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Hier finden Sie alle Referenzen, welche im Buch in dem jeweiligen Kapitel zitiert wurden.

Contents

Kapitel 1

E. Schrödinger (1999): Was ist Leben?
Type: book by Piper Verlag {GmbH}.

E. Sackmann (1996): Supported membranes: scientific and practical applications
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/8539599
Abstract:

Scientific and practical applications of supported lipid-protein bilayers are described. Membranes can be covalently coupled to or separated from solids by ultrathin layers of water or soft polymer cushions. The latter systems maintain the structural and dynamic properties of free bilayers, forming a class of models of biomembranes that allow the application of a manifold of surface-sensitive techniques. They form versatile models of low-dimensionality complex fluids, which can be used to study interfacial forces and wetting phenomena, and enable the design of phantom cells to explore the interplay of lock-and-key forces (such as receptor-ligand binding) and universal forces for cell adhesion. Practical applications are the design of (highly selective) receptor surfaces of biosensors on electrooptical devices or the biofunctionalization of inorganic solids.

E. Mayr (2002): Die Entwicklung der biologischen Gedankenwelt: Vielfalt, Evolution und Vererbung
Type: book by Springer, Berlin.

E. Mach (1963): Die Mechanik
Type: book by Wissenschaftl. Buchgesellschaft.

P. M. Kulesa, S. E. Fraser (2002): Cell dynamics during somite boundary formation revealed by time-lapse analysis
Type: article by Science {(New} York, {N.Y.)}.
doi: 10.1126/science.1075544
link: http://www.ncbi.nlm.nih.gov/pubmed/12411697
Abstract:

We follow somite segmentation in living chick embryos and find that the shaping process is not a simple periodic slicing of tissue blocks but a much more carefully choreographed separation in which the somite pulls apart from the segmental plate. Cells move across the presumptive somite boundary and violate gene expression boundaries thought to correlate with the site of the somite boundary. Similarly, cells do not appear to be preassigned to a given somite as they leave the node. The results offer a detailed picture of somite shaping and provide a spatiotemporal framework for linking gene expression with cell movements.

J. Keckes, I. Burgert, K. Frühmann, M. Müller, K. Kölln, M. Hamilton, M. Burghammer, S. V. Roth, S. Stanzl-Tschegg, P. Fratzl (2003): Cell-wall recovery after irreversible deformation of wood
Type: article by Nature Materials.
doi: 10.1038/nmat1019
link: http://www.ncbi.nlm.nih.gov/pubmed/14625541
Abstract:

The remarkable mechanical properties of biological materials reside in their complex hierarchical architecture and in specific molecular mechanistic phenomena. The fundamental importance of molecular interactions and bond recovery has been suggested by studies on deformation and fracture of bone and nacre. Like these mineral-based materials, wood also represents a complex nanocomposite with excellent mechanical performance, despite the fact that it is mainly based on polymers. In wood, however, the mechanistic contribution of processes in the cell wall is not fully understood. Here we have combined tensile tests on individual wood cells and on wood foils with simultaneous synchrotron X-ray diffraction analysis in order to separate deformation mechanisms inside the cell wall from those mediated by cell-cell interactions. We show that tensile deformation beyond the yield point does not deteriorate the stiffness of either individual cells or foils. This indicates that there is a dominant recovery mechanism that re-forms the amorphous matrix between the cellulose microfibrils within the cell wall, maintaining its mechanical properties. This stick-slip mechanism, rather like Velcro operating at the nanometre level, provides a 'plastic response' similar to that effected by moving dislocations in metals. We suggest that the molecular recovery mechanism in the cell matrix is a universal phenomenon dominating the tensile deformation of different wood tissue types.

J. L. van Hemmen (2001): Die Karte im Kopf - Wie stellt das Gehirn seine Umwelt dar?
Type: article by Physikalische Blätter.

H. von Helmholtz, A. Wangerin (2009): Über die Erhaltung der Kraft
Type: book by Deutsch {(Harri)}.

M. Fritz, A. Belcher, M. Radmacher, D. Walters, P. Hansma, G. Stucky, D. Morse, S. Mann (1994): Flat pearls from biofabrication of organized composites on inorganic substrates
Type: article by Nature.
link: http://dx.doi.org/10.1038/371049a0

P. Fratzl (2002): Von Knochen, Holz und Zähnen
Type: article by Physik Journal.
Abstract:

Biologische Materialien wie Holz, Knochen

oder Zähne sind im Laufe der Evolution von der Natur für ihre jeweilige Anwendung optimiert worden. Die Bauprinzipien dieser Gewebe, ihre Eigenschaften und ihre Funktion liefern für die Materialwissenschaft wichtige Erkenntnisse, die sich für „biomimetisches“ Design von neuartigen Werkstoffen einsetzen lassen. Anstatt viele (teure) Grundstoffe zu verwenden, kommt die Natur für den Großteil ihrer Materialien mit relativ wenigen Grundelementen aus, die gezielt strukturiert werden. Die meisten dieser Prinzipien sind noch unbekannt oder physikalisch unverstanden und bieten ein noch kaum erkundetes Betätigungsfeld für den Materialphysiker. Mögliche Anwendungen liegen in der Entwicklung von Werkstoffen für die Biomedizin (z. B. Knochenersatzmaterialien), aber auch für neuartige Sensoren oder intelligente Materialien.

E. Arzt, S. Gorb, R. Spolenak (2003): From micro to nano contacts in biological attachment devices
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.1534701100
link: http://www.ncbi.nlm.nih.gov/pubmed/12960386
Abstract:

Animals with widely varying body weight, such as flies, spiders, and geckos, can adhere to and move along vertical walls and even ceilings. This ability is caused by very efficient attachment mechanisms in which patterned surface structures interact with the profile of the substrate. An extensive microscopic study has shown a strong inverse scaling effect in these attachment devices. Whereas microm dimensions of the terminal elements of the setae are sufficient for flies and beetles, geckos must resort to sub-microm devices to ensure adhesion. This general trend is quantitatively explained by applying the principles of contact mechanics, according to which splitting up the contact into finer subcontacts increases adhesion. This principle is widely spread in design of natural adhesive systems and may also be transferred into practical applications.

L. Addadi, D. Joester, F. Nudelman, S. Weiner (2006): Mollusk shell formation: a source of new concepts for understanding biomineralization processes.
Type: article by Chemistry {(Weinheim} an der Bergstrasse, Germany).
link: http://dx.doi.org/10.1002/chem.200500980
Abstract:

The biological approach to forming crystals is proving to be most surprising. Mollusks build their shells by using a hydrophobic silk gel, very acidic aspartic acid rich proteins, and apparently also an amorphous precursor phase from which the crystals form. All this takes place in a highly structured chitinous framework. Here we present ideas on how these disparate components work together to produce the highly structured pearly nacreous layer of the mollusk shell.

Kapitel 2

T. D. Pollard, W. C. Earnshaw, J. Lippincott-Schwartz (2007): Cell Biology
Type: book by Saunders.

L. Margulis, K. V. Schwartz (1989): Die fünf Reiche der Organismen. Ein Leitfaden
Type: book by Heidelberg : Spektrum der Wissenschaft.

H. Lodish, A. Berk, C. A. Kaiser, M. Krieger, M. P. Scott, A. Bretscher (2007): Molecular Cell Biology
Type: book by Palgrave Macmillan.

R. Lipowsky, E. Sackmann (1996): Architecture and Function. Handbook of Biological Physics Vol I
Type: book by Elsevier.
Abstract:

The first volume of the Handbook deals with the amazing world of biomembranes and lipid bilayers. Part A describes all aspects related to the morphology of these membranes, beginning with the complex architecture of biomembranes, continues with a description of the bizarre morphology of lipid bilayers and concludes with technological applications of these membranes. The first two chapters deal with biomembranes, providing an introduction to the membranes of eucaryotes and a description of the evolution of membranes. The following chapters are concerned with different aspects of lipids including the physical properties of model membranes composed of lipid-protein mixtures, lateral phase separation of lipids and proteins and measurement of lipid-protein bilayer diffusion. Other chapters deal with the flexibility of fluid bilayers, the closure of bilayers into vesicles which attain a large variety of different shapes, and applications of lipid vesicles and liposomes.

Part B covers membrane adhesion, membrane fusion and the interaction of biomembranes with polymer networks such as the cytoskeleton. The first two chapters of this part discuss the generic interactions of membranes from the conceptual point of view. The following two chapters summarize the experimental work on two different bilayer systems. The next chapter deals with the process of contact formation, focal bounding and macroscopic contacts between cells. The cytoskeleton within eucaryotic cells consists of a network of relatively stiff filaments of which three different types of filaments have been identified. As explained in the next chapter much has been recently learned about the interaction of these filaments with the cell membrane. The final two chapters deal with membrane fusion.

S. F. Gilbert, S. R. Singer (2006): Developmental Biology
Type: book by Palgrave Macmillan.

W. Fritsche (2001): Mikrobiologie
Type: book by Spektrum Akademischer Verlag.

J. M. Berg, L. Stryer, J. L. Tymoczko (2007): Biochemie
Type: book by Spektrum Akademischer Verlag.

B. Alberts, A. Johnson, P. Walter, J. Lewis, M. Raff, K. Roberts (2008): Molecular Biology of the Cell
Type: book by Taylor & Francis.


Kapitel 3

I. Tinoco, K. Sauer (2003): Physical Chemistry: Principles and Applications in Biological Sciences
Type: book by Pearson Education {(US)}.

G. Thews, E. Mutschler, P. Vaupel (2007): Anatomie, Physiologie, Pathophysiologie des Menschen
Type: book by Wissenschaftliche Verlagsgesellschaft.

F. Reif, W. Muschik (1987): Statistische Physik und Theorie der Wärme
Type: book by Gruyter.

D. J. Randall, W. Burggren, K. French (2001): Eckert Animal Physiology
Type: book by Palgrave Macmillan.

L. D. Landau, E. M. Lifschitz (1987): Lehrbuch der theoretischen Physik, 10 Bde., Bd.5, Statistische Physik: {BD} 5
Type: book by Deutsch {(Harri)}.

T. L. Hill (1988): An Introduction to Statistical Thermodynamics
Type: book by Dover Pubn Inc..

K. A. Dill, S. Bromberg (2002): Molecular driving forces: statistical thermodynamics in chemistry and biology
Type: book by Garland Pub.

R. Cahn, W. Ludwig (1985): Theorie der Wärme.
Type: book by Springer, Berlin.

G. B. Benedek, F. M. H. Villars (2000): Physics With Illustrative Examples From Medicine and Biology: Volume 2: Statistical Physics
Type: book by Springer, Berlin.


Kapitel 4

G. Wedler (2004): Lehrbuch der Physikalischen Chemie: Funfte, Vollstandig Uberarbeitete Und Aktualisierte Auflage
Type: book by {Wiley-VCH}.

I. Tinoco, K. Sauer (2003): Physical Chemistry: Principles and Applications in Biological Sciences
Type: book by Pearson Education {(US)}.

U. Schindewolf (1968): Formation and Properties of Solvated Electrons
Type: article by Angewandte Chemie International Edition in English.
doi: 10.1002/anie.196801901
link: http://dx.doi.org/10.1002/anie.196801901
Abstract:

In the formulation of many chemical reactions, electrons are regarded as readily transferable particles, though their participation in these reactions cannot be directly observed. However, the discovery that electrons can be produced in various ways in suitable solutions and that they are stabilized by solvation and can thus be studied directly has recently led to a rapid growth of interest in these, the simplest and most reactive particles of chemistry. The solvated electron has physical properties that permit its detection by various methods even at very low concentrations, so that it is also possible to follow its many reactions, most of which are extremely fast.

D. Marx, M. E. Tuckerman, J. Hutter, M. Parrinello (1999): The nature of the hydrated excess proton in water
Type: article by Nature.
doi: 10.1038/17579
link: http://dx.doi.org/10.1038/17579

I. N. Levine (2009): Physical Chemistry
Type: book by {Mcgraw-Hill} {Publ.Comp.}.

G. Kortüm, W. Vogel (1970): Lehrbuch der Elektrochemie
Type: book by Verl. Chemie.

F. Kohlrausch, A. Heydweiller (1894): Über reines Wasser
Type: article by Annalen der Physik.
link: http://adsabs.harvard.edu/abs/1894AnP...289..209K

P. Karlson, D. Doenecke, J. Koolman, G. Fuchs, W. Gerok (2005): Karlsons Biochemie und Pathobiochemie
Type: book by Thieme, Stuttgart.

M. Eigen (1964): Proton transfer, acid-base catalysis, and enzymatic hydrolysis. Part I: elementary processes
Type: article by Angewandte Chemie International Edition in English.

J. O'M Bockris, A. K. N. Reddy (1995): Modern Electrochemistry
Type: book by Kluwer Academic / Plenum Publishers.

G. J. Bignold, A. D. Brewer, B. Hearn (1971): Specific conductivity and ionic product of water between 50 and 271 {[degree]C}
Type: article by Transactions of the Faraday Society.
link: http://dx.doi.org/10.1039/TF9716702419
Abstract:

The specific conductivity of high-purity water has been measured at temperatures between 51[degree] and {271[degree]C} along the saturated vapour pressure curve. Correction has been made for traces of contamination. The frequency dispersion of the impedance of the water-filled cell has been analyzed in terms of an equivalent electrical circuit. The data have been used to calculate the ionic product constant of water over this temperature range.

J. M. Berg, L. Stryer, J. L. Tymoczko (2007): Biochemie
Type: book by Spektrum Akademischer Verlag.


Kapitel 5

H. Beyer, W. Francke, W. Walter (2004): Lehrbuch der Organischen Chemie
Type: book by Hirzel, Stuttgart.

D. E. Metzler, C. M. Metzler (2000): Biochemistry Vol. 1. The Chemical Reactions of Living Cells
Type: book by Academic Press.

T. E. Creighton (1993): Proteins: Structures and Molecular Properties
Type: book by W. H. Freeman & Co Ltd.

P. Karlson, D. Doenecke, J. Koolman, G. Fuchs, W. Gerok (2005): Karlsons Biochemie und Pathobiochemie
Type: book by Thieme, Stuttgart.

P. McCaldon, P. Argos (1988): Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences
Type: article by Proteins.
doi: 10.1002/prot.340040204
link: http://www.ncbi.nlm.nih.gov/pubmed/3227018
Abstract:

We have examined oligopeptides with lengths ranging from 2 to 11 residues in protein sequences that show no obvious evolutionary relationship. All sequences in the Protein Identification Resource database were carefully classified by sensitive homology searches into superfamilies to obtain unbiased oligopeptide counts. The results, contrary to previous studies, show clear prejudices in protein sequences. The oligopeptide preferences were used to help decide the significance of sequence homologies and to improve the more general methods for detecting protein coding regions within nucleotide sequences.

J. M. Berg, L. Stryer, J. L. Tymoczko (2007): Biochemie
Type: book by Spektrum Akademischer Verlag.


Kapitel 6

K. E. van Holde, C. Johnson, P. S. Ho (2005): Principles of Physical Biochemistry
Type: book by {Prentice-Hall}.

B. Lee (1991): Solvent reorganization contribution to the transfer thermodynamics of small nonpolar molecules
Type: article by Biopolymers.
doi: 10.1002/bip.360310809
link: http://www.ncbi.nlm.nih.gov/pubmed/1782360
Abstract:

The experimental thermodynamic data for the dissolution of five simple hydrocarbon molecules in water were combined with the solute-solvent interaction energy from a computer simulation study to yield data on the enthalpy change of solvent reorganization. Similar data were generated for dissolving these same solute molecules in their respective neat solvents using the equilibrium vapor pressure and the heat of vaporization data for the pure liquid. The enthalpy and the free energy changes upon cavity formation were also estimated using the temperature dependence of the solute-solvent interaction energy. Both the enthalpy and T delta S for cavity formation rapidly increase with temperature in both solvent types, and the free energy of cavity formation can be reproduced accurately by the scaled particle theory over the entire temperature range in all cases. These results indicate that the characteristic structure formation around an inert solute molecule in water produces compensating changes in enthalpy and entropy, and that the hydrophobicity arises mainly from the difference in the excluded volume effect.

D. Hall, A. P. Minton (2003): Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges
Type: article by Biochimica Et Biophysica Acta.
link: http://www.ncbi.nlm.nih.gov/pubmed/12878031
Abstract:

The concept of excluded volume and the theory of effects of excluded volume on the equilibria and rates of macromolecular reactions in fluid media containing high total concentrations of macromolecules ('crowded' media) are summarized. Reports of experimental studies of crowding effects published during the last year are tabulated. Limitations of current excluded volume theory are discussed, and a determination is made of conditions under which this theory may and may not be validly applied. Recently suggested novel approaches to quantitative analysis of crowding phenomena, which may help to overcome some of the limitations of current theory, are summarized.

H. S. Ashbaugh, L. R. Pratt (2006): Colloquium: Scaled particle theory and the length scales of hydrophobicity
Type: article by Reviews of Modern Physics.
link: http://adsabs.harvard.edu/abs/2006RvMP...78..159A
Abstract:

Hydrophobic hydration plays a crucial role in self-assembly processes

over multiple length scales, from the microscopic origins of inert gas solubility in water, to the mesoscopic organization of proteins and surfactant structures, to macroscopic phase separation. Many theoretical studies focus on the molecularly detailed interactions between oil and water, but the extrapolation of molecular-scale models to larger-length-scale hydration phenomena is sometimes not warranted. Scaled particle theories are based upon an interpolative view of that microscopic{textless}--{textgreater}macroscopic issue. This Colloquium revisits the scaled particle theory proposed 30 years ago by Stillinger {[J.} Solution Chem. 2, 141 (1973)], adopts a practical generalization, and considers the implications for hydrophobic hydration in light of our current understanding. The generalization is based upon identifying a molecular length, implicit in previous applications of scaled particle models, which provides an effective radius for joining microscopic and macroscopic descriptions. It will be demonstrated that the generalized theory correctly reproduces many of the anomalous thermodynamic properties of hydrophobic hydration for molecularly sized solutes, including solubility minima and entropy convergence, successfully interpolates between the microscopic and macroscopic extremes, and provides new insights into the underlying molecular mechanisms. The model considered here serves as a reference for theories that bridge microscopic and macroscopic hydrophobic effects. The results are discussed in terms of length scales associated with component phenomena. In particular, first there is a discussion of the microscopic-macroscopic joining radius identified by the theory; then follows a discussion of the Tolman length that describes curvature corrections to a surface area model of hydrophobic hydration free energies and the length scales on which entropy convergence of hydration free energies are expected.

J. Cavanagh, W. J. Fairbrother, A. G. Palmer, N. J. Skelton, M. Rance (2006): Protein {NMR} Spectroscopy. Principles and Practice
Type: book by Academic Press.

P. C. Hiemenz, R. Rajagopalan (1997): Principles of Colloid and Surface Chemistry
Type: book by Marcel Dekker Inc.

D. T. Bowron (2004): Structure and interactions in simple solutions.
Type: article by Philosophical Transactions of the Royal Society B: Biological Sciences.
doi: 10.1098/rstb.2004.1496
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1693403&rendertype=abstract

H. Reiss, H. L. Frisch, J. L. Lebowitz (1959): Statistical Mechanics of Rigid Spheres
Type: article by The Journal of Chemical Physics.
doi: 10.1063/1.1730361
link: http://link.aip.org/link/?JCP/31/369/1

N. T. Southall, K. A. Dill, A. D. J. Haymet (2002): A View of the Hydrophobic Effect
Type: article by The Journal of Physical Chemistry B.
doi: 10.1021/jp020104r
link: http://dx.doi.org/10.1021/jp020104r

A. G. Ogston (1958): The spaces in a uniform random suspension of fibres
Type: article by Transactions of the Faraday Society.
link: http://dx.doi.org/10.1039/TF9585401754

J. L. Finney (2004): Water? What's so special about it?
Type: article by Philosophical Transactions of the Royal Society B: Biological Sciences.
doi: 10.1098/rstb.2004.1495
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1693413&rendertype=abstract

J. N. Israelachvili (1991): Intermolecular and Surface Forces: With Applications to Colloidal and Biological Systems
Type: book by Academic Pr Inc.

P. M. Chaikin, T. C. Lubensky (2000): Principles of Condensed Matter Physics
Type: book by Cambridge University Press.

T. E. Creighton (1993): Proteins: Structures and Molecular Properties
Type: book by W. H. Freeman & Co Ltd.

J. M. Ziman (1979): Models of Disorder: The Theoretical Physics of Homogeneously Disordered Systems
Type: book by Cambridge University Press.

S. Asakura, F. Oosawa (1954): On Interaction between Two Bodies Immersed in a Solution of Macromolecules
Type: article by Journal of Chemical Physics.
link: http://adsabs.harvard.edu/abs/1954JChPh..22.1255A
Abstract:

Not Available

T. C. Laurent, J. J. Killander (1964): A theory of gel filtration and its experimental verification
Type: article by Journal of Chromatography.
Abstract:

The separation of molecules according to size when chromatographed on granulated gels was explained in terms of sterical exclusion of the molecules from the gel grains.

The gel was assumed to be made up of a three-dimensional random network of fibers and the exclusion was calculated for spherical molecules of varying diameter. Theoretical values agreed with experimental data.

D. F. Evans, H. K. Wennerström (1999): The Colloidal Domain: Where Physics, Chemistry, Biology, and Technology Meet
Type: book by {Wiley-Vch}.

J. L. Lebowitz, E. Helfand, E. Praestgaard (1965): Scaled Particle Theory of Fluid Mixtures
Type: article by The Journal of Chemical Physics.
doi: 10.1063/1.1696842
link: http://link.aip.org/link/?JCP/43/774/1

V. A. Parsegian (2005): Van Der Waals Forces: A Handbook for Biologists, Chemists, Engineers, and Physicists
Type: book by Cambridge University Press.

C. Tanford (1980): The Hydrophobic Effect: Formation of Micelles and Biological Membranes
Type: book by John Wiley & Sons Inc.

S. Leikin, V. A. Parsegian, D. C. Rau, R. P. Rand (1993): Hydration Forces
Type: article by Annual Review of Physical Chemistry.
doi: 10.1146/annurev.pc.44.100193.002101
link: http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.pc.44.100193.002101

S. Marcelja, N. Radic (1976): Repulsion of interfaces due to boundary water
Type: article by Chemical Physics Letters.
link: http://adsabs.harvard.edu/abs/1976CPL....42..129M

R. S. Berry, S. A. Rice, J. Ross (2000): Physical Chemistry
Type: book by Oxford University Press.



Kapitel 7

J. SantaLucia, D. Hicks (2004): The thermodynamics of {DNA} structural motifs
Type: article by Annual Review of Biophysics and Biomolecular Structure.
doi: 10.1146/annurev.biophys.32.110601.141800
link: http://www.ncbi.nlm.nih.gov/pubmed/15139820
Abstract:

{DNA} secondary structure plays an important role in biology, genotyping diagnostics, a variety of molecular biology techniques, in vitro-selected {DNA} catalysts, nanotechnology, and {DNA-based} computing. Accurate prediction of {DNA} secondary structure and hybridization using dynamic programming algorithms requires a database of thermodynamic parameters for several motifs including {Watson-Crick} base pairs, internal mismatches, terminal mismatches, terminal dangling ends, hairpins, bulges, internal loops, and multibranched loops. To make the database useful for predictions under a variety of salt conditions, empirical equations for monovalent and magnesium dependence of thermodynamics have been developed. Bimolecular hybridization is often inhibited by competing unimolecular folding of a target or probe {DNA.} Powerful numerical methods have been developed to solve multistate-coupled equilibria in bimolecular and higher-order complexes. This review presents the current parameter set available for making accurate {DNA} structure predictions and also points to future directions for improvement.

P. Hänggi, P. Talkner, M. Borkovec (1990): Reaction-rate theory: fifty years after Kramers
Type: article by Reviews of Modern Physics.
link: http://adsabs.harvard.edu/abs/1990RvMP...62..251H
Abstract:

The calculation of rate coefficients is a discipline of nonlinear

science of importance to much of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on thermally activated barrier crossing, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry. Theoretical as well as numerical approaches are discussed for single- and many-dimensional metastable systems (including fields) in gases and condensed phases. The role of many-dimensional transition-state theory is contrasted with Kramers' reaction-rate theory for moderate-to-strong friction; the authors emphasize the physical situation and the close connection between unimolecular rate theory and Kramers' work for weakly damped systems. The rate theory accounting for memory friction is presented, together with a unifying theoretical approach which covers the whole regime of weak-to-moderate-to-strong friction on the same basis (turnover theory). The peculiarities of noise-activated escape in a variety of physically different metastable potential configurations is elucidated in terms of the mean-first-passage-time technique. Moreover, the role and the complexity of escape in driven systems exhibiting possibly multiple, metastable stationary nonequilibrium states is identified. At lower temperatures, quantum tunneling effects start to dominate the rate mechanism. The early quantum approaches as well as the latest quantum versions of Kramers' theory are discussed, thereby providing a description of dissipative escape events at all temperatures. In addition, an attempt is made to discuss prominent experimental work as it relates to Kramers' reaction-rate theory and to indicate the most important areas for future research in theory and experiment.

C. L. Stevens, G. Felsenfeld (1964): The Conversion of {Two-Stranded} Poly {(A+U)} to {Three-Strand} Poly {(A+2U)} and Poly A by Heat
Type: article by Biopolymers 2.

K. E. van Holde, C. Johnson, P. S. Ho (2005): Principles of Physical Biochemistry
Type: book by {Prentice-Hall}.

H. Frauenfelder, F. Parak, R. D. Young (1988): Conformational substates in proteins
Type: article by Annual Review of Biophysics and Biophysical Chemistry.
doi: 10.1146/annurev.bb.17.060188.002315
link: http://www.ncbi.nlm.nih.gov/pubmed/3293595

J. I. Steinfeld, J. S. Francisco, W. L. Hase (1998): Chemical Kinetics and Dynamics
Type: book by Prentice Hall.

M. Karplus, J. A. McCammon (2002): Molecular dynamics simulations of biomolecules
Type: article by Nature Structural Biology.
doi: 10.1038/nsb0902-646
link: http://dx.doi.org/10.1038/nsb0902-646

P. W. Fenimore, H. Frauenfelder, B. H. McMahon, F. G. Parak (2002): Slaving: Solvent fluctuations dominate protein dynamics and functions
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.212637899
link: http://www.pnas.org/content/99/25/16047.abstract
Abstract:

Protein motions are essential for function. Comparing protein processes with the dielectric fluctuations of the surrounding solvent shows that they fall into two classes: nonslaved and slaved. Nonslaved processes are independent of the solvent motions; their rates are determined by the protein conformation and vibrational dynamics. Slaved processes are tightly coupled to the solvent; their rates have approximately the same temperature dependence as the rate of the solvent fluctuations, but they are smaller. Because the temperature dependence is determined by the activation enthalpy, we propose that the solvent is responsible for the activation enthalpy, whereas the protein and the hydration shell control the activation entropy through the energy landscape. Bond formation is the prototype of nonslaved processes; opening and closing of channels are quintessential slaved motions. The prevalence of slaved motions highlights the importance of the environment in cells and membranes for the function of proteins.

R. Elber, M. Karplus (1990): Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
Type: article by Journal of the American Chemical Society.
doi: 10.1021/ja00181a020
link: http://dx.doi.org/10.1021/ja00181a020

M. F. Perutz, A. J. Wilkinson, M. Paoli, G. G. Dodson (1998): {THE} {STEREOCHEMICAL} {MECHANISM} {OF} {THE} {COOPERATIVE} {EFFECTS} {IN} {HEMOGLOBIN} {REVISITED}
Type: article by Annual Review of Biophysics and Biomolecular Structure.
doi: 10.1146/annurev.biophys.27.1.1
link: http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biophys.27.1.1

R. H. Austin, K. W. Beeson, L. Eisenstein, H. Frauenfelder, I. C. Gunsalus (1975): Dynamics of ligand binding to myoglobin
Type: article by Biochemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/1191643
Abstract:

Myoglobin rebinding of carbon monoxide and dioxygen after photodissociation has been observed in the temperature range between 40 and 350 K. A system was constructed that records the change in optical absorption at 436 nm smoothly and without break between 2 musec and 1 ksec. Four different rebinding processes have been found. Between 40 and 160 K, a single process is observed. It is not exponential in time, but approximately given by N(t) = (1 + t/to)-n, where to and n are temperature-dependent, ligand-concentration independent, parameters. At about 170 K, a second and at 200 K, a third concentration-independent process emerge. At 210 K, a concentration-dependent process sets in. If myoglobin is embedded in a solid, only the first three can be seen, and they are all nonexponential. In a liquid glycerol-water solvent, rebinding is exponential. To interpret the data, a model is proposed in which the ligand molecule, on its way from the solvent to the binding site at the ferrous heme iron, encounters four barriers in succession. The barriers are tentatively identified with known features of myoglobin. By computer-solving the differential equation for the motion of a ligand molecule over four barriers, the rates for all important steps are obtained. The temperature dependences of the rates yield enthalpy, entropy, and free-energy changes at all barriers. The free-energy barriers at 310 K indicate how myoglobin achieves specificity and order. For carbon monoxide, the heights of these barriers increase toward the inside; carbon monoxide consequently is partially rejected at each of the four barriers. Dioxygen, in contrast, sees barriers of about equal height and moves smoothly toward the binding site. The entropy increases over the first two barriers, indicating a rupturing of bonds or displacement of residues, and then smoothly decreases, reaching a minimum at the binding site. The magnitude of the decrease over the innermost barrier implies participation of heme and/or protein. The nonexponential rebinding observed at low temperatures and in solid samples implies that the innermost barrier has a spectrum of activation energies. The shape of the spectrum has been determined; its existence can be explained by assuming the presence of many conformational states for myoglobin. In a liquid at temperatures above about 230 K, relaxation among conformational states occurs and rebinding becomes exponential.

J. Monod, J. Wyman, J. P. CHANGEUX (1965): {ON} {THE} {NATURE} {OF} {ALLOSTERIC} {TRANSITIONS:} A {PLAUSIBLE} {MODEL}
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/14343300

H. A. Kramers (1940): Brownian motion in a field of force and the diffusion model of chemical reactions
Type: article by Physica.
link: http://adsabs.harvard.edu/abs/1940Phy.....7..284K

T. E. Creighton (1993): Proteins: Structures and Molecular Properties
Type: book by W. H. Freeman & Co Ltd.

R. Hill (1936): Oxygen Dissociation Curves of Muscle Haemoglobin
Type: article by Royal Society of London Proceedings Series B.
link: http://adsabs.harvard.edu/abs/1936RSPSB.120..472H

B. H. Zimm, J. K. Bragg (1959): Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains
Type: article by The Journal of Chemical Physics.
doi: 10.1063/1.1730390
link: http://link.aip.org/link/?JCP/31/526/1

F. Colonna-Cesari, D. Perahia, M. Karplus, H. Eklund, C. I. Brädén, O. Tapia (1986): Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode
Type: article by The Journal of Biological Chemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/3771574
Abstract:

A study of the hinge bending mode in the enzyme liver alcohol dehydrogenase is made by use of empirical energy functions. The enzyme is a dimer, with each monomer composed of a coenzyme binding domain and a catalytic domain with a large cleft between the two. Superposition of the apoenzyme and holoenzyme crystal structures is used to determine a rigid rotation axis for closing of the cleft. It is shown that a rigid body transformation of the apoenzyme to the holoenzyme structure corresponds to a 10 degrees rotation of the catalytic domain about this axis. The rotation is not along the least-motion path for closing of the cleft but instead corresponds to the catalytic domain coming closer to the coenzyme binding domain by a sliding motion. Estimation of the energy associated with the interdomain motion of the apoenzyme over a range of 90 degrees (-40 to 50 degrees, where 0 degrees corresponds to the minimized crystal structure) demonstrates that local structural relaxation makes possible large-scale rotations with relatively small energy increments. A variety of structural rearrangements associated with the domain motion are characterized. They involve the hinge region residues that provide the covalent connections between the two domains and certain loop regions that are brought into contact by the rotation. Differences between the energy minimized and the holoenzyme structures point to the existence of alternative conformations for loops and to the importance of the ligands in the structural rearrangements.

J. Grotendorst, D. Marx, A. Muramatsu (2002): Quantum Simulations of Complex {Many-Body} Systems: From Theory to Algorithms {(G.} Sutmann {"Classical} Molecular Dynamics")
Type: book by Forschungszentrum Jülich.

P. Doty, J. T. Yang (1956): {POLYPEPTIDES.} {VII.} {POLY-γ-BENZYL-L-GLUTAMATE:} {THE} {HELIX-COIL} {TRANSITION} {IN} {SOLUTION1}
Type: article by Journal of the American Chemical Society.
doi: 10.1021/ja01583a070
link: http://dx.doi.org/10.1021/ja01583a070

H. J. Dyson, P. E. Wright (2005): Intrinsically unstructured proteins and their functions
Type: article by Nature Reviews. Molecular Cell Biology.
doi: 10.1038/nrm1589
link: http://www.ncbi.nlm.nih.gov/pubmed/15738986
Abstract:

Many gene sequences in eukaryotic genomes encode entire proteins or large segments of proteins that lack a well-structured three-dimensional fold. Disordered regions can be highly conserved between species in both composition and sequence and, contrary to the traditional view that protein function equates with a stable three-dimensional structure, disordered regions are often functional, in ways that we are only beginning to discover. Many disordered segments fold on binding to their biological targets (coupled folding and binding), whereas others constitute flexible linkers that have a role in the assembly of macromolecular arrays.

A. D. Jr. MacKerell, D. Bashford, M. Aepfelbacher, R. L. Jr. Dunbrack, J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, M. Karplus (1998): {All-Atom} Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
Type: article by The Journal of Physical Chemistry B.
doi: 10.1021/jp973084f
link: http://dx.doi.org/10.1021/jp973084f
Abstract:

New protein parameters are reported for the all-atom empirical energy function in the {CHARMM} program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solventsolvent, solventsolute, and solutesolute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein phi, chi angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published {CHARMM} all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.

J. Marmur, P. Doty (1959): Heterogeneity in Deoxyribonucleic Acids: I. Dependence on Composition of the Configurational Stability of Deoxyribonucleic Acids
Type: article by Nature.
doi: 10.1038/1831427a0
link: http://dx.doi.org/10.1038/1831427a0

M. F. Perutz (1970): Stereochemistry of Cooperative Effects in Haemoglobin: {Haem-Haem} Interaction and the Problem of Allostery
Type: article by Nature.
doi: 10.1038/228726a0
link: http://dx.doi.org/10.1038/228726a0

K. A. Dill (1999): Polymer principles and protein folding.
Type: article by Protein Science : A Publication of the Protein Society.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2144345&rendertype=abstract

J. A. Subirana, P. Doty (1966): Kinetics of renaturation of denatured {DNA.} I. Spectrophotometric results
Type: article by Biopolymers.
doi: 10.1002/bip.1966.360040204
link: http://dx.doi.org/10.1002/bip.1966.360040204
Abstract:

The kinetics of renaturation of heat- or formamide-denatured {DNA} have been studied by following the change of optical density at a constant temperature. Solvents of different ionic strength and various {DNA} samples have been used. At the lower ionic strengths studied, the reaction follows second-order kinetics, substantiating the hypothesis that strands of native {DNA} separate upon denaturation and recombine during renaturation. As the ionic strength is increased at a constant temperature, the reaction deviates from simple second-order behavior. This appears to be the result of the inhibition to rewinding caused by short helical segments in the denatured {DNA} which are more stable at the higher ionic strenth.

D. E. Anderson, R. J. Peters, B. Wilk, D. A. Agard (1999): Alpha-lytic protease precursor: characterization of a structured folding intermediate
Type: article by Biochemistry.
doi: 10.1021/bi982165e
link: http://www.ncbi.nlm.nih.gov/pubmed/10200160
Abstract:

The bacterial alpha-lytic protease {(alphaLP)} is synthesized as a precursor containing a large N-terminal pro region {(Pro)} transiently required for correct folding of the protease {[Silen,} J. L., and Agard, D. A. (1989) Nature 341, 462-464]. Upon folding, the precursor is autocatalyticly cleaved to yield a tight-binding inhibitory complex of the pro region and the fully folded protease {(Pro/alphaLP).} An in vitro purification and refolding protocol has been developed for production of the disulfide-bonded precursor. A combination of spectroscopic approaches have been used to compare the structure and stability of the precursor with either the {Pro/alphaLP} complex or isolated Pro. The precursor and complex have significant similarities in secondary structure but some differences in tertiary structure, as well as a dramatic difference in stability. Correlations with isolated Pro suggest that the pro region part of the precursor is fully folded and acts to stabilize and structure the {alphaLP} region. Precursor folding is shown to be biphasic with the fast phase matching the rate of pro region folding. Further, the rate-limiting step in oxidative folding is formation of the disulfide bonds and autocatalytic processing occurs rapidly thereafter. These studies suggests a model in which the pro region folds first and catalyzes folding of the protease domain, forming the active site and finally causing autocatalytic cleavage of the bond separating pro region and protease. This last processing step is critical as it allows the protease N-terminus to rearrange, providing the majority of net stabilization of the product {Pro/alphaLP} complex.

C. J. Tsai, S. Kumar, B. Ma, R. Nussinov (1999): Folding funnels, binding funnels, and protein function
Type: article by Protein Science: A Publication of the Protein Society.
doi: 10.1110/ps.8.6.1181
link: http://www.ncbi.nlm.nih.gov/pubmed/10386868
Abstract:

Folding funnels have been the focus of considerable attention during the last few years. These have mostly been discussed in the general context of the theory of protein folding. Here we extend the utility of the concept of folding funnels, relating them to biological mechanisms and function. In particular, here we describe the shape of the funnels in light of protein synthesis and folding; flexibility, conformational diversity, and binding mechanisms; and the associated binding funnels, illustrating the multiple routes and the range of complexed conformers. Specifically, the walls of the folding funnels, their crevices, and bumps are related to the complexity of protein folding, and hence to sequential vs. nonsequential folding. Whereas the former is more frequently observed in eukaryotic proteins, where the rate of protein synthesis is slower, the latter is more frequent in prokaryotes, with faster translation rates. The bottoms of the funnels reflect the extent of the flexibility of the proteins. Rugged floors imply a range of conformational isomers, which may be close on the energy landscape. Rather than undergoing an induced fit binding mechanism, the conformational ensembles around the rugged bottoms argue that the conformers, which are most complementary to the ligand, will bind to it with the equilibrium shifting in their favor. Furthermore, depending on the extent of the ruggedness, or of the smoothness with only a few minima, we may infer nonspecific, broad range vs. specific binding. In particular, folding and binding are similar processes, with similar underlying principles. Hence, the shape of the folding funnel of the monomer enables making reasonable guesses regarding the shape of the corresponding binding funnel. Proteins having a broad range of binding, such as proteolytic enzymes or relatively nonspecific endonucleases, may be expected to have not only rugged floors in their folding funnels, but their binding funnels will also behave similarly, with a range of complexed conformations. Hence, knowledge of the shape of the folding funnels is biologically very useful. The converse also holds: If kinetic and thermodynamic data are available, hints regarding the role of the protein and its binding selectivity may be obtained. Thus, the utility of the concept of the funnel carries over to the origin of the protein and to its function.

D. Thorn Leeson, D. A. Wiersma, K. Fritsch, J. Friedrich (1997): The Energy Landscape of Myoglobin: An Optical Study
Type: article by The Journal of Physical Chemistry B.
doi: 10.1021/jp970908k
link: http://dx.doi.org/10.1021/jp970908k
Abstract:

In this paper we demonstrate how the potential energy surface of a protein, which determines its conformational degrees of freedom, can be constructed from a series of advanced nonlinear optical experiments. The energy landscape of myoglobin was probed by studying its low-temperature structural dynamics, using several spectral hole burning and photon echo techniques. The spectral diffusion of the heme group of the protein was studied on a time scale ranging from nanoseconds to several days while covering a temperature range from 100 {mK} to 23 K. The spectral line broadening, as measured in three-pulse stimulated photon echo experiments, occurs in a stepwise fashion, while the exact time dependence of the line width is critically dependent on temperature. From these results we obtained the energy barriers between the conformational states of the protein. Aging time dependent hole-burning experiments show that, at 100 {mK,} it takes several days for the protein to reach thermal equilibrium. When, after this period a spectral hole is burned, the line broadening induced by well-defined temperature cycles is partly reversed over a period of several hours. From this we conclude that a rough structure is superimposed on the overall shape of the potential energy surface of the protein. By combining the hole burning and photon echo results, we construct a detailed image of this energy landscape, supporting the general concept of a structural hierarchy. More specifically, we show that the number of conformational substates in the lower hierarchical tiers is much lower than was previously anticipated and, in fact, is comparable to the number of taxonomic substates.

Y. S. Lazurkin, M. D. Frank-Kamenetskii, E. N. Trifonov (1970): Melting of {DNA:} its study and application as a research method
Type: article by Biopolymers.
doi: 10.1002/bip.1970.360091102
link: http://www.ncbi.nlm.nih.gov/pubmed/4922326

H. Risken, T. Frank (1996): The {Fokker-Planck} Equation: Methods of Solutions and Applications
Type: book by Springer, Berlin.

J. Applequist (1963): On the {Helix-Coil} Equilibrium in Polypeptides
Type: article by The Journal of Chemical Physics.
doi: 10.1063/1.1733787
link: http://link.aip.org/link/?JCP/38/934/1

F. Schwabl (2006): Statistische Mechanik: Mit 186 Aufgaben
Type: book by Springer, Berlin.

C. R. Cantor, P. R. Schimmel (1980): Biophysical Chemistry: Part {III:} The Behavior of Biological Macromolecules: Pt.3
Type: book by W. H. Freeman & Co Ltd.

D. Hamada, S. Segawa, Y. Goto (1996): Non-native [alpha]-helical intermediate in the refolding of [beta]-lactoglobulin, a predominantly [beta]-sheet protein
Type: article by Nature Structural Biology.
doi: 10.1038/nsb1096-868
link: http://dx.doi.org/10.1038/nsb1096-868

F. Chiti, C. M. Dobson (2006): Protein misfolding, functional amyloid, and human disease
Type: article by Annual Review of Biochemistry.
doi: 10.1146/annurev.biochem.75.101304.123901
link: http://www.ncbi.nlm.nih.gov/pubmed/16756495
Abstract:

Peptides or proteins convert under some conditions from their soluble forms into highly ordered fibrillar aggregates. Such transitions can give rise to pathological conditions ranging from neurodegenerative disorders to systemic amyloidoses. In this review, we identify the diseases known to be associated with formation of fibrillar aggregates and the specific peptides and proteins involved in each case. We describe, in addition, that living organisms can take advantage of the inherent ability of proteins to form such structures to generate novel and diverse biological functions. We review recent advances toward the elucidation of the structures of amyloid fibrils and the mechanisms of their formation at a molecular level. Finally, we discuss the relative importance of the common main-chain and side-chain interactions in determining the propensities of proteins to aggregate and describe some of the evidence that the oligomeric fibril precursors are the primary origins of pathological behavior.

J. D. Bryngelson, J. N. Onuchic, N. D. Socci, P. G. Wolynes (1995): Funnels, pathways, and the energy landscape of protein folding: a synthesis
Type: article by Proteins: Structure, Function and Genetics.
doi: 10.1002/prot.340210302
link: http://www.ncbi.nlm.nih.gov/pubmed/7784423
Abstract:

The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation, that is, to the energy landscape. The statistical energy landscape approach explains when and why unique behaviors, such as specific folding pathways, occur in some proteins and more generally explains the distinction between folding processes common to all sequences and those peculiar to individual sequences. This approach also gives new, quantitative insights into the interpretation of experiments and simulations of protein folding thermodynamics and kinetics. Specifically, the picture provides simple explanations for folding as a two-state first-order phase transition, for the origin of metastable collapsed unfolded states and for the curved Arrhenius plots observed in both laboratory experiments and discrete lattice simulations. The relation of these quantitative ideas to folding pathways, to uniexponential vs. multiexponential behavior in protein folding experiments and to the effect of mutations on folding is also discussed. The success of energy landscape ideas in protein structure prediction is also described. The use of the energy landscape approach for analyzing data is illustrated with a quantitative analysis of some recent simulations, and a qualitative analysis of experiments on the folding of three proteins. The work unifies several previously proposed ideas concerning the mechanism protein folding and delimits the regions of validity of these ideas under different thermodynamic conditions.

F. Parak, E. W. Knapp, D. Kucheida (1982): Protein dynamics: Mössbauer spectroscopy on deoxymyoglobin crystals
Type: article by Journal of Molecular Biology.
doi: 10.1016/0022-2836(82)90285-6
Abstract:

Mössbauer absorption experiments on {57Fe} of deoxygenated myoglobin crystals and on K4 {57Fe(CN)6} dissolved in the water of metmyoglobin crystals were performed over a large temperature range. At low temperatures the mean square displacements, x2, of the iron indicate solid-like behaviour of the whole system, whereas at higher temperatures protein-specific modes of motion contribute to x2{textgreater}. The protein dynamics are correlated with the mobility of the water within the protein crystals. A Brownian oscillator is used to model the protein-specific modes of motion measured at the {57Fe} nucleus. Three modes are necessary for understanding the Mössbauer spectrum. Two of them correspond to an extremely overdamped Brownian oscillator. The third mode can be understood as quasi-free diffusion. Whereas the protein molecule is frozen in conformational substates in the low temperature regime, it reaches transition states with a finite probability in the high temperature regime. The surface water mediates a possible trigger mechanism that switches on protein dynamics within a narrow temperature interval. Results from Mössbauer spectroscopy and from X-ray structure analysis are compared. *1 This work was supported by the Deutsche Forschungs Gemeinschaft {(Pa} 178/8 and {SFB} 143 C2).

C. Bossa, M. Anselmi, D. Roccatano, A. Amadei, B. Vallone, M. Brunori, A. Di Nola (2004): Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin
Type: article by Biophysical Journal.
doi: 10.1529/biophysj.103.037432
link: http://www.ncbi.nlm.nih.gov/pubmed/15189882
Abstract:

We report the results of an extended molecular dynamics simulation on the migration of photodissociated carbon monoxide in wild-type sperm whale myoglobin. Our results allow following one possible ligand migration dynamics from the distal pocket to the Xe1 cavity via a path involving the other xenon binding cavities and momentarily two additional packing defects along the pathway. Comparison with recent time resolved structural data obtained by Laue crystallography with subnanosecond to millisecond resolution shows a more than satisfactory agreement. In fact, according to time resolved crystallography, {CO,} after photolysis, can occupy the Xe1 and Xe4 cavities. However, no information on the trajectory of the ligand from the distal pocket to the Xe1 is available. Our results clearly show one possible path within the protein. In addition, although our data refer to a single trajectory, the local dynamics of the ligand in each cavity is sufficiently equilibrated to obtain local structural and thermodynamic information not accessible to crystallography. In particular, we show that the {CO} motion and the protein fluctuations are strictly correlated: free energy calculations of the migration between adjacent cavities show that the migration is not a simple diffusion but is kinetically or thermodynamically driven by the collective motions of the protein; conversely, the protein fluctuations are influenced by the ligand in such a way that the opening/closure of the passage between adjacent cavities is strictly correlated to the presence of {CO} in its proximity. The compatibility between time resolved crystallographic experiments and molecular dynamics simulations paves the way to a deeper understanding of the role of internal dynamics and packing defects in the control of ligand binding in heme proteins.

Kapitel 8

B. Alberts, A. Johnson, P. Walter, J. Lewis, M. Raff, K. Roberts (2008): Molecular Biology of the Cell
Type: book by Taylor & Francis.

R. Cahn, W. Ludwig (1985): Theorie der Wärme.
Type: book by Springer, Berlin.

H. G. Hansma, J. H. Hoh (1994): Biomolecular Imaging with the Atomic Force Microscope
Type: article by Annual Review of Biophysics and Biomolecular Structure.
doi: 10.1146/annurev.bb.23.060194.000555
link: http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.bb.23.060194.000555

D. T. Gillespie (1996): The mathematics of Brownian motion and Johnson noise
Type: article by American Journal of Physics.
doi: 10.1119/1.18210
link: http://link.aip.org/link/?AJP/64/225/1

N. Voiculetz, I. Motoc (1993): Specific Interactions and Biological Recognition Processes
Type: book by {CRC} Press Inc.

M. Radermacher Single molecules feel the force
Type: misc
link: http://physicsworld.com/cws/article/print/955
It was published through http://physicsworld.com/cws/article/print/955
Abstract:

Biophysicists are now able to study a whole host of living processes with unprecedented accuracy thanks to a microscope normally associated with surface science.

O. Livnah, E. A. Bayer, M. Wilchek, J. L. Sussman (1993): Three-dimensional structures of avidin and the avidin-biotin complex
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 90
link: http://www.pnas.org/content/90/11/5076.abstract
Abstract:

The crystal structures of a deglycosylated form of the egg-white glycoprotein avidin and of its complex with biotin have been determined to 2.6 and 3.0 A, respectively. The structures reveal the amino acid residues critical for stabilization of the tetrameric assembly and for the exceptionally tight binding of biotin. Each monomer is an eight-stranded antiparallel beta-barrel, remarkably similar to that of the genetically distinct bacterial analog streptavidin. As in streptavidin, binding of biotin involves a highly stabilized network of polar and hydrophobic interactions. There are, however, some differences. The presence of additional hydrophobic and hydrophilic groups in the binding site of avidin (which are missing in streptavidin) may account for its higher affinity constant. Two amino acid substitutions are proposed to be responsible for its susceptibility to denaturation relative to streptavidin. Unexpectedly, a residual N-acetylglucosamine moiety was detected in the deglycosylated avidin monomer by difference Fourier synthesis.

R. Merkel, P. Nassoy, A. Leung, K. Ritchie, E. Evans (1999): Energy landscapes of receptor-ligand bonds explored with dynamic force spectroscopy
Type: article by Nature.
doi: 10.1038/16219
link: http://dx.doi.org/10.1038/16219

B. Essevaz-Roulet, U. Bockelmann, F. Heslot (1997): Mechanical separation of the complementary strands of {DNA}
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/9342340
Abstract:

We describe the mechanical separation of the two complementary strands of a single molecule of bacteriophage lambda {DNA.} The 3' and 5' extremities on one end of the molecule are pulled progressively apart, and this leads to the opening of the double helix. The typical forces along the opening are in the range of 10-15 {pN.} The separation force signal is shown to be related to the local {GC} vs. {AT} content along the molecule. Variations of this content on a typical scale of 100-500 bases are presently detected.

L. Bergmann, C. Schaefer (2008): Lehrbuch der Experimentalphysik: Lehrbuch der Experimentalphysik 1. Mechanik - Akkustik - Wärme: Bd 1: Band 1
Type: book by Gruyter.

M. P. Sheetz (1998): Laser Tweezers in Cell Biology
Type: book by Academic Press.

F. Colonna-Cesari, D. Perahia, M. Karplus, H. Eklund, C. I. Brädén, O. Tapia (1986): Interdomain motion in liver alcohol dehydrogenase. Structural and energetic analysis of the hinge bending mode
Type: article by The Journal of Biological Chemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/3771574
Abstract:

A study of the hinge bending mode in the enzyme liver alcohol dehydrogenase is made by use of empirical energy functions. The enzyme is a dimer, with each monomer composed of a coenzyme binding domain and a catalytic domain with a large cleft between the two. Superposition of the apoenzyme and holoenzyme crystal structures is used to determine a rigid rotation axis for closing of the cleft. It is shown that a rigid body transformation of the apoenzyme to the holoenzyme structure corresponds to a 10 degrees rotation of the catalytic domain about this axis. The rotation is not along the least-motion path for closing of the cleft but instead corresponds to the catalytic domain coming closer to the coenzyme binding domain by a sliding motion. Estimation of the energy associated with the interdomain motion of the apoenzyme over a range of 90 degrees (-40 to 50 degrees, where 0 degrees corresponds to the minimized crystal structure) demonstrates that local structural relaxation makes possible large-scale rotations with relatively small energy increments. A variety of structural rearrangements associated with the domain motion are characterized. They involve the hinge region residues that provide the covalent connections between the two domains and certain loop regions that are brought into contact by the rotation. Differences between the energy minimized and the holoenzyme structures point to the existence of alternative conformations for loops and to the importance of the ligands in the structural rearrangements.

M. Rief, J. M. Fernandez, H. E. Gaub (1998): Elastically Coupled {Two-Level} Systems as a Model for Biopolymer Extensibility
Type: article by Physical Review Letters.
link: http://adsabs.harvard.edu/abs/1998PhRvL..81.4764R
Abstract:

We present Monte Carlo simulations for the elasticity of biopolymers

consisting of segments that can undergo conformational transitions. Based on the thermodynamics of an elastically coupled two-level system, the probability for a transition and a related change in length of each segment was calculated. Good agreement between this model description and measured data was found for both the polysaccharide dextran where the conformational changes are fast and the muscle protein titin where the marked rate dependence of the transition forces could be explained by nonequilibrium processes.

M. Rief, M. Gautel, F. Oesterhelt, J. M. Fernandez, H. E. Gaub (1997): Reversible Unfolding of Individual Titin Immunoglobulin Domains by {AFM}
Type: article by Science.
doi: 10.1126/science.276.5315.1109
link: http://www.sciencemag.org/cgi/content/abstract/276/5315/1109

R. Alon, D. A. Hammer, T. A. Springer (1995): Lifetime of the P-selectin-carbohydrate bond and its response to tensile force in hydrodynamic flow
Type: article by Nature.
doi: 10.1038/374539a0
link: http://dx.doi.org/10.1038/374539a0

L. Tskhovrebova, J. Trinick, J. A. Sleep, R. M. Simmons (1997): Elasticity and unfolding of single molecules of the giant muscle protein titin
Type: article by Nature.
doi: 10.1038/387308a0
link: http://dx.doi.org/10.1038/387308a0

D. E. Koshland (1958): Application of a Theory of Enzyme Specificity to Protein Synthesis
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 44
link: http://www.pnas.org/content/44/2/98.short

D. A. Simson, M. Strigl, M. Hohenadl, R. Merkel (1999): Statistical Breakage of Single Protein {A-IgG} Bonds Reveals Crossover from Spontaneous to {Force-Induced} Bond Dissociation
Type: article by Physical Review Letters.
link: http://adsabs.harvard.edu/abs/1999PhRvL..83..652S
Abstract:

Dynamic force spectroscopy was applied to single specific bonds between

immunoglobulins of type G and protein A, a staphylococcal receptor for {IgG.} The resulting spectra of yield forces indicated the crossover from force induced to spontaneous bond dissociation. Moreover, failure of unloaded bonds was observed directly. Extrapolation to vanishing loading rate and direct observation yielded coinciding results.

G. I. Bell (1978): Models for the specific adhesion of cells to cells
Type: article by Science.
doi: 10.1126/science.347575
link: http://www.sciencemag.org/cgi/content/abstract/200/4342/618
Abstract:

A theoretical framework is proposed for the analysis of adhesion between cells or of cells to surfaces when the adhesion is mediated by reversible bonds between specific molecules such as antigen and antibody, lectin and carbohydrate, or enzyme and substrate. From a knowledge of the reaction rates for reactants in solution and of their diffusion constants both in solution and on membranes, it is possible to estimate reaction rates for membrane-bound reactants. Two models are developed for predicting the rate of bond formation between cells and are compared with experiments. The force required to separate two cells is shown to be greater than the expected electrical forces between cells, and of the same order of magnitude as the forces required to pull gangliosides and perhaps some integral membrane proteins out of the cell membrane.

E. Evans, K. Ritchie (1997): Dynamic strength of molecular adhesion bonds.
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1184350&rendertype=abstract

T. A. Steitz, M. Shoham, W. S. Bennett (1981): Structural Dynamics of Yeast Hexokinase During Catalysis
Type: article by Royal Society of London Philosophical Transactions Series B.
link: http://adsabs.harvard.edu/abs/1981RSPTB.293...43S
Abstract:

The binding of the substrate glucose to yeast hexokinase results in a

substantial enzyme conformational change that is essential for catalysis and may be important for the enzyme's specificity, as well as the control of its activity. From high-resolution crystal structures of the monomeric enzyme crystallized both in the presence and in the absence of glucose, we find that glucose binds into the deep cleft that separates the molecule into two lobes and causes these two lobes to move together and close off the cleft. The structure of the hexokinase crystallized in the presence of xylose and {ADP} is being determined at low resolution. In this crystal form, the enzyme was thought to be in the conformation of the ternary complex. However, a low-resolution structure of this crystal form shows clearly that the enzyme is in the `open' form and is not a ternary complex. Crystals of the A isozyme with glucose and {ADP} may be. Further, chemically sequenced tryptic peptides are being incorporated into the model obtained by crystallographic refinement at 2.1 A resolution. Completion of the sequence and the structure of the ternary complex should allow a detailed description of the enzymatic mechanism of this kinase and the role of substrate-induced conformational changes in catalysis and control.

M. Carrion-Vazquez, A. F. Oberhauser, S. B. Fowler, P. E. Marszalek, S. E. Broedel, J. Clarke, J. M. Fernandez (1999): Mechanical and chemical unfolding of a single protein: A comparison
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 96
link: http://www.pnas.org/content/96/7/3694.abstract
Abstract:

Is the mechanical unraveling of protein domains by atomic force microscopy {(AFM)} just a technological feat or a true measurement of their unfolding? By engineering a protein made of tandem repeats of identical Ig modules, we were able to get explicit {AFM} data on the unfolding rate of a single protein domain that can be accurately extrapolated to zero force. We compare this with chemical unfolding rates for untethered modules extrapolated to 0 M denaturant. The unfolding rates obtained by the two methods are the same. Furthermore, the transition state for unfolding appears at the same position on the folding pathway when assessed by either method. These results indicate that mechanical unfolding of a single protein by {AFM} does indeed reflect the same event that is observed in traditional unfolding experiments. The way is now open for the extensive use of {AFM} to measure folding reactions at the single-molecule level. Single-molecule {AFM} recordings have the added advantage that they define the reaction coordinate and expose rare unfolding events that cannot be observed in the absence of chemical denaturants.

P. R. Kuser, S. Krauchenco, O. A. C. Antunes, I. Polikarpov (2000): The High Resolution Crystal Structure of Yeast Hexokinase {PII} with the Correct Primary Sequence Provides New Insights into Its Mechanism of Action
Type: article by Journal of Biological Chemistry.
doi: 10.1074/jbc.M910412199
link: http://www.jbc.org/cgi/content/abstract/275/27/20814
Abstract:

Hexokinase is the first enzyme in the glycolytic pathway, catalyzing the transfer of a phosphoryl group from {ATP} to glucose to form glucose 6-phosphate and {ADP.} Two yeast hexokinase isozymes are known, namely {PI} and {PII.} The crystal structure of yeast hexokinase {PII} from Saccharomyces cerevisiae without substrate or competitive inhibitor is determined and refined in a tetragonal crystal form at {2.2-A} resolution. The folding of the peptide chain is very similar to that of Schistosoma mansoni and previous yeast hexokinase models despite only 30% sequence identity between them. Distinct differences in conformation are found that account for the absence of glucose in the binding site. Comparison of the current model with S. mansoni and yeast hexokinase {PI} structures both complexed with glucose shows in atomic detail the rigid body domain closure and specific loop movements as glucose binds. A hydrophobic channel formed by strictly conserved hydrophobic residues in the small domain of the hexokinase is identified. The channel's mouth is close to the active site and passes through the small domain to its surface. The possible role of the observed channel in proton transfer is discussed.

J. DeChancie, K. N. Houk (2007): The Origins of Femtomolar {Protein–Ligand} Binding: Hydrogen Bond Cooperativity and Desolvation Energetics in the {Biotin–(Strept)Avidin} Binding Site
Type: article by Journal of the American Chemical Society.
doi: 10.1021/ja066950n
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2527462

U. Bockelmann, B. Essevaz-Roulet, F. Heslot (1997): Molecular {Stick-Slip} Motion Revealed by Opening {DNA} with Piconewton Forces
Type: article by Physical Review Letters.
doi: 10.1103/PhysRevLett.79.4489
link: http://link.aps.org/abstract/PRL/v79/p4489
Abstract:

We have pulled apart the two strands of a {DNA} double helix. The forces measured during this process show a sequence specific variation on the piconewton scale. Opening two helical molecules with the same sequence from opposite sides gives two signatures which are not simply related by symmetry. In a theoretical model, this is explained as a molecular stick-slip motion which does not involve instabilities and is determined by the sequence.

S. Chu (1992): Laser Trapping of neutral Particles
Type: article by Scientific American.
Abstract:

Lasers can be used to trap and manipulate electrically neutral particles. These techniques have allowed scientists to cool vapors to near absolute zero, develop new atomic clocks, and stretch single molecules of {DNA}

M. S. Z. Kellermayer, S. B. Smith, H. L. Granzier, C. Bustamante (1997): {Folding-Unfolding} Transitions in Single Titin Molecules Characterized with Laser Tweezers
Type: article by Science.
doi: 10.1126/science.276.5315.1112
link: http://www.sciencemag.org/cgi/content/abstract/276/5315/1112

J. M. Berg, L. Stryer, J. L. Tymoczko (2007): Biochemie
Type: book by Spektrum Akademischer Verlag.

E. Fischer (1894): Einfluss der Configuration auf die Wirkung der Enzyme
Type: article by Berichte der deutschen chemischen Gesellschaft.
link: http://dx.doi.org/10.1002/cber.18940270364
Abstract:

No Abstract.

M. Radmacher (1999): Single molecules feel the force
Type: article by Physics World.

K. Berg-Sørensen, H. Flyvbjerg (2004): Power spectrum analysis for optical tweezers
Type: article by Review of Scientific Instruments.
link: http://adsabs.harvard.edu/abs/2004RScI...75..594B
Abstract:

The force exerted by an optical trap on a dielectric bead in a fluid is

often found by fitting a Lorentzian to the power spectrum of Brownian motion of the bead in the trap. We present explicit functions of the experimental power spectrum that give the values of the parameters fitted, including error bars and correlations, for the best such χ2 fit in a given frequency range. We use these functions to determine the information content of various parts of the power spectrum, and find, at odds with lore, much information at relatively high frequencies. Applying the method to real data, we obtain perfect fits and calibrate tweezers with less than 1% error when the trapping force is not too strong. Relatively strong traps have power spectra that cannot be fitted properly with any Lorentzian, we find. This underscores the need for better understanding of the power spectrum than the Lorentzian provides. This is achieved using old and new theory for Brownian motion in an incompressible fluid, and new results for a popular photodetection system. The trap and photodetection system are then calibrated simultaneously in a manner that makes optical tweezers a tool of precision for force spectroscopy, local viscometry, and probably other applications.


Kapitel 9

T. M. Allen, P. R. Cullis (2004): Drug Delivery Systems: Entering the Mainstream
Type: article by Science.
doi: 10.1126/science.1095833
link: http://www.sciencemag.org/cgi/content/abstract/303/5665/1818
Abstract:

Drug delivery systems {(DDS)} such as lipid- or polymer-based nanoparticles can be designed to improve the pharmacological and therapeutic properties of drugs administered parenterally. Many of the early problems that hindered the clinical applications of particulate {DDS} have been overcome, with several {DDS} formulations of anticancer and antifungal drugs now approved for clinical use. Furthermore, there is considerable interest in exploiting the advantages of {DDS} for in vivo delivery of new drugs derived from proteomics or genomics research and for their use in ligand-targeted therapeutics.

G. Blobel (1980): Intracellular protein topogenesis
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=348522&rendertype=abstract

M. Tanaka, E. Sackmann (2005): Polymer-supported membranes as models of the cell surface
Type: article by Nature.
doi: 10.1038/nature04164
link: http://dx.doi.org/10.1038/nature04164

S. L. Hardt (1979): Rates of diffusion controlled reactions in one, two and three dimensions
Type: article by Biophysical Chemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/16997220
Abstract:

The dimensionality of diffusion may markedly affect the rate and economy of diffusion controlled reactions. Moreover, the degree of dependence of the steady state rate of these reactions on the concentration of each of the two reacting species is also dictated by the dimensionality and it ranges from linear dependence in the three dimensional case to a nearly square dependence in the one dimensional case. These theoretical observations emerge from a direct analysis of the steady state diffusion controlled rates which are derived here using a simple straightforward approach. This approach is based on the conjecture that in the steady state the rate of diffusional encounters between the two reaction partners equals to the sum of the encounter rates of two independent processes which are obtained by alternately immobilizing one of the reaction partners while the other partner diffuses freely. Unlike Smoluchowski's classical approach, the presented point of view permits to obtain in a unified fashion reaction rates for all dimensionalities.

E. Sackmann, E. Bausch, L. Vonna (2002): Physics of Composite Cell Membrane and Actin Based Cytoskeleton
Type: incollection
link: http://dx.doi.org/10.1007/3-540-45701-1_7
Abstract:

The composite cell envelope is an impressive example of nature’s strategy to design complex materials and machineries with

unique and stunning physical properties by self-assembly of hierarchical structures. The most simple prototype of a composite cell membrane is the envelope (often called plasma membrane) of red blood cells.

E. Townes-Anderson, R. F. Dacheux, E. Raviola (1988): Rod photoreceptors dissociated from the adult rabbit retina
Type: article by Journal of Neuroscience.
link: http://www.jneurosci.org/cgi/content/abstract/8/1/320

J. A. F. Op den Kamp (1979): Lipid Asymmetry in Membranes
Type: article by Annual Review of Biochemistry.
doi: 10.1146/annurev.bi.48.070179.000403
link: http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.bi.48.070179.000403

R. Lipowsky, E. Sackmann (1996): Architecture and Function. Handbook of Biological Physics Vol I
Type: book by Elsevier.
Abstract:

The first volume of the Handbook deals with the amazing world of biomembranes and lipid bilayers. Part A describes all aspects related to the morphology of these membranes, beginning with the complex architecture of biomembranes, continues with a description of the bizarre morphology of lipid bilayers and concludes with technological applications of these membranes. The first two chapters deal with biomembranes, providing an introduction to the membranes of eucaryotes and a description of the evolution of membranes. The following chapters are concerned with different aspects of lipids including the physical properties of model membranes composed of lipid-protein mixtures, lateral phase separation of lipids and proteins and measurement of lipid-protein bilayer diffusion. Other chapters deal with the flexibility of fluid bilayers, the closure of bilayers into vesicles which attain a large variety of different shapes, and applications of lipid vesicles and liposomes.

Part B covers membrane adhesion, membrane fusion and the interaction of biomembranes with polymer networks such as the cytoskeleton. The first two chapters of this part discuss the generic interactions of membranes from the conceptual point of view. The following two chapters summarize the experimental work on two different bilayer systems. The next chapter deals with the process of contact formation, focal bounding and macroscopic contacts between cells. The cytoskeleton within eucaryotic cells consists of a network of relatively stiff filaments of which three different types of filaments have been identified. As explained in the next chapter much has been recently learned about the interaction of these filaments with the cell membrane. The final two chapters deal with membrane fusion.

W. Fritsche (2001): Mikrobiologie
Type: book by Spektrum Akademischer Verlag.

B. W. Shen, R. Josephs, T. L. Steck (1986): Ultrastructure of the intact skeleton of the human erythrocyte membrane
Type: article by Journal of Cell Biology.
doi: 10.1083/jcb.102.3.997
link: http://jcb.rupress.org/cgi/content/abstract/102/3/997

P. Michaely, D. R. Tomchick, M. Machius, R. G. W. Anderson (2002): Crystal structure of a 12 {ANK} repeat stack from human {ankyrinR}
Type: article by The {EMBO} Journal.
link: http://www.ncbi.nlm.nih.gov/pubmed/12456646
Abstract:

Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. The N-terminal, 'membrane-binding' domain of ankyrins contains 24 {ANK} repeats and mediates most binding activities. Repeats 13-24 are especially active, with known sites of interaction for the {Na/K} {ATPase,} {Cl/HCO(3)} anion exchanger, voltage-gated sodium channel, clathrin heavy chain and L1 family cell adhesion molecules. Here we report the crystal structure of a human {ankyrinR} construct containing {ANK} repeats 13-24 and a portion of the spectrin-binding domain. The {ANK} repeats are observed to form a contiguous spiral stack with which the spectrin-binding domain fragment associates as an extended strand. The structural information has been used to construct models of all 24 repeats of the membrane-binding domain as well as the interactions of the repeats with the {Cl/HCO(3)} anion exchanger and clathrin. These models, together with available binding studies, suggest that ion transporters such as the anion exchanger associate in a large central cavity formed by the {ANK} repeat spiral, while clathrin and cell adhesion molecules associate with specific regions outside this cavity.

E. Sackmann (2006): Thermo-elasticity and adhesion as regulators of cell membrane architecture and function
Type: article by Journal of Physics: Condensed Matter.
link: http://www.iop.org/EJ/abstract/0953-8984/18/45/R02/
Abstract:

Elastic forces and structural phase transitions control the

architecture and function of bio-membranes from the molecular to the microscopic scale of organization. The multi-component lipid bilayer matrix behaves as a pseudo-ternary system. Together with elastically and electrostatically mediated specific lipid-protein interaction mechanisms, fluid-fluid phase separation can occur at physiological temperatures. This can drive the transient generation of micro-domains of distinct composition within multi-component lipid-protein alloys, enabling cells to optimize the efficiency of biochemical reactions by facilitating or inhibiting the access of enzymes by distinct substrates or regulatory proteins. Together with global shape changes governed by the principle of minimum bending energy and induced curvature by macromolecular adsorption, phase separation processes can also play a key role for the sorting of lipids and proteins between intracellular compartments during the vesicle mediated intracellular material transport. Cell adhesion is another example of mechanical force controlled membrane processes. By interplay of attractive lock and key forces, long range disjoining pressures mediated by repeller molecules or membrane undulations and elastic interfacial forces, adhesion induced domain formation can play a dual role for the immunological stimulation of lymphocytes and for the rapid control of the adhesion strength. The present picture of the thermo-elastic control of membrane processes based on concepts of local thermal equilibrium is still rudimentary and has to be extended in the future to account for the intrinsic non-equilibrium situation associated with the constant restructuring of the cellular compartments on a timescale of minutes.

U. Kaupp, K. Koch (1986): Mechanism of photoreception in vertebrate vision
Type: article by Trends in Biochemical Sciences.
doi: 10.1016/0968-0004(86)90232-X
link: https://www.cell.com/trends/biochemical-sciences/abstract/0968-0004(86)90232-X

G. Lee, K. Abdi, Y. Jiang, P. Michaely, V. Bennett, P. E. Marszalek (2006): Nanospring behaviour of ankyrin repeats
Type: article by Nature.
doi: 10.1038/nature04437
link: http://dx.doi.org/10.1038/nature04437

U. Seifert (1997): Configurations of fluid membranes and vesicles
Type: article by Advances in Physics.
link: http://adsabs.harvard.edu/abs/1997AdPhy..46...13S
Abstract:

Vesicles consisting of a bilayer membrane of amphiphilic lipid molecules

are remarkably flexible surfaces that show an amazing variety of shapes of different symmetry and topology. Owing to the fluidity of the membrane, shape transitions such as budding can be induced by temperature changes or the action of optical tweezers. Thermally excited shape fluctuations are both strong and slow enough to be visible by video microscopy. Depending on the physical conditions, vesicles adhere to and unbind from each other or a {substrate.This} article describes the systematic physical theory developed to understand the static and dynamic aspects of membrane and vesicle configurations. The preferred shapes arise from a competition between curvature energy, which derives from the bending elasticity of the membrane, geometrical constraints such as fixed surface area and fixed enclosed volume, and a signature of the bilayer aspect. These shapes of lowest energy are arranged into phase diagrams, which separate regions of different symmetry by continuous or discontinuous transitions. The geometrical constraints affect the fluctuations around these shapes by creating an effective {tension.For} vesicles of non-spherical topology, the conformal invariance of the curvature energy leads to conformal diffusion, which signifies a one-fold degeneracy of the ground state. Unbinding and adhesion transitions arise from the balance between attractive interactions and entropic repulsion or a cost in bending energy, respectively. Both the dynamics of equilibrium fluctuations and the dynamics of shape transformations are governed not only by viscous damping in the surrounding liquid but also by internal friction if the two monolayers slip over each other. More complex membranes such as that of the red blood cell exhibit a variety of new phenomena because of coupling between internal degrees of freedom and external geometry.

J. Kyte, R. F. Doolittle (1982): A simple method for displaying the hydropathic character of a protein
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/7108955

H. Lodish, A. Berk, C. A. Kaiser, M. Krieger, M. P. Scott, A. Bretscher (2007): Molecular Cell Biology
Type: book by Palgrave Macmillan.

S. Manno, Y. Takakuwa, K. Nagao, N. Mohandas (1995): Modulation of Erythrocyte Membrane Mechanical Function by {beta-Spectrin} Phosphorylation and Dephosphorylation
Type: article by Journal of Biological Chemistry.
doi: 10.1074/jbc.270.10.5659
link: http://www.jbc.org/cgi/content/abstract/270/10/5659
Abstract:

The mechanical properties of human erythrocyte membrane are largely regulated by submembranous protein skeleton whose principal components are [alpha]- and [beta]-spectrin, actin, protein 4.1, adducin, and dematin. All of these proteins, except for actin, are phosphorylated by various kinases present in the erythrocyte. In vitro studies with purified skeletal proteins and various kinases has shown that while phosphorylation of these proteins can modify some of the binary and ternary protein interactions, it has no effect on certain other interactions between these proteins. Most importantly, at present there is no direct evidence that phosphorylation of skeletal protein(s) alters the function of the intact membrane. To explore this critical issue, we have developed experimental strategies to determine the functional consequences of phosphorylation of [beta]spectrin on mechanical properties of intact erythrocyte membrane. We have been able to document that membrane mechanical stability is exquisitely regulated by phosphorylation of [beta]-spectrin by membrane-bound casein kinase I. Increased phosphorylation of [beta]-spectrin decreases membrane mechanical stability while decreased phosphorylation increases membrane mechanical stability. Our data for the first time demonstrate that phosphorylation of a skeletal protein in situ can modulate physiological function of native erythrocyte membrane.

R. B. Gennis (1989): Biomembranes. Molecular Structure and Function
Type: book by Springer, Berlin.

R. R. Kopito, H. F. Lodish (1985): Primary structure and transmembrane orientation of the murine anion exchange protein
Type: article by Nature.
doi: 10.1038/316234a0
link: http://dx.doi.org/10.1038/316234a0

G. Wald (1968): Molecular basis of visual excitation
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/4877437

V. Gerke, C. E. Creutz, S. E. Moss (2005): Annexins: linking Ca2+ signalling to membrane dynamics
Type: article by Nature Reviews. Molecular Cell Biology.
doi: 10.1038/nrm1661
link: http://www.ncbi.nlm.nih.gov/pubmed/15928709
Abstract:

Eukaryotic cells contain various Ca(2+)-effector proteins that mediate cellular responses to changes in intracellular Ca(2+) levels. A unique class of these proteins - annexins - can bind to certain membrane phospholipids in a Ca(2+)-dependent manner, providing a link between Ca(2+) signalling and membrane functions. By forming networks on the membrane surface, annexins can function as organizers of membrane domains and membrane-recruitment platforms for proteins with which they interact. These and related properties enable annexins to participate in several otherwise unrelated events that range from membrane dynamics to cell differentiation and migration.

R. Beckmann, D. Bubeck, R. Grassucci, P. Penczek, A. Verschoor, G. Blobel, J. Frank (1997): Alignment of Conduits for the Nascent Polypeptide Chain in the {Ribosome-Sec61} Complex
Type: article by Science.
doi: 10.1126/science.278.5346.2123
link: http://www.sciencemag.org/cgi/content/abstract/278/5346/2123

D. N. Wang (1994): Band 3 protein: structure, flexibility and function
Type: article by {FEBS} Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/8206153
Abstract:

The electroneutral exchange of chloride and bicarbonate across the human erythrocyte membrane is facilitated by Band 3, a 911 amino acid glycoprotein. The 43 {kDa} amino-terminal cytosolic domain binds the cytoskeleton, haemoglobin and glycolytic enzymes. The 52 {kDa} carboxyl-terminal membrane domain mediates anion transport. The protein is a functional dimer, in which the two subunits probably interact with one another by an allosteric mechanism. It is proposed that the link between the mobile cytoplasmic and the membrane-spanning domains of the protein is flexible, based on recent biochemical, biophysical and structural data. This explains the long-standing puzzle that attachment to the cytoskeletal spectrin and actin does not appear to restrict the rotational movement of the Band 3 protein in the erythrocyte membrane. In the Band 3 isoform from the Southeast Asian Ovalocytes {(SAO)} this link is altered, resulting a tighter attachment of the cytoskeleton to the plasma membrane and a more rigid red blood cell.

P. F. Devaux (1988): Phospholipid flippases
Type: article by {FEBS} Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/3292284
Abstract:

Protein mediated phospholipid translocation through membranes has been observed in rat liver endoplasmic reticulum and in the plasma membrane of erythrocytes as well as in a few other cell membranes. Lipid translocation in plasma membranes is {ATP} dependent and selectively accumulates aminophospholipids on the inner monolayers.

K. Palczewski, T. Kumasaka, T. Hori, C. A. Behnke, H. Motoshima, B. A. Fox, I. Le Trong, D. C. Teller, T. Okada, R. E. Stenkamp, M. Yamamoto, M. Miyano (2000): Crystal Structure of Rhodopsin: A G {Protein-Coupled} Receptor
Type: article by Science.
doi: 10.1126/science.289.5480.739
link: http://www.sciencemag.org/cgi/content/abstract/289/5480/739

G. A. Jamieson (1977): Mammalian Cell Membranes: Volume Two: The Diversity of Membranes
Type: book by {Butterworth-Heinemann} Ltd.

J. M. Berg, L. Stryer, J. L. Tymoczko (2007): Biochemie
Type: book by Spektrum Akademischer Verlag.

V. Bennett (2005): {Spectrin-Based} Membrane Skeleton: A Multipotential Adaptor Between Plasma Membrane and Cytoplasm
Type: article by Physiological Reviews.
link: http://physrev.physiology.org/cgi/content/abstract/71/1/330-r
Abstract:

Pages 1029-1065: Vann Bennett. {"Spectrin-Based} Membrane Skeleton: A Multipotential Adaptor Between Plasma Membrane and Cytoplasm." Page 1056: Ref. 36 should read {BENNETT,} H., and J. {CONDEELIS.} Isolation of an immunoreactive analogue of brain fodrin that is associated with the cell cortex of Dictyostelium amoebae. Cell Motil. Cytoskeleton 11: 303-317, 1988.

W. R. Bishop, R. M. Bell (1988): Assembly of phospholipids into cellular membranes: biosynthesis, transmembrane movement and intracellular translocation
Type: article by Annual Review of Cell Biology.
doi: 10.1146/annurev.cb.04.110188.003051
link: http://www.ncbi.nlm.nih.gov/pubmed/3058167

E. Ritter, K. Zimmermann, M. Heck, K. P. Hofmann, F. J. Bartl (2004): Transition of rhodopsin into the active metarhodopsin {II} state opens a new light-induced pathway linked to Schiff base isomerization
Type: article by The Journal of Biological Chemistry.
doi: 10.1074/jbc.M406857200
link: http://www.ncbi.nlm.nih.gov/pubmed/15322129
Abstract:

Rhodopsin bears 11-cis-retinal covalently bound by a protonated Schiff base linkage. 11-cis/all-trans isomerization, induced by absorption of green light, leads to active metarhodopsin {II,} in which the Schiff base is intact but deprotonated. The subsequent metabolic retinoid cycle starts with Schiff base hydrolysis and release of photolyzed all-trans-retinal from the active site and ends with the uptake of fresh 11-cis-retinal. To probe chromophore-protein interaction in the active state, we have studied the effects of blue light absorption on metarhodopsin {II} using infrared and time-resolved {UV-visible} spectroscopy. A light-induced shortcut of the retinoid cycle, as it occurs in other retinal proteins, is not observed. The predominantly formed illumination product contains all-trans-retinal, although the spectra reflect Schiff base reprotonation and protein deactivation. By its kinetics of formation and decay, its low temperature photointermediates, and its interaction with transducin, this illumination product is identified as metarhodopsin {III.} This species is known to bind all-trans-retinal via a reprotonated Schiff base and forms normally in parallel to retinal release. We find that its generation by light absorption is only achieved when starting from active metarhodopsin {II} and is not found with any of its precursors, including metarhodopsin I. Based on the finding of others that metarhodopsin {III} binds retinal in {all-trans-C(15)-syn} configuration, we can now conclude that light-induced formation of metarhodopsin {III} operates by Schiff base isomerization ("second switch"). Our reaction model assumes steric hindrance of the retinal polyene chain in the active conformation, thus preventing central double bond isomerization.

M. J. F. Broderick, S. J. Winder (2002): Towards a complete atomic structure of spectrin family proteins
Type: article by Journal of Structural Biology.
doi: 10.1006/jsbi.2002.4465
link: http://www.ncbi.nlm.nih.gov/pubmed/12064945
Abstract:

The spectrin family of proteins represents a discrete group of cytoskeletal proteins comprising principally alpha-actinin, spectrin, dystrophin, and homologues and isoforms. They all share three main structural and functional motifs, namely, the spectrin repeat, {EF-hands,} and a {CH} domain-containing actin-binding domain. These proteins are variously involved in organisation of the actin cytoskeleton, membrane cytoskeleton architecture, cell adhesion, and contractile apparatus. The highly modular nature of these molecules has been a hindrance to the determination of their complete structures due to the inherent flexibility imparted on the proteins, but has also been an asset, inasmuch as the individual modules were of a size amenable to structural analysis by both crystallographic and {NMR} approaches. Representative structures of all the major domains shared by spectrin family proteins have now been solved at atomic resolution, including in some cases multiple domains from several family members. High-resolution structures, coupled with lower resolution methods to determine the overall molecular shape of these proteins, allow us for the first time to build complete atomic structures of the spectrin family of proteins.

R. F. Schmidt, G. Thews, F. Lang (2000): Physiologie des Menschen
Type: book by Springer Berlin.

S. C. Liu, L. H. Derick, J. Palek (1987): Visualization of the hexagonal lattice in the erythrocyte membrane skeleton
Type: article by Journal of Cell Biology.
doi: 10.1083/jcb.104.3.527
link: http://jcb.rupress.org/cgi/content/abstract/104/3/527


Kapitel 10

M. Tanaka, E. Sackmann (2005): Polymer-supported membranes as models of the cell surface
Type: article by Nature.
doi: 10.1038/nature04164
link: http://dx.doi.org/10.1038/nature04164

P. F. F. Almeida, W. L. C. Vaz (1995): Lateral Diffusion in Membranes
Type: book by Elsevier Science, Amsterdam.

E. Evans, D. Needham (1987): Physical properties of surfactant bilayer membranes: thermal transitions, elasticity, rigidity, cohesion and colloidal interactions
Type: article by The Journal of Physical Chemistry.
doi: 10.1021/j100300a003
link: http://dx.doi.org/10.1021/j100300a003

P. C. Hiemenz, R. Rajagopalan (1997): Principles of Colloid and Surface Chemistry
Type: book by Marcel Dekker Inc.

M. Tomishige, A. Kusumi (1999): Compartmentalization of the Erythrocyte Membrane by the Membrane Skeleton: Intercompartmental Hop Diffusion of Band 3
Type: article by Molecular Biology of the Cell.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=25476

J. Seelig (1977): Deuterium magnetic resonance: theory and application to lipid membranes
Type: article by Quarterly Reviews of Biophysics.
link: http://www.ncbi.nlm.nih.gov/pubmed/335428

H. H. Mantsch, R. N. McElhaney (1991): Phospholipid phase transitions in model and biological membranes as studied by infrared spectroscopy
Type: article by Chemistry and Physics of Lipids.
link: http://www.ncbi.nlm.nih.gov/pubmed/2054905
Abstract:

Fourier transform infrared {(FT-IR)} spectroscopy is an extremely powerful yet non-perturbing physical technique for monitoring the conformation and dynamics of all portions of the phospholipid molecule. In this brief review we summarize some recent {FT-IR} spectroscopic studies of phospholipid phase transitions in model lipid bilayer and in biological membranes which illustrate the great utility of this technique. We show that {FT-IR} spectroscopy can accurately monitor the gel to liquid-crystalline phase transition and can provide a large amount of detailed information about phospholipid structure and organization in both the gel and liquid-crystalline states of lipid bilayers.

J. H. Ipsen, O. G. Mouritsen, M. J. Zuckermann (1989): Theory of thermal anomalies in the specific heat of lipid bilayers containing cholesterol.
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1280522&rendertype=abstract

H. Heller, M. Schaefer, K. Schulten (1993): Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase
Type: article by The Journal of Physical Chemistry.
doi: 10.1021/j100133a034
link: http://dx.doi.org/10.1021/j100133a034

J. N. Israelachvili (1991): Intermolecular and Surface Forces: With Applications to Colloidal and Biological Systems
Type: book by Academic Pr Inc.

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.7, Elastizitätstheorie: {BD} 7
Type: book by Deutsch {(Harri)}.

E. Sackmann (2006): Thermo-elasticity and adhesion as regulators of cell membrane architecture and function
Type: article by Journal of Physics: Condensed Matter.
link: http://www.iop.org/EJ/abstract/0953-8984/18/45/R02/
Abstract:

Elastic forces and structural phase transitions control the

architecture and function of bio-membranes from the molecular to the microscopic scale of organization. The multi-component lipid bilayer matrix behaves as a pseudo-ternary system. Together with elastically and electrostatically mediated specific lipid-protein interaction mechanisms, fluid-fluid phase separation can occur at physiological temperatures. This can drive the transient generation of micro-domains of distinct composition within multi-component lipid-protein alloys, enabling cells to optimize the efficiency of biochemical reactions by facilitating or inhibiting the access of enzymes by distinct substrates or regulatory proteins. Together with global shape changes governed by the principle of minimum bending energy and induced curvature by macromolecular adsorption, phase separation processes can also play a key role for the sorting of lipids and proteins between intracellular compartments during the vesicle mediated intracellular material transport. Cell adhesion is another example of mechanical force controlled membrane processes. By interplay of attractive lock and key forces, long range disjoining pressures mediated by repeller molecules or membrane undulations and elastic interfacial forces, adhesion induced domain formation can play a dual role for the immunological stimulation of lymphocytes and for the rapid control of the adhesion strength. The present picture of the thermo-elastic control of membrane processes based on concepts of local thermal equilibrium is still rudimentary and has to be extended in the future to account for the intrinsic non-equilibrium situation associated with the constant restructuring of the cellular compartments on a timescale of minutes.

H. Träuble (1971): The movement of molecules across lipid membranes: A molecular theory
Type: article by Journal of Membrane Biology.
doi: 10.1007/BF02431971
link: http://dx.doi.org/10.1007/BF02431971
Abstract:

Summary The movement of molecules across membranes is discussed in terms of thermal fluctuations in the hydrocarbon chains of the

membrane lipids. The thermal motion of the hydrocarbon chains results in the formation of conformational isomers, so-called kink-isomers of the hydrocarbon chains. {“Kinks”} may be pictured as mobile structural defects which represent small, mobile free volumes in the hydrocarbon phase of the membrane. The diffusion coefficient of kinks is calculated to be 10−5 cm2/sec; thus kinks diffusion is a fast process. Small molecules can enter into the free volumes of kinks and migrate across the membrane together with the kinks; thus kinks may be regarded as intrinsic carriers of lipid membranes. An expression is derived from this model for the flow of molecules through lipid membranes. The calculated value for the water permeability is compatible with measurements on lipid bilayers.

G. Buldt, H. U. Gally, A. Seelig, J. Seelig, G. ZACCAI (1978): Neutron diffraction studies on selectively deuterated phospholipid bilayers
Type: article by Nature.
doi: 10.1038/271182a0
link: http://dx.doi.org/10.1038/271182a0

A. Ben-Shaul Molecular theory of chain packing, elasticity and lipid-protein interaction in lipid bilayers
Type: article

P. G. Saffman, M. Delbrück (1975): Brownian motion in biological membranes
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 72
link: http://www.pnas.org/content/72/8/3111.abstract
Abstract:

Brownian motion (diffusion) of particles in membranes occurs in a highly anisotropic environment. For such particles a translational mobility (independent of velocity) can be defined if the viscosity of the liquid embedding the membrane is taken into account. The results of a model calculation are presented. They suggest that for a realistic situation translational diffusion should be about four times faster in relation to rotational diffusion than in the isotropic case.

O. Albrecht, H. Gruler, E. Sackmann (1978): Polymorphism of phospholipid monolayers
Type: article by Journal de Physique.
doi: 10.1051/jphys:01978003903030100

S. T. Hess, S. Huang, A. A. Heikal, W. W. Webb (2002): Biological and Chemical Applications of Fluorescence Correlation Spectroscopy: A Review†
Type: article by Biochemistry.
doi: 10.1021/bi0118512
link: http://dx.doi.org/10.1021/bi0118512

P. Schwille, E. Haustein (2001): Fluorescence Correlation Spectroscopy
Type: book
Abstract:

The recent development of single molecule detection techniques has opened new horizons for the study of individual macromolecules under physiological conditions. Conformational subpopulations, internal dynamics and activity of single biomolecules, parameters that have so far been hidden in large ensemble averages, are now being unveiled. Herein, we review a particular attractive solution-based single molecule technique, fluorescence correlation spectroscopy {(FCS).} This time-averaging fluctuation analysis which is usually performed in Confocal setups combines maximum sensitivity with high statistical confidence. {FCS} has proven to be a very versatile and powerful tool for detection and temporal investigation of biomolecules at ultralow concentrations on surfaces, in solution, and in living cells. The introduction of dual-color cross-correlation and two-photon excitation in {FCS} experiments is currently increasing the number of promising applications of {FCS} to biological research.

S. König, W. Pfeiffer, T. Bayerl, D. Richter, E. Sackmann (1992): Molecular dynamics of lipid bilayers studied by incoherent quasi-elastic neutron scattering
Type: article by Journal de Physique {II}.
doi: 10.1051/jp2:1992100

H. E. Stanley (1971): Introduction to Phase Transitions and Critical Phenomena
Type: book by {Oxf.U.P.}.

O. G. Mouritsen, M. Bloom (1984): Mattress model of lipid-protein interactions in membranes.
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1435039&rendertype=abstract

E. Evans, E. Sackmann (1988): Translational and Rotational Drag Coefficients for a Disk Moving in a Liquid Membrane Associated with a Rigid Substrate
Type: article by Journal of Fluid Mechanics Digital Archive.
doi: 10.1017/S0022112088003106
link: http://journals.cambridge.org/action/displayAbstract;jsessionid=D698D6F9D374DDAE983E12893A26D888.tomcat1?fromPage=online&aid=394801

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.6, Hydrodynamik: {BD} 6
Type: book by Deutsch {(Harri)}.

J. Rika, T. Binkert (1989): Direct measurement of a distinct correlation function by fluorescence cross correlation
Type: article by Physical Review A..
link: http://www.ncbi.nlm.nih.gov/pubmed/9901536

G. J. Schütz, G. Kada, V. P. Pastushenko, H. Schindler (2000): Properties of lipid microdomains in a muscle cell membrane visualized by single molecule microscopy
Type: article by The {EMBO} Journal.
doi: 10.1093/emboj/19.5.892
link: http://www.ncbi.nlm.nih.gov/pubmed/10698931
Abstract:

The lateral motion of single fluorescence labeled lipid molecules was imaged in native cell membranes on a millisecond time scale and with positional accuracy of approximately 50 nm, using 'single dye tracing'. This first application of single molecule microscopy to living cells rendered possible the direct observation of lipid-specific membrane domains. These domains were sensed by a lipid probe with saturated acyl chains as small areas in a liquid-ordered phase: the probe showed confined but fast diffusion, with high partitioning (approximately 100-fold) and long residence time (approximately 13 s). The analogous probe with mono-unsaturated chains diffused predominantly unconfined within the membrane. With approximately 15 saturated probes per domain, the locations, sizes, shapes and motions of individual domains became clearly visible. Domains had a size of 0.7 micrometer (0.2-2 micrometer), covering approximately 13% of total membrane area. Both the liquid-ordered phase characteristics and the sizes of domains match properties of membrane fractions described as detergent-resistant membranes {(DRMs),} strongly suggesting that the domains seen are the in vivo correlate of {DRMs} and thus may be identified as lipid rafts.

J. M. Seddon, R. H. Templer (1995): Polymorphism of {Lipid-Water} Systems in Structure and Dynamics of Membranes. From Cells to Vesicles
Type: article by Structure and Dynamics of Membranes, Generic and Specific Interaction, Handbook of Biological Physics, Elsevier, Amsterdam.

G. Breton, J. Danyluk, F. Ouellet, F. Sarhan (2000): Biotechnological applications of plant freezing associated proteins
Type: article by Biotechnology Annual Review.
link: http://www.ncbi.nlm.nih.gov/pubmed/11193297
Abstract:

Plants use a wide array of proteins to protect themselves against low temperature and freezing conditions. The identification of these freezing tolerance associated proteins and the elucidation of their cryoprotective functions will have important applications in several fields. Genes encoding structural proteins, osmolyte producing enzymes, oxidative stress scavenging enzymes, lipid desaturases and gene regulators have been used to produce transgenic plants. These studies have revealed the potential capacity of different genes to protect against temperature related stresses. In some cases, transgenic plants with significant cold tolerance have been produced. Furthermore, the biochemical characterization of the cold induced antifreeze proteins and dehydrins reveals many applications in the food and the medical industries. These proteins are being considered as food additives to improve the quality and shelf-life of frozen foods, as cryoprotective agents for organ and cell cryopreservation, and as chemical adjuvant in cancer cryosurgery.

M. Bee (1988): Quasielastic Neutron Scattering: Principles and Applications in Solid State Chemistry, Biology and Materials Science
Type: book by Institute of Physics Publishing.

D. Axelrod, D. E. Koppel, J. Schlessinger, E. Elson, W. W. Webb (1976): Mobility measurement by analysis of fluorescence photobleaching recovery kinetics.
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1334945&rendertype=abstract

H. Möhwald (1996): Phospholipid Monolayers
Type: article by Handbook of Biological Physics, Elsevier.

H. J. Galla, W. Hartmann, U. Theilen, E. Sackmann (1979): On two-dimensional passive random walk in lipid bilayers and fluid pathways in biomembranes
Type: article by The Journal of Membrane Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/40032
Abstract:

The lateral mobility of pyrene, pyrene decanoic acid, and 1-palmitoyl-2-pyrene decanoyl-phosphatidyl choline (pyrene lecithin) in lipid bilayers is determined by the excimer formation technique. This method is applied to vesicles of lecithins differing in chain length and in the degree of saturation of the hydrocarbon chains. These values are compared with results in cephalins of different chain length and in dipalmitoyl phosphatidic acid at variable {pH.} The influence of cholesterol is investigated. The results are analyzed in terms of the Montroll model of two-dimensional random walk. The jump frequency of the probe molecule within the lipid lattice is obtained. The advantage of this measure of transport in lipid layers is that it does not involve lipid lattice parameters. The main results of the present work are: (i) The lateral mobility of a given solute molecule in lamellae of saturated lecithins is independent of hydrocarbon chain length and rather a universal function of temperature. (ii) In unsaturated dioleyl lecithin the amphiphatic molecules have lateral mobilities of the same size as in saturated lipids. The jump frequency of pyrene, however, is by a factor of two larger in the unsaturated lecithin. (iii) The jump frequencies in phosphatidyl ethanolamines are about equal to those in lecithins. (iv) In phosphatidic acid layers the hopping frequencies depend on the charges of the head groups of both the lipids and the probes. (v) Cholesterol strongly reduces the jump frequency in fluid layers. (vi) The lateral mobility in biological membranes is comparable to that in artificial lipid bilayers. The experimental results are discussed in terms of the free volume model of diffusion in fluids. Good agreement with the predictions made from this model is found. A striking result is the observation of a tilt in dioleyl-lecithin bilayer membranes from the hopping frequencies of pyrene and pyrene lecithin. A tilt angle of phi = 17 degrees is estimated.

C. Tanford (1980): The Hydrophobic Effect: Formation of Micelles and Biological Membranes
Type: book by John Wiley & Sons Inc.

T. Köchy, T. M. Bayerl (1993): Lateral diffusion coefficients of phospholipids in spherical bilayers on a solid support measured by {2H-nuclear-magnetic-resonance} relaxation
Type: article by Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics.
link: http://www.ncbi.nlm.nih.gov/pubmed/9960231

C. Gliss, O. Randel, H. Casalta, E. Sackmann, R. Zorn, T. Bayerl (1999): Anisotropic motion of cholesterol in oriented {DPPC} bilayers studied by quasielastic neutron scattering: the liquid-ordered phase.
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1300333&rendertype=abstract

J. F. Nagle, R. Zhang, S. Tristram-Nagle, W. Sun, H. I. Petrache, R. M. Suter (1996): X-ray structure determination of fully hydrated L alpha phase dipalmitoylphosphatidylcholine bilayers.
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1225068&rendertype=abstract

K. Tu, M. L. Klein, D. J. Tobias (1998): Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer.
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1299887&rendertype=abstract

L. Saiz, M. L. Klein (2002): Computer simulation studies of model biological membranes
Type: article by Accounts of chemical research.

G. Büldt, H. U. Gally, J. Seelig, G. Zaccai (1979): Neutron diffraction studies on phosphatidylcholine model membranes. I. Head group conformation
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/537074

M. Bloom, E. Evans, O. G. Mouritsen (1991): Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective
Type: article by Quarterly Reviews of Biophysics.
link: http://www.ncbi.nlm.nih.gov/pubmed/1749824

J. H. Ipsen, O. G. Mouritsen, M. Bloom (1990): Relationships between lipid membrane area, hydrophobic thickness, and acyl-chain orientational order. The effects of cholesterol.
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1280735&rendertype=abstract

F. Jähnig (1976): Electrostatic free energy and shift of the phase transition for charged lipid membranes
Type: article by Biophysical Chemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/953150
Abstract:

For a charged membrane in an electrolyte solution the electrostatic free energy is derived treating the system as a diffuse double layer. The dependence of the energy on external parameters like surface charge density and temperature is obtained and the physical basis discussed. As an application the charges are shown to exert an electrostatic surface pressure on the lipid chain packing which leads to a shift in the phase transition of membranes. The results confirm the interpretation of experimental data as given by Träuble et al. in the accompanying paper.

K. Mortensen, W. Pfeiffer, E. Sackmann, W. Knoll (1988): Structural properties of a phosphatidylcholine-cholesterol system as studied by small-angle neutron scattering: ripple structure and phase diagram
Type: article by Biochimica Et Biophysica Acta.
link: http://www.ncbi.nlm.nih.gov/pubmed/3191122
Abstract:

Small-angle neutron scattering has been used to study structural features of lamellar bilayer membranes of dimyristoylphosphatidylcholine {(DMPC)} and {DMPC} mixed with various amount of cholesterol. The studies were recorded at a fixed hydration level of 17% {2H2O,} i.e. just below saturation. Bragg reflections gives information on the ripple structure and on the bilayer periodicity. The crystalline Lc phase, which was stabilized after long time storage at low temperature, exhibits major small angle scattering when cholesterol is mixed into the membrane. The intermediate P beta' gel-phase, which is characteristic by the rippled structure, is dramatically stabilized by the introduction of cholesterol. The ripple structure depends significantly both on the cholesterol content and on the temperature. At high temperatures, T greater than 15 degrees C, the inverse ripple periodicity varies basically linearly with cholesterol content, and approach zero (i.e. periodicity goes to infinite) at 20 mol% cholesterol, approximately. At lower temperatures the correlation is more complex. The data indicate additional phase boundaries below 2 mol% and at approx. 8 mol%. Secondary rippled structures are observed in the low temperature L beta'-phase for cholesterol content below approx. 8 mol%. The data gives detailed insight into the phosphatidylcholine cholesterol phase diagram, which is discussed on the basis of a simple model in which the cholesterol complexes are fixed to the defect stripes of the rippled structure.

A. Tardieu, V. Luzzati, F. C. Reman (1973): Structure and polymorphism of the hydrocarbon chains of lipids: a study of lecithin-water phases
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/4738730

E. Evans, F. Ludwig (2000): Dynamic strengths of molecular anchoring and material cohesion in fluid biomembranes
Type: article by Journal of Physics Condensed Matter.
link: http://adsabs.harvard.edu/abs/2000JPCM...12..315E
Abstract:

Building on Kramers' theory for reaction kinetics in liquids and using

laboratory experiments, we show how strengths of molecular anchoring and material cohesion in fluid-lipid membranes increase with rate of force and tension loading. Expressed on a scale of log(loading rate), the dynamic spectra of pull-out forces and rupture tensions image the microscopic and mesoscopic energy barriers traversed in molecular extraction and membrane failure. To capture such images, we have pulled single molecules from membranes with force rates from 1 to 104 {pN} s-1 and ruptured giant membrane vesicles with tension rates from 10-2 to 102 {mN} m-1 s-1 .

D. Turnbull, M. H. Cohen (1961): {Free-Volume} Model of the Amorphous Phase: Glass Transition
Type: article by The Journal of Chemical Physics.
doi: 10.1063/1.1731549
link: http://link.aip.org/link/?JCP/34/120/1
Abstract:

Free volume vf is defined as that part of the thermal expansion, or excess volume Deltav-bar which can be redistributed without energy change. Assuming a {Lennard-Jones} potential function for a molecule within its cage in the condensed phase, it can be shown that at small Deltav-bar considerable energy is required to redistribute the excess volume; however, at Deltav-bar considerably greater than some value deltav-bar g (corresponding to potentials within the linear region), most of the volume added can be redistributed freely. The transition from glass to liquid may be associated with the introduction of appreciable free volume into the system. Free volume will be distributed at random within the amorphous phase and there is a contribution to the entropy from this randomness which is not present in the entropy of the crystalline phase. According to our model all liquids would become glasses at sufficiently low temperature if crystallization did not intervene. Therefore whether or not a glass forms is determined by the crystallization kinetic constants and the cooling rate of the liquid. The experience on the glass formation is consistent with the generalization: at a given level of cohesive energy the glass-forming tendency of a substance in a particular class is greater the less is the ratio of the energy to the entropy of crystallization.

M. A. Medina, P. Schwille (2002): Fluorescence correlation spectroscopy for the detection and study of single molecules in biology
Type: article by {BioEssays}.
doi: 10.1002/bies.10118
link: http://dx.doi.org/10.1002/bies.10118
Abstract:

The recent development of single molecule detection techniques has opened new horizons for the study of individual macromolecules under physiological conditions. Conformational subpopulations, internal dynamics and activity of single biomolecules, parameters that have so far been hidden in large ensemble averages, are now being unveiled. Herein, we review a particular attractive solution-based single molecule technique, fluorescence correlation spectroscopy {(FCS).} This time-averaging fluctuation analysis which is usually performed in Confocal setups combines maximum sensitivity with high statistical confidence. {FCS} has proven to be a very versatile and powerful tool for detection and temporal investigation of biomolecules at ultralow concentrations on surfaces, in solution, and in living cells. The introduction of dual-color cross-correlation and two-photon excitation in {FCS} experiments is currently increasing the number of promising applications of {FCS} to biological research. {BioEssays} 24:758-764, 2002. © 2002 Wiley Periodicals, Inc.

L. van Hove (1954): Temperature Variation of the Magnetic Inelastic Scattering of Slow Neutrons
Type: article by Physical Review.
doi: 10.1103/PhysRev.93.268
link: http://link.aps.org/abstract/PR/v93/p268
Abstract:

The main features of the temperature variation of the magnetic inelastic scattering of slow neutrons in iron, recently measured by Palevsky and Hughes, are accounted for, by use of a theoretical description of the scattering in terms of the correlation between pairs of spins at different positions and different times. Proofs will be given in a later paper devoted to a general discussion of space-time correlations and of their use in scattering theory.


Kapitel 11

A. Zilker, M. Ziegler, E. Sackmann (1992): Spectral analysis of erythrocyte flickering in the 0.3–4-mum-1 regime by microinterferometry combined with fast image processing
Type: article by Physical Review A.
doi: 10.1103/PhysRevA.46.7998
link: http://link.aps.org/abstract/PRA/v46/p7998
Abstract:

Reflection interference microscopy in combination with real-time image processing was applied to determine the spatial spectrum of the mean-square amplitude of erythrocyte flickering in the wave-vector regime 0.3≤q≤4 μm-1. The mean-square amplitude scales as q4±ε for q≥0.7 μm-1, suggesting that flickering is dominated mainly by bending stiffness. We measured a bending modulus of Kc=(2±0.5)×10-20 N m as compared to Kc=(5±1.5)×10-20 N m found for dimyristoylphosphatidylcholine {(DMPC)} vesicles with the same technique.

T. Auth, S. A. Safran, N. S. Gov (2007): Fluctuations of coupled fluid and solid membranes with application to red blood cells
Type: article by Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics.
link: http://www.ncbi.nlm.nih.gov/pubmed/18233690
Abstract:

The fluctuation spectra and the intermembrane interaction of two membranes at a fixed average distance are investigated. Each membrane can either be a fluid or a solid membrane, and in isolation, its fluctuations are described by a bare or a wave-vector-dependent bending modulus, respectively. The membranes interact via their excluded-volume interaction; the average distance is maintained by an external, homogeneous pressure. For strong coupling, the fluctuations can be described by a single, effective membrane that combines the elastic properties. For weak coupling, the fluctuations of the individual, noninteracting membranes are recovered. The case of a composite membrane consisting of one fluid and one solid membrane can serve as a microscopic model for the plasma membrane and cytoskeleton of the red blood cell. We find that, despite the complex microstructure of bilayers and cytoskeletons in a real cell, the fluctuations with wavelengths lambda greater, similar 400 nm are well described by the fluctuations of a single, polymerized membrane (provided that there are no inhomogeneities of the microstructure). The model is applied to the fluctuation data of discocytes ("normal" red blood cells), a stomatocyte, and an echinocyte. The elastic parameters of the membrane and an effective temperature that quantifies active, metabolically driven fluctuations are extracted from the experiments.

E. A. Evans (1974): Bending Resistance and Chemically Induced Moments in Membrane Bilayers
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1334588&rendertype=abstract

R. Cahn, W. Ludwig (1985): Theorie der Wärme.
Type: book by Springer, Berlin.

Y. C. Fung (1993): Biomechanics. Mechanical Properties of Living Tissues
Type: book by {Springer-Verlag} {GmbH}.

R. W. Cahn, P. Haasen (1996): Physical Metallurgy, Revised and Enhanced Edition 3 Volume Set
Type: book by Elsevier Science & Technology.

Mark A. Peterson (1992): Linear response of the human erythrocyte to mechanical stress
Type: article by Physical Review A.
doi: 10.1103/PhysRevA.45.4116
link: http://link.aps.org/abstract/PRA/v45/p4116
Abstract:

The human erythrocyte readily changes its shape in response to mechanical stress. Geometrical methods are used to analyze this effect in three experiments: thermal shape fluctuation (flicker), electrodeformation, and tank treading, which is the circulation of the membrane around the interior fluid in a shear flow. Comparison with existing data indicates that both flicker and tank treading represent the motion of a fluid membrane. At the same time it is a solid membrane (i.e., possessing a shear modulus) that resists large-scale shape change. This combination of fluid and solid membrane properties is in some ways paradoxical.

S. Svetina, B. Zeks (1989): Membrane bending energy and shape determination of phospholipid vesicles and red blood cells
Type: article by European Biophysics Journal: {EBJ}.
link: http://www.ncbi.nlm.nih.gov/pubmed/2766997
Abstract:

A procedure is developed to calculate red blood cell and phospholipid vesicle shapes within the bilayer couple model of the membrane. The membrane is assumed to consist of two laterally incompressible leaflets which are in close contact but unconnected. Shapes are determined by minimizing the membrane bending energy at a given volume of a cell {(V),} given average membrane area {(A)} and given difference of the areas of two leaflets (delta A). Different classes of shapes exist in parts of the v/delta a phase diagram, where v and delta a are the volume and the leaflet area difference relative to the sphere with area A. The limiting shapes are composed of sections of spheres with only two values allowed for their radii. Two low energy axisymmetrical classes, which include discocyte and stomatocyte shapes are studied and their phase diagrams are analyzed. For v= 0.6, the discocyte is the lowest energy shape, which transforms by decreasing delta a continuously into a stomatocyte. The spontaneous membrane curvature {(C0)} and compressibility of membrane leaflets can be incorporated into the model. A model, where delta A is free and C0 determines the shapes at given V and A, is also studied. In this case, by decreasing C0, a discocyte transforms discontinuously into an almost closed stomatocyte.

H. P. Duwe, E. Sackmann (1990): Bending elasticity and thermal excitations of lipid bilayer vesicles: Modulation by solutes
Type: article by Physica A Statistical Mechanics and its Applications.
link: http://adsabs.harvard.edu/abs/1990PhyA..163..410D
Abstract:

We present high-precision measurements of the bending elastic moduli of

bilayers of a variety of different lipids and of modifications of the flexural rigidity by solutes. The measurements are based on the Fourier analysis of thermally excited membrane undulations (vesicle shape fluctuations) using a recently developed dynamic image processing method. Measurements of the bending modulus as a function of the undulation wave vector provide information on the limitation of the excitations by the constraint of finite membrane area (surface tension effects) and by transient lateral tensions arising in each monolayer by restricted diffusion at high wave vectors. Measurements of the autocorrelation function of the undulation amplitudes provide a further test of the theoretical models. Studies of the effect of solutes show that cholesterol increases the bending modulus of dimyristoylphosphatidylcholine from Kc = 1. 1 � 10-12 erg to 4.2 � 10-12 erg (at 30 mol%). Incorporation of a short bipolar lipid reduces Kc to the order of {kT.} Finally we present a variety of shape changes of vesicle and provide evidence for the stabilization of metastable non-equilibrium shapes by lateral phase separation.

H.-G. Döbereiner, E. Evans, M. Kraus, U. Seifert, M. Wortis (1997): Mapping vesicle shapes into the phase diagram: A comparison of experiment and theory
Type: article by Physical Review E.
doi: 10.1103/PhysRevE.55.4458
link: http://link.aps.org/abstract/PRE/v55/p4458
Abstract:

Phase-contrast microscopy is used to monitor the shapes of micron-scale fluid-phase phospholipid-bilayer vesicles in an aqueous solution. At fixed temperature, each vesicle undergoes thermal shape fluctuations. We are able, experimentally, to characterize the thermal shape ensemble by digitizing the vesicle outline in real time and storing the time sequence of images. Analysis of this ensemble using the area-difference-elasticity {(ADE)} model of vesicle shapes allows us to associate (map) each time sequence to a point in the zero-temperature (shape) phase diagram. Changing the laboratory temperature modifies the control parameters (area, volume, etc.) of each vesicle, so it sweeps out a trajectory across the theoretical phase diagram. It is a nontrivial test of the {ADE} model to check that these trajectories remain confined to regions of the phase diagram where the corresponding shapes are locally stable. In particular, we study the thermal trajectories of three prolate vesicles which, upon heating, experienced a mechanical instability leading to budding. We verify that the position of the observed instability and the geometry of the budded shape are in reasonable accord with the theoretical predictions. The inability of previous experiments to detect the ``hidden control parameters (relaxed area difference and spontaneous curvature) make this the first direct quantitative confrontation between vesicle-shape theory and experiment.

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.7, Elastizitätstheorie: {BD} 7
Type: book by Deutsch {(Harri)}.

R. Mukhopadhyay, G. Lim H W, M. Wortis (2002): Echinocyte shapes: bending, stretching, and shear determine spicule shape and spacing
Type: article by Biophysical Journal.
link: http://www.ncbi.nlm.nih.gov/pubmed/11916836
Abstract:

We study the shapes of human red blood cells using continuum mechanics. In particular, we model the crenated, echinocytic shapes and show how they may arise from a competition between the bending energy of the plasma membrane and the stretching/shear elastic energies of the membrane skeleton. In contrast to earlier work, we calculate spicule shapes exactly by solving the equations of continuum mechanics subject to appropriate boundary conditions. A simple scaling analysis of this competition reveals an elastic length Lambda(el), which sets the length scale for the spicules and is, thus, related to the number of spicules experimentally observed on the fully developed echinocyte.

J. Käs, E. Sackmann (1991): Shape transitions and shape stability of giant phospholipid vesicles in pure water induced by area-to-volume changes
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(91)82117-8
link: http://www.ncbi.nlm.nih.gov/pubmed/1742455
Abstract:

Shape transformations of vesicles of dimyristoylphosphatidylcholine (= {DMPC)} and palmitoyloleylphosphatidylcholine (= {POPC)} in ion-free water were induced by changing the area-to-volume ratio via temperature variations. Depending on the pretreatment we find several types of shape changes for {DMPC} (in pure water) at increasing area-to-volume ratio: (a) budding transitions leading to the formation of a chain of vesicles at further increase of the area-to-volume ratio, (b) discocyte-stomatocyte transitions, (c) reentrant dumbbell-pear-dumbbell transitions, and (d) spontaneous blebbing and/or tether formation of spherical vesicles. Beside these transitions a more exotic dumbbell-discocyte transition (e) was found which proceeded via local instabilities. Pears, discocytes, and stomatocytes are stable with respect to small temperature variations unless the excess area is close to values corresponding to limiting shapes of budded vesicles where temperature variations of less than or equal to 0.1 degree C lead to spontaneous budding to the inside or the outside. For {POPC} we observed only budding transitions to the inside leading either to chains of vesicles or to distributions of equally sized daughter vesicles protruding to the inside of the vesicle. Preliminary experiments concerning the effect of solutes are also reported. The first three types of shape transitions can be explained in terms of the bilayer coupling model assuming small differences in thermal expansivities of the two monolayers. This does not hold for the observed instabilities close to the limiting shapes.

W. Helfrich (1978): Steric Interaction of Fluid Membranes in Multilayer Systems
Type: article by Zeitschrift Naturforschung Teil A.
link: http://adsabs.harvard.edu/abs/1978ZNatA..33..305H

U. Seifert (1997): Configurations of fluid membranes and vesicles
Type: article by Advances in Physics.
link: http://adsabs.harvard.edu/abs/1997AdPhy..46...13S
Abstract:

Vesicles consisting of a bilayer membrane of amphiphilic lipid molecules

are remarkably flexible surfaces that show an amazing variety of shapes of different symmetry and topology. Owing to the fluidity of the membrane, shape transitions such as budding can be induced by temperature changes or the action of optical tweezers. Thermally excited shape fluctuations are both strong and slow enough to be visible by video microscopy. Depending on the physical conditions, vesicles adhere to and unbind from each other or a {substrate.This} article describes the systematic physical theory developed to understand the static and dynamic aspects of membrane and vesicle configurations. The preferred shapes arise from a competition between curvature energy, which derives from the bending elasticity of the membrane, geometrical constraints such as fixed surface area and fixed enclosed volume, and a signature of the bilayer aspect. These shapes of lowest energy are arranged into phase diagrams, which separate regions of different symmetry by continuous or discontinuous transitions. The geometrical constraints affect the fluctuations around these shapes by creating an effective {tension.For} vesicles of non-spherical topology, the conformal invariance of the curvature energy leads to conformal diffusion, which signifies a one-fold degeneracy of the ground state. Unbinding and adhesion transitions arise from the balance between attractive interactions and entropic repulsion or a cost in bending energy, respectively. Both the dynamics of equilibrium fluctuations and the dynamics of shape transformations are governed not only by viscous damping in the surrounding liquid but also by internal friction if the two monolayers slip over each other. More complex membranes such as that of the red blood cell exhibit a variety of new phenomena because of coupling between internal degrees of freedom and external geometry.

E. Evans, W. Rawicz (1990): Entropy-driven tension and bending elasticity in condensed-fluid membranes
Type: article by Physical Review Letters.
doi: 10.1103/PhysRevLett.64.2094
link: http://link.aps.org/abstract/PRL/v64/p2094
Abstract:

Sensitive micropipet methods have been used to measure the relation between tension and the projected surface area in fluid membranes of vesicles over a 4-order-of-magnitude range in tension (10-3–10 dyn/cm). In the low-tension regime ({textless}0.5 dyn/cm), the data confirm the prediction of equilibrium theory that the projected area should increase logarithmically with tension as shape fluctuations become progressively restricted. The slope of log(tension) versus area dilation yields and the elastic bending modulus of the membrane. In the high-tension regime, the projected area crosses over to vary linearly with tension due to direct expansion of area per molecule.

R. Lipowsky Generic interactions of flexible membranes
Type: article

E. Sackmann Physical basis of self-organization and function of membranes: physics of vesicles
Type: article

W. Helfrich (1973): Elastic properties of lipid bilayers: theory and possible experiments
Type: article by Zeitschrift Für Naturforschung. Teil C: Biochemie, Biophysik, Biologie, Virologie.
link: http://www.ncbi.nlm.nih.gov/pubmed/4273690

H. Noguchi, G. Gompper (2005): Shape transitions of fluid vesicles and red blood cells in capillary flows
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.0504243102
link: http://www.pnas.org/content/102/40/14159.abstract
Abstract:

The dynamics of fluid vesicles and red blood cells {(RBCs)} in cylindrical capillary flow is studied by using a three-dimensional mesoscopic simulation approach. As flow velocity increases, a model {RBC} is found to transit from a nonaxisymmetric discocyteto an axisymmetric parachute shape (coaxial with the flow axis), while a fluid vesicle is found to transit from a discocyte to a prolate ellipsoid. Both shape transitions reduce the flow resistance. The critical velocities of the shape transitions are linearly dependent on the bending rigidity and on the shear modulus of the membrane. Slipper-like shapes of the {RBC} model are observed around the transition velocities. Our results are in good agreement with experiments on {RBCs.}

C. Rotsch (2000): {Drug-Induced} Changes of Cytoskeletal Structure and Mechanics in Fibroblasts: An Atomic Force Microscopy Study
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(00)76614-8
link: http://www.cell.com/biophysj/abstract/S0006-3495(00)76614-8
Abstract:

The effect of various drugs affecting the integrity of different components of the cytoskeleton on the elasticity of two fibroblast cell lines was investigated by elasticity measurements with an atomic force microscope {(AFM).} Disaggregation of actin filaments always resulted in a distinct decrease in the cells average elastic modulus indicating the crucial importance of the actin network for the mechanical stability of living cells. Disruption or chemical stabilization of microtubules did not affect cell elasticity. For the f-actin-disrupting drugs different mechanisms of drug action were observed. Cytochalasins B and D and Latrunculin A disassembled stress fibers. For Cytochalasin D this was accompanied by an aggregation of actin within the cytosol. Jasplakinolide disaggregated actin filaments but did not disassemble stress fibers. Fibrous structures found in {AFM} images and elasticity maps of fibroblasts could be identified as stress fibers by correlation of {AFM} data and fluorescence images.

D. Boal (2001): Mechanics of the Cell
Type: book by Cambridge University Press.

D. W. Thompson (1992): On Growth and Form: The Complete Revised Edition
Type: book by Dover Publications.

B. Fourcade, M. Mutz, D. Bensimon (1992): Experimental and theoretical study of toroidal vesicles
Type: article by Physical Review Letters.
doi: 10.1103/PhysRevLett.68.2551
link: http://link.aps.org/abstract/PRL/v68/p2551
Abstract:

We report the observation of toroidal and higher genus vesicles of diacetylenic phospholipids, a class of polymerizable amphiphiles. When unpolymerized, the vesicles exhibit different toroidal shapes in quantitative agreement with recent theoretical predictions. When partially polymerized, only a specific family of shapes has been observed: the Clifford torus or the branch of nonaxisymmetric shapes obtained by its conformal transformations. Assuming that partially polymerized vesicles are permeable on short time scale, we give a physical explanation of our findings. We also report the results of a variational calculation which approximates the nonaxisymmetric shape problem for finite spontaneous curvature.

J. O. Rädler, T. J. Feder, H. H. Strey, E. Sackmann (1995): Fluctuation analysis of tension-controlled undulation forces between giant vesicles and solid substrates
Type: article by Physical Review E.
doi: 10.1103/PhysRevE.51.4526
link: http://link.aps.org/abstract/PRE/v51/p4526
Abstract:

Using reflection interference contrast microscopy, we studied the thermal fluctuations of giant vesicles that weakly adhere to flat solid substrates. The absolute membrane-substrate separation distance was imaged and the average contact contour, including the contact area, the contact rounding, and the asymptotic contact angle, was determined. The static fluctuations in the flat, adhering part of the vesicle were analyzed. The spectrum of mean square amplitudes yielded the lateral membrane tension and the second derivative of the interaction potential. The vertical roughness and lateral correlation length were measured from the spatial autocorrelation of the undulations. The roughness was shown to obey the behavior predicted by functional renormalization in the observed tension regime of 10-6 to 10-4 J/m2. Moreover, the measured separation distances can be explained within the framework of undulation and van der Waals forces and confirmed the model of tension-induced adhesion. However, the adhesion energies as well as the measured separation distances exhibit a weaker dependence on the membrane tension than predicted.

F. Brochard, J. F. Lennon (1975): Frequency spectrum of the flicker phenomenon in erythrocytes
Type: article by Journal de Physique.

Z. Guttenberg, B. Lorz, E. Sackmann, A. Boulbitch (2001): First-order transition between adhesion states in a system mimicking cell-tissue interaction
Type: article by Europhysics Letters.
link: http://adsabs.harvard.edu/abs/2001EL.....54..826G
Abstract:

We establish a model of cell-tissue interaction consisting of vesicles

carrying lipopolymers (to mimic the glycocalix) and mobile specific ligands of the blood platelet integrin {alphaIIbbeta3} covering the substrate. We find the phase diagram with a first-order transition between a gravity-controlled weak state of the vesicle-substrate adhesion and a strong-adhesion state governed by receptor-ligand interaction. Adhesion energy ɛadh is measured as a function of ligand and repeller concentration by interferometric contour analysis on the basis of a new refined model of soft shell adhesion (accounting for the membrane bending and stretching at the adhesion rim of the ellipsoidal vesicle). At ligand densities comparable to integrin density, ɛadh decreases sharply. Increasing the repeller content weakens the adhesion strength.

W. Häckl, U. Seifert, E. Sackmann (1997): Effects of Fully and Partially Solubilized Amphiphiles on Bilayer Bending Stiffness and Temperature Dependence of the Effective Tension of Giant Vesicles
Type: article by Journal de Physique {II}.
link: http://adsabs.harvard.edu/abs/1997JPhy2...7.1141H
Abstract:

We report the modification of the bending elastic modulus k_c of lipid

bilayers (here {DMPC)} by small amounts (c leq 5 mol %) of (i) small amphiphiles which exchange between the bilayer and the aqueous phase (e.g. the ion carrier valinomycin and the Ca{textasciicircum}{++} carrier A23187) and (ii) amphiphiles solubilized in the membrane (cholanic acid). Large reductions of the bending stiffness may be induced by a few percent of the solutes, e.g. 1 mol % of valinomycin reduce k_c by a factor of two. The effect is rationalised in terms of local thinning of the bilayer. The strong effect of solutes on k_c contrasts with its weak dependence on the lipid structure since the {C18:0/C18:1-lipid} stearoyl-oleoyl-phosphatidyl-choline {(SOPC)} exhibits only a 15% higher value of k_c than {DMPC.} The effect of temperature on the flicker behaviour was analysed in order to establish correlations between the effective tension and the excess area of the quasi-spherical vesicles. The temperature dependence of the bilayer excess area for a {DMPC} vesicle leads to the thermal expansion coefficient, beta, for which a value of beta = 10.4 � 10{textasciicircum}{-3} K{textasciicircum}{-1} is obtained. A much stronger tendency for budding on mum-scale (micro budding) during thermal area expansion of {POPC} and {SOPC} compared to {DMPC} was observed.

R. Lipowsky (1995): The morphology of lipid membranes
Type: article by Current Opinion in Structural Biology.

U. Seifert, R. Lipowsky (1995): Morphology of vesicles
Type: article by Handbook of biological physics.

H. S. Seung, D. R. Nelson (1988): Defects in flexible membranes with crystalline order
Type: article by Physical Review. A.
link: http://www.ncbi.nlm.nih.gov/pubmed/9900464

H. Engelhardt, E. Sackmann (1988): On the measurement of shear elastic moduli and viscosities of erythrocyte plasma membranes by transient deformation in high frequency electric fields
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(88)82982-5
Abstract:

Sensitive micropipet methods have been used to measure the relation between tension and the projected surface area in fluid membranes of vesicles over a 4-order-of-magnitude range in tension (10-3–10 dyn/cm). In the low-tension regime ({textless}0.5 dyn/cm), the data confirm the prediction of equilibrium theory that the projected area should increase logarithmically with tension as shape fluctuations become progressively restricted. The slope of log(tension) versus area dilation yields and the elastic bending modulus of the membrane. In the high-tension regime, the projected area crosses over to vary linearly with tension due to direct expansion of area per molecule.

J. L. van Hemmen, C. Leibold (2007): Elementary excitations of biomembranes: Differential geometry of undulations in elastic surfaces
Type: article by Physics Reports.
doi: 10.1016/j.physrep.2006.12.007

R. R. Netz (1995): Complete unbinding of fluid membranes in the presence of short-ranged forces
Type: article by Physical Review E.
doi: 10.1103/PhysRevE.51.2286
link: http://link.aps.org/abstract/PRE/v51/p2286
Abstract:

Lipid or surfactant bilayers which are bound by an external pressure and intereact via an additional short-ranged potential are studied theoretically. If the latter potential is not strong enough to bind the lamellae by itself, it has asymptotically no effect on the (complete) unbinding transition, which occurs in the limit of vanishing pressure; the separation and correlation lengths diverge as power laws as a function of the pressure, with the amplitudes being determined by characteristic amplitude ratios. If the potential strength exceeds the critical value, the bilayers are bound even for zero external pressure (incomplete unbinding). Exactly at the critical potential strength, all length scales again diverge as a function of the pressure. The critical exponents are found to be identical to those for a less attractive potential, but the asymptotic amplitude ratios have different values; also, the fluctuation amplitude, which measures the strength of the fluctuation-induced repulsion between the bilayers, is reduced by a factor of 12 as compared to the subcritical case. These results are obtained directly by Monte Carlo simulations of two fluid membranes and agree with exact calculations for the analogous system of two strings in 1+1 dimensions. Experimentally, the effects of short-ranged van der Waals attraction on the fluctuation amplitude cfl should be observable for suitable systems by small-angle x-ray scattering on lamellar phases.

B. T. Stokke, A. Mikkelsen, A. Elgsaeter (1986): Spectrin, human erythrocyte shapes, and mechanochemical properties
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(86)83644-X

A. Zidovska, E. Sackmann (2006): Brownian Motion of Nucleated Cell Envelopes Impedes Adhesion
Type: article by Physical Review Letters.
doi: 10.1103/PhysRevLett.96.048103
link: http://link.aps.org/abstract/PRL/v96/e048103

Kapitel 12

T. Baumgart, S. T. Hess, W. W. Webb (2003): Imaging coexisting fluid domains in biomembrane models coupling curvature and line tension
Type: article by Nature.
doi: 10.1038/nature02013
link: http://dx.doi.org/10.1038/nature02013
Abstract:

Lipid bilayer membranes—ubiquitous in biological systems and closely associated with cell function—exhibit rich shape-transition behaviour, including bud formation1 and vesicle fission2. Membranes formed from multiple lipid components can laterally separate into coexisting liquid phases, or domains, with distinct compositions. This process, which may resemble raft formation in cell membranes, has been directly observed in giant unilamellar vesicles3, 4. Detailed theoretical frameworks5, 6, 7, 8, 9, 10, 11 link the elasticity of domains and their boundary properties to the shape adopted by membranes and the formation of particular domain patterns, but it has been difficult to experimentally probe and validate these theories. Here we show that high-resolution fluorescence imaging using two dyes preferentially labelling different fluid phases directly provides a correlation between domain composition and local membrane curvature. Using freely suspended membranes of giant unilamellar vesicles, we are able to optically resolve curvature and line tension interactions of circular, stripe and ring domains. We observe long-range domain ordering in the form of locally parallel stripes and hexagonal arrays of circular domains, curvature-dependent domain sorting, and membrane fission into separate vesicles at domain boundaries. By analysing our observations using available membrane theory, we are able to provide experimental estimates of boundary tension between fluid bilayer domains.

E. Karatekin, O. Sandre, H. Guitouni, N. Borghi, P.-H. Puech, F. Brochard-Wyart (2003): Cascades of Transient Pores in Giant Vesicles: Line Tension and Transport
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302742
Abstract:

Under ordinary circumstances, the membrane tension of a giant unilamellar vesicle is essentially nil. Using visible light, we stretch the vesicles, increasing the membrane tension until the membrane responds by the sudden opening of a large pore (several micrometers in size). Only a single pore is observed at a time in a given vesicle. However, a cascade of transient pores appear, up to 30–40 in succession, in the same vesicle. These pores are transient: they reseal within a few seconds as the inner liquid leaks out. The membrane tension, which is the driving force for pore opening, is relaxed with the opening of a pore and the leakage of the inner liquid; the line tension of the pore's edge is then able to drive the closure of a pore. We use fluorescent membrane probes and real-time videomicroscopy to study the dynamics of the pores. These can be visualized only if the vesicles are prepared in a viscous solution to slow down the leakout of the internal liquid. From measurements of the closure velocity of the pores, we are able to infer the line tension, T. We have studied the effect of the shape of inclusion molecules on T. Cholesterol, which can be modeled as an inverted cone-shaped molecule, increases the line tension when incorporated into the bilayers. Conversely, addition of cone-shaped detergents reduces T. The effect of some detergents can be dramatic, reducing Tby two orders of magnitude, and increasing pore lifetimes up to several minutes. We give some examples of transport through transient pores and present a rough measurement of the leakout velocity of the inner liquid through a pore. We discuss how our results can be extended to less viscous aqueous solutions which are more relevant for biological systems and biotechnological applications.

L. Chernomordik, A. Chanturiya, J. Green, J. Zimmerberg (1995): The hemifusion intermediate and its conversion to complete fusion: regulation by membrane composition
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(95)79966-0
link: http://www.ncbi.nlm.nih.gov/pubmed/8519992
Abstract:

To fuse, membranes must bend. The energy of each lipid monolayer with respect to bending is minimized at the spontaneous curvature of the monolayer. Two lipids known to promote opposite spontaneous curvatures, lysophosphatidylcholine and arachidonic acid, were added to different sides of planar phospholipid membranes. Lysophosphatidylcholine added to the contacting monolayers of fusing membranes inhibited the hemifusion we observed between lipid vesicles and planar membranes. In contrast, fusion pore formation depended upon the distal monolayer of the planar membrane; lysophosphatidylcholine promoted and arachidonic acid inhibited. Thus, the intermediates of hemifusion and fusion pores in phospholipid membranes involve different membrane monolayers and may have opposite net curvatures, Biological fusion may proceed through similar intermediates.

S. Mabrey, P. L. Mateo, J. M. Sturtevant (1978): High-sensitivity scanning calorimetric study of mixtures of cholesterol with dimyristoyl- and dipalmitoylphosphatidylcholines
Type: article by Biochemistry.
doi: 10.1021/bi00605a034
link: http://dx.doi.org/10.1021/bi00605a034

R. B. Sutton, D. Fasshauer, R. Jahn, A. T. Brunger (1998): Crystal structure of a {SNARE} complex involved in synaptic exocytosis at 2.4 A resolution
Type: article by Nature.
doi: 10.1038/26412
link: http://www.ncbi.nlm.nih.gov/pubmed/9759724
Abstract:

The evolutionarily conserved {SNARE} proteins and their complexes are involved in the fusion of vesicles with their target membranes; however, the overall organization and structural details of these complexes are unknown. Here we report the X-ray crystal structure at 2.4 A resolution of a core synaptic fusion complex containing syntaxin-1 A, {synaptobrevin-II} and {SNAP-25B.} The structure reveals a highly twisted and parallel four-helix bundle that differs from the bundles described for the haemagglutinin and {HIV/SIV} gp41 membrane-fusion proteins. Conserved leucine-zipper-like layers are found at the centre of the synaptic fusion complex. Embedded within these leucine-zipper layers is an ionic layer consisting of an arginine and three glutamine residues contributed from each of the four alpha-helices. These residues are highly conserved across the entire {SNARE} family. The regions flanking the leucine-zipper-like layers contain a hydrophobic core similar to that of more general four-helix-bundle proteins. The surface of the synaptic fusion complex is highly grooved and possesses distinct hydrophilic, hydrophobic and charged regions. These characteristics may be important for membrane fusion and for the binding of regulatory factors affecting neurotransmission.

R. Cahn, W. Ludwig (1985): Theorie der Wärme.
Type: book by Springer, Berlin.

H. G. Döbereiner, J. Käs, D. Noppl, I. Sprenger, E. Sackmann (1993): Budding and fission of vesicles
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(93)81203-7
link: http://www.ncbi.nlm.nih.gov/pubmed/8274633
Abstract:

We report on budding and fission of protein-free vesicles swollen from a natural lipid mixture of bovine brain sphingomyelins. Budding was induced by increasing the area-to-volume ratio through heating. Morphological changes were monitored by phase contrast microscopy and correlated with the thermal behavior of the bilayer by differential scanning calorimetry. Freeze fracture electron microscopy revealed that budding and fission are not restricted to giant vesicles but also occur on length scales relevant for cellular processes. We also observed osmotically induced budding and fission in mixtures of dimyristoyl phosphatidylcholine with cholesterol. We find that these shape transitions are driven by liquid/gel domain formation and/or coupling of the spontaneous curvature of the membrane to the local lipid composition. Our results provide evidence that coat proteins are not necessary for budding and fission of vesicles. The physics of the lipid bilayer is rich enough to explain the observed behavior.

S. May, A. Ben-Shaul (2000): A molecular model for lipid-mediated interaction between proteins in membranes
Type: article by Physical Chemistry Chemical Physics.
link: http://dx.doi.org/10.1039/b003570j
Abstract:

The loss of conformational freedom experienced by lipid chains in the vicinity of one, or two, impenetrable walls, representing the surfaces of hydrophobic transmembrane proteins, is calculated using a mean-field molecular-level chain packing theory. The hydrophobic thickness of the protein is set equal to that of the unperturbed lipid membrane (i.e., no " hydrophobic mismatch"). The probability distributions of chain conformations, at all distances from the walls, are calculated by generating all conformations according to the rotational-isomeric-state model, and subjecting the system free energy to the requirement that the hydrophobic core of the membrane is liquid-like, and hence uniformly packed by chain segments. As long as the two protein surfaces are far apart, their interaction zones do not overlap, each extending over several molecular diameters. When the interaction zones begin to overlap, inter-protein repulsion sets in. At some intermediate distance the interaction turns strongly attractive, resulting from the depletion of (highly constrained) lipid tails from the volume separating the two surfaces. The chains confined between the hydrophobic surfaces are tilted away from the walls. Their tilt angle decreases monotonically with the distance from the walls, and with the distance between the walls. A nonmonotonic variation of the lipid-mediated interaction free energy between hydrophobic surfaces in membranes is also obtained using a simple, analytical, model in which chain conformations are grouped according to their director (end-to-end vector) orientations.

B. Bechinger (1996): Towards membrane protein design: {pH-sensitive} topology of histidine-containing polypeptides
Type: article by Journal of Molecular Biology.
doi: 10.1006/jmbi.1996.0614
link: http://www.ncbi.nlm.nih.gov/pubmed/8947574
Abstract:

Hydrophobic and amphipathic alpha-helices act as independent functional units in immunogenic or fusogenic polypeptides and constitute important structural building blocks in larger membrane proteins. In order to quantitatively assess the interactions that determine the alignment of membrane-associated alpha-helices, hydrophobic model peptides containing histidine residues at selected sites were prepared by solid-phase peptide synthesis. {CD} and solution {NMR} spectroscopy show that these peptides assume alpha-helical secondary structures in micellar environments. The chemical shift alterations of the histidine side-chain protons during {pH} titration experiments indicate that the {pK} values of the histidine imidazole protons range from 4.9 to 6.6 in the presence of dodecylphosphocholine micelles. {15N} solid-state {NMR} spectroscopy was used to determine the membrane alignment of these peptide alpha-helices in uniaxially oriented phospholipid bilayers. The observed {pH-dependent} change of orientation of one of these model peptides is quantitatively described by a dynamic equilibrium governed by both electrostatic and hydrophobic protein-lipid interactions. The thermodynamic equations presented provide a means for the prediction of membrane protein structure and topology, as well as the future design of peptide channels and pharmaceuticals.

M. Ø. Jensen, O. G. Mouritsen (2004): Lipids do influence protein function-the hydrophobic matching hypothesis revisited
Type: article by Biochimica Et Biophysica Acta.
doi: 10.1016/j.bbamem.2004.06.009
link: http://www.ncbi.nlm.nih.gov/pubmed/15519316
Abstract:

A topical review of the current state of lipid-protein interactions is given with focus on the physical interactions between lipids and integral proteins in lipid-bilayer membranes. The concepts of hydrophobic matching and curvature stress are revisited in light of recent data obtained from experimental and theoretical studies which demonstrate that not only do integral proteins perturb the lipids, but the physical state of the lipids does also actively influence protein function. The case of the trans-membrane water-channel protein aquaporin {GlpF} from E. coli imbedded in lipid-bilayer membranes is discussed in some detail. Numerical data obtained from Molecular Dynamics simulations show on the one side that the lipid bilayer adapts to the channel by a hydrophobic matching condition which reflects the propensity of the lipid molecules for forming curved structures. On the other side, it is demonstrated that the transport function of the channel is modulated by the matching condition and/or the curvature stress in a lipid-specific manner.

T. Sintes, A. Baumgärtner (1997): Protein attraction in membranes induced by lipid fluctuations
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(97)78257-2
link: http://www.ncbi.nlm.nih.gov/pubmed/9370422
Abstract:

The nonspecific lipid-mediated attraction between two proteins embedded in a bilayer membrane have been investigated for a model system using Monte Carlo simulations. We found two types of attraction with different regimes. A depletion-induced attraction in the range r {textless} {sigmaL,} where {sigmaL} is the diameter of a lipid and r is the distance between the surfaces of the two proteins, and a fluctuation-induced attraction in the range 1 {textless} {r/sigmaL} {textless} 6, which originates from the gradients of density and orientational fluctuations of the lipids around each protein. The effective potential of the latter type of attraction decays exponentially with U(r) approximately exp(r/vi) where the correlation length is {vi/sigmaL} approximately 3.2 in the present model system.

E. Sackmann (2006): Thermo-elasticity and adhesion as regulators of cell membrane architecture and function
Type: article by Journal of Physics: Condensed Matter.
link: http://www.iop.org/EJ/abstract/0953-8984/18/45/R02/
Abstract:

Elastic forces and structural phase transitions control the

architecture and function of bio-membranes from the molecular to the microscopic scale of organization. The multi-component lipid bilayer matrix behaves as a pseudo-ternary system. Together with elastically and electrostatically mediated specific lipid-protein interaction mechanisms, fluid-fluid phase separation can occur at physiological temperatures. This can drive the transient generation of micro-domains of distinct composition within multi-component lipid-protein alloys, enabling cells to optimize the efficiency of biochemical reactions by facilitating or inhibiting the access of enzymes by distinct substrates or regulatory proteins. Together with global shape changes governed by the principle of minimum bending energy and induced curvature by macromolecular adsorption, phase separation processes can also play a key role for the sorting of lipids and proteins between intracellular compartments during the vesicle mediated intracellular material transport. Cell adhesion is another example of mechanical force controlled membrane processes. By interplay of attractive lock and key forces, long range disjoining pressures mediated by repeller molecules or membrane undulations and elastic interfacial forces, adhesion induced domain formation can play a dual role for the immunological stimulation of lymphocytes and for the rapid control of the adhesion strength. The present picture of the thermo-elastic control of membrane processes based on concepts of local thermal equilibrium is still rudimentary and has to be extended in the future to account for the intrinsic non-equilibrium situation associated with the constant restructuring of the cellular compartments on a timescale of minutes.

A. Ben-Shaul Molecular theory of chain packing, elasticity and lipid-protein interaction in lipid bilayers
Type: article

H. Reinl, T. Brumm, T. Bayerl (1992): Changes of the physical properties of the liquid-ordered phase with temperature in binary mixtures of {DPPC} with {cholesterolA} {2H-NMR,} {FT-IR,} {DSC,} and neutron scattering study
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(92)81910-0
link: http://www.cell.com/biophysj/abstract/S0006-3495(92)81910-0
Abstract:

The structure of the so-called liquid-ordered (lo) phase of binary mixtures of {DPPC-d62} with cholesterol was studied between 2050 mol% cholesterol using {2H-NMR,} {FT-IR,} {DSC,} and neutron specular reflection. Different model systems such as multilamellar vesicles, spherical supported vesicles, and oriented multilayers were used. We observed significant changes of the lo phase structure in the physiological relevant temperature region between {3045C.} {2H-NMR} in combination with lineshape simulations provides evidence for a drastic effect of cholesterol on the shape of multilamellar vesicles due to magnetic field orientation. Moreover, the data indicates a significant change of the extent of this partial orientation for {DPPC-d62} multilamellar vesicles containing 25 mol% cholesterol between {3642C.} The semiaxes ratio of the (due to magnetic field orientation) ellipsoidal multilamellar vesicles changes over this temperature range by ≈25%. {2H-NMR} and {FT-IR} measurements indicate changes of the average orientational order at the bilayer center in the same temperature range and a significant increase of the number of end-gauche conformers while the majority of the methylene groups remain in an all-trans conformation. Additionally, specular reflection of neutrons shows a concomitant reduction of the bilayer thickness by 4Å. Based on a model of the arrangement of {DPPC} and cholesterol in the lo phase, a molecular mechanism is proposed in which increasing the temperature between 30 and {45C} has the effect of driving cholesterol from the bilayer center towards the head group region

R. Lipowsky Generic interactions of flexible membranes
Type: article

R. F. M. de Almeida, A. Fedorov, M. Prieto (2003): Sphingomyelin/phosphatidylcholine/cholesterol phase diagram: boundaries and composition of lipid rafts
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(03)74664-5
link: http://www.ncbi.nlm.nih.gov/pubmed/14507704
Abstract:

The ternary system palmitoylsphingomyelin {(PSM)/palmitoyloleoylphosphatidylcholine} {(POPC)/cholesterol} is used to model lipid rafts. The phase behavior of the three binary systems {PSM/POPC,} {PSM/cholesterol,} and {POPC/cholesterol} is first experimentally determined. Phase coexistence boundaries are then determined for ternary mixtures at room temperature (23 degrees C) and the ternary phase diagram at that temperature is obtained. From the diagram at 23 degrees C and the binary phase diagrams, a reasonable expectation is drawn for the ternary phase diagram at 37 degrees C. Several photophysical methodologies are employed that do not involve detergent extraction, in addition to literature data (e.g., differential scanning calorimetry) and thermodynamic rules. For the ternary phase diagrams, some tie-lines are calculated, including the one that contains the {PSM/POPC/} cholesterol 1:1:1 mixture, which is often used in model raft studies. The diagrams here described are used to rationalize literature results, some of them apparently discrepant, and to discuss lipid rafts within the framework of liquid-ordered/liquid-disordered phase coexistence.

R. Waugh (1979): Thermoelasticity of red blood cell membrane
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(79)85239-X
link: http://www.cell.com/biophysj/abstract/S0006-3495(79)85239-X
Abstract:

The elastic properties of the human red blood cell membrane have been measured as functions of temperature. The area compressibility modulus and the elastic shear modulus, which together characterize the surface elastic behavior of the membrane, have been measured over the temperature range of 250 degrees C with micropipette aspiration of flaccid and osmotically swollen red cells. In addition, the fractional increase in membrane surface area from 250 degrees C has been measured to give a value for the thermal area expansivity. The value of the elastic shear modulus at 25 degrees C was measured to be 6.6 X 10(-3) dyne/cm. The change in the elastic shear modulus with temperature was -6 X 10(-5) dyne/cm degrees C. Fractional forces were shown to be only on the order of 1015%. The area compressibility modulus at 25 degrees C was measured to be 450 dyne/cm. The change in the area compressibility modulus with temperature was -6 dyne/cm degrees C. The thermal area expansivity for red cell membrane was measured to be 1.2 X 10(-3)/degrees C. With this data and thermoelastic relations the heat of expansion is determined to be 110200 ergs/cm2; the heat of extension is 2 X 10(-2) ergs/cm2 for unit extension of the red cell membrane. The heat of expansion is of the order anticipated for a lipid bilayer idealized as twice the behavior of a monolayer at an oil-water interface. The observation that the heat of extension is positive demonstrates that the entropy of the material increases with extension, and that the dominant mechanism of elastic energy storage is energetic. Assuming that the red cell membrane shear rigidity is associated with "spectrin," unit extension of the membrane increases the configurational entropy of spectrin by 500 cal/mol.

W. Helfrich (1973): Elastic properties of lipid bilayers: theory and possible experiments
Type: article by Zeitschrift Für Naturforschung. Teil C: Biochemie, Biophysik, Biologie, Virologie.
link: http://www.ncbi.nlm.nih.gov/pubmed/4273690

S. A. Safran, T. L. Kuhl, J. N. Israelachvili (2001): Polymer-induced membrane contraction, phase separation, and fusion via Marangoni flow
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(01)75730-X
link: http://www.ncbi.nlm.nih.gov/pubmed/11463614
Abstract:

Experiments have shown that the depletion of polymer in the region between two apposed (contacting or nearly contacting) bilayer membranes leads to fusion. In this paper we show theoretically that the addition of nonadsorbing polymer in solution can promote lateral contraction and phase separation of the lipids in the outer monolayers of the membranes exposed to the polymer solution, i.e., outside the contact zone. This initial phase coexistence of higher- and lower-density lipid domains in the outer monolayer results in surface tension gradients in the outer monolayer. Initially, the inner layer lipids are not exposed to the polymer solution and remain in their original "unstressed" state. The differential stresses on the bilayers give rise to a Marangoni flow of lipid from the outer monolayers in the "contact zone" (where there is little polymer and hence a uniform phase) to the outer monolayers in the "reservoir" (where initially the surface tension gradients are large due to the polymer-induced phase separation). As a result, the low-density domains of the outer monolayers in the contact zone expose their hydrophobic chains, and those of the inner monolayers, to the solvent and to each other across the narrow water gap, allowing fusion to occur via a hydrophobic interaction. More generally, this type of mechanism suggests that fusion and other intermembrane interactions may be triggered by Marangoni flows induced by surface tension gradients that provide "action at a distance" far from the fusion or interaction zone.

M. R. Vist, J. H. Davis (1990): Phase equilibria of cholesterol/dipalmitoylphosphatidylcholine mixtures: deuterium nuclear magnetic resonance and differential scanning calorimetry
Type: article by Biochemistry.
doi: 10.1021/bi00454a021
link: http://dx.doi.org/10.1021/bi00454a021

D. Langosch, J. M. Crane, B. Brosig, A. Hellwig, L. K. Tamm, J. Reed (2001): Peptide mimics of {SNARE} transmembrane segments drive membrane fusion depending on their conformational plasticity
Type: article by Journal of Molecular Biology.
doi: 10.1006/jmbi.2001.4889
link: http://www.ncbi.nlm.nih.gov/pubmed/11518525
Abstract:

{SNARE} proteins are essential for different types of intracellular membrane fusion. Whereas interaction between their cytoplasmic domains is held responsible for establishing membrane proximity, the role of the transmembrane segments in the fusion process is currently not clear. Here, we used an in vitro approach based on lipid mixing and electron microscopy to examine a potential fusogenic activity of the transmembrane segments. We show that the presence of synthetic peptides representing the transmembrane segments of the presynaptic soluble N-ethylmaleimide-sensitive factor attachment protein receptors {(SNAREs)} synaptobrevin {II} (also referred to as {VAMP} {II)} or syntaxin {1A,} but not of an unrelated control peptide, in liposomal membranes drives their fusion. Liposome aggregation by millimolar Ca(2+) concentrations strongly potentiated the effect of the peptides; this indicates that juxtaposition of the bilayers favours their fusion in the absence of the cytoplasmic {SNARE} domains. Peptide-driven fusion is reminiscent of natural membrane fusion, since it was suppressed by lysolipid and involved both bilayer leaflets. This suggests transient presence of a hemifusion intermediate followed by complete membrane merger. Structural studies of the peptides in lipid bilayers performed by Fourier transform infrared spectroscopy indicated mixtures of alpha-helical and beta-sheet conformations. In isotropic solution, circular dichroism spectroscopy showed the peptides to exist in a concentration-dependent equilibrium of alpha-helical and beta-sheet structures. Interestingly, the fusogenic activity decreased with increasing stability of the alpha-helical solution structure for a panel of variant peptides. Thus, structural plasticity of transmembrane segments may be important for {SNARE} protein function at a late step in membrane fusion.

M. R. Brzustowicz, V. Cherezov, M. Caffrey, W. Stillwell, S. R. Wassall (2002): Molecular organization of cholesterol in polyunsaturated membranes: microdomain formation
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(02)75394-0
link: http://www.ncbi.nlm.nih.gov/pubmed/11751316
Abstract:

The molecular organization of cholesterol in phospholipid bilayers composed of 1,2-diarachidonylphosphatidylcholine {(20:4-20:4PC),} 1-stearoyl-2-arachidonylphosphatidylcholine {(18:0-20:4PC),} and {20:4-20:4PC/18:0-20:4PC} (1/1 mol) was investigated by solid-state {(2)H} {NMR} and by low- and wide-angle x-ray diffraction {(XRD).} On the basis of distinct quadrupolar powder patterns arising from [3 {alpha-(2)H(1)]cholesterol} intercalated into the membrane and phase separated as solid, solubility {chi(NMR)(chol)} = 17 +/- 2 mol% and tilt angle alpha(0) = 25 +/- 1 degrees in {20:4-20:4PC} were determined. The corresponding values in {18:0-20:4PC} were chi {(NMR)(chol)} {textgreater} or = 50 mol% and alpha(0) = 16 +/- 1 degrees. Cholesterol solubility determined by {XRD} was {chi(NMR)(chol)} = 15 +/- 2 mol% and {chi(NMR)(chol)} = 49 +/- 1 mol% for {20:4-20:4PC} and {18:0-20:4PC,} respectively. {XRD} experiments show that the solid sterol is monohydrate crystals presumably residing outside the bilayer. The {(2)H} {NMR} spectrum for equimolar [3 {alpha-(2)H(1)]cholesterol} added to mixed {20:4-20:4PC/18:0-20:4PC} (1/1 mol) membranes is consistent with segregation of cholesterol into {20:4-20:4PC} and {18:0-20:4PC} microdomains of {textless}160 A in size that preserve the molecular organization of sterol in the individual phospholipid constituents. Our results demonstrate unambiguously that cholesterol has low affinity to polyunsaturated fatty acids and support hypotheses of lateral phase separation of membrane constituents into sterol-poor/polyunsaturated fatty acid-rich and sterol-rich/saturated fatty acid-rich microdomains.

C. Böttcher, K. Ludwig, A. Herrmann, M. van Heel, H. Stark (1999): Structure of influenza haemagglutinin at neutral and at fusogenic {pH} by electron cryo-microscopy
Type: article by {FEBS} Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/10606732
Abstract:

The three-dimensional structures of the complete haemagglutinin {(HA)} of influenza virus {A/Japan/305/57} {(H2N2)} in its native (neutral {pH)} and membrane fusion-competent (low {pH)} form by electron cryo-microscopy at a resolution of 10 A and 14 A, respectively, have been determined. In the fusion-competent form the subunits remain closely associated preserving typical overall features of the trimeric ectodomain at neutral {pH.} Rearrangements of the tertiary structure in the distal and the stem parts are associated with the formation of a central cavity through the entire ectodomain. We suggest that the cavity is essential for relocation of the so-called fusion sequence of {HA} towards the target membrane.

M. S. Bretscher, S. Munro (1993): Cholesterol and the Golgi apparatus
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/8362242

D. N. Wang (1994): Band 3 protein: structure, flexibility and function
Type: article by {FEBS} Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/8206153
Abstract:

The electroneutral exchange of chloride and bicarbonate across the human erythrocyte membrane is facilitated by Band 3, a 911 amino acid glycoprotein. The 43 {kDa} amino-terminal cytosolic domain binds the cytoskeleton, haemoglobin and glycolytic enzymes. The 52 {kDa} carboxyl-terminal membrane domain mediates anion transport. The protein is a functional dimer, in which the two subunits probably interact with one another by an allosteric mechanism. It is proposed that the link between the mobile cytoplasmic and the membrane-spanning domains of the protein is flexible, based on recent biochemical, biophysical and structural data. This explains the long-standing puzzle that attachment to the cytoskeletal spectrin and actin does not appear to restrict the rotational movement of the Band 3 protein in the erythrocyte membrane. In the Band 3 isoform from the Southeast Asian Ovalocytes {(SAO)} this link is altered, resulting a tighter attachment of the cytoskeleton to the plasma membrane and a more rigid red blood cell.

A. Schlegel, M. P. Lisanti (2000): A molecular dissection of caveolin-1 membrane attachment and oligomerization. Two separate regions of the caveolin-1 C-terminal domain mediate membrane binding and oligomer/oligomer interactions in vivo
Type: article by The Journal of Biological Chemistry.
doi: 10.1074/jbc.M002558200
link: http://www.ncbi.nlm.nih.gov/pubmed/10801850
Abstract:

Caveolins form interlocking networks on the cytoplasmic face of caveolae. The cytoplasmically directed N and C termini of caveolins are separated by a central hydrophobic segment, which is believed to form a hairpin within the membrane. Here, we report that the caveolin scaffolding domain {(CSD,} residues 82-101), and the C terminus (residues 135-178) of caveolin-1 are each sufficient to anchor green fluorescent protein {(GFP)} to membranes in vivo. We also show that the first 16 residues of the C terminus (i.e. residues 135-150) are necessary and sufficient to attach {GFP} to membranes. When fused to the caveolin-1 C terminus, {GFP} co-localizes with two {trans-Golgi} markers and is excluded from caveolae. In contrast, the {CSD} targets {GFP} to caveolae, albeit less efficiently than full-length caveolin-1. Thus, caveolin-1 contains at least two membrane attachment signals: the {CSD,} dictating caveolar localization, and the C terminus, driving {trans-Golgi} localization. Additionally, we find that caveolin-1 oligomer/oligomer interactions require the distal third of the caveolin-1 C terminus. Thus, the caveolin-1 C-terminal domain has two separate functions: (i) membrane attachment (proximal third) and (ii) protein/protein interactions (distal third).

S. H. W. Wu, H. M. McConnell (1975): Phase separations in phospholipid membranes
Type: article by Biochemistry.
doi: 10.1021/bi00675a032
link: http://dx.doi.org/10.1021/bi00675a032

D. Boal (2001): Mechanics of the Cell
Type: book by Cambridge University Press.

C. Gliss, O. Randel, H. Casalta, E. Sackmann, R. Zorn, T. Bayerl (1999): Anisotropic motion of cholesterol in oriented {DPPC} bilayers studied by quasielastic neutron scattering: the liquid-ordered phase.
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1300333&rendertype=abstract

K. Tu, M. L. Klein, D. J. Tobias (1998): Constant-pressure molecular dynamics investigation of cholesterol effects in a dipalmitoylphosphatidylcholine bilayer.
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1299887&rendertype=abstract

R. J. Mashl, R. F. Bruinsma (1998): Spontaneous-curvature theory of clathrin-coated membranes
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(98)77993-7
link: http://www.ncbi.nlm.nih.gov/pubmed/9635740
Abstract:

Clathrin-coated membranes are precursors to coated vesicles in the receptor-mediated endocytic pathway. In this paper we present a physical model for the first steps of the transformation of a clathrin-coated membrane into a coated vesicle. The theory is based on in vitro cytoplasmic acidification experiments of Heuser {(J.} Cell Biol. 108:401-411) that suggest the transformation proceeds by changes in the chemical environment of the clathrin lattice, wherein the chemical environment determines the amount of intrinsic, or spontaneous, curvature of the network. We show that a necessary step of the transformation, formation of free pentagons in the clathrin network, can proceed via dislocation unbinding, driven by changes in the spontaneous curvature. Dislocation unbinding is shown to favor formation of coated vesicles that are quite small compared to those predicted by the current continuum theories, which do not include the topology of the clathrin lattice.

T. P. McMullen, R. N. McElhaney (1995): New aspects of the interaction of cholesterol with dipalmitoylphosphatidylcholine bilayers as revealed by high-sensitivity differential scanning calorimetry
Type: article by Biochimica Et Biophysica Acta.
link: http://www.ncbi.nlm.nih.gov/pubmed/7880863
Abstract:

We have investigated the effects of cholesterol on the thermotropic phase behavior of annealed and unannealed aqueous dispersions of dipalmitoylphosphatidylcholine {(DPPC)} using high-sensitivity differential scanning calorimetry {(DSC),} concentrating particularly on the cholesterol concentration range from 0 to 20 mol%. We find that the incorporation of cholesterol into low-temperature annealed {DPPC} bilayers decreases the enthalpy of the subtransition without affecting the transition temperature, such that the subtransition is abolished by 20 mol% cholesterol. Similarly, the incorporation of cholesterol progressively decreases the temperature and enthalpy of the pretransition and abolishes it entirely at cholesterol concentrations above 5 mol%. The incorporation of increasing quantities of cholesterol also alters the main or chain-melting phase transition. At cholesterol concentrations of 2 to 20 mol% cholesterol, the {DSC} endotherm arising from the main transition consists of superimposed sharp and broad components, the former due to the melting of cholesterol-poor and the latter to the melting of the cholesterol-rich {DPPC} domains. The temperature and cooperativity of the sharp component decreases slightly with increasing cholesterol concentration whereas the enthalpy decreases markedly, becoming zero at 20-25 mol% cholesterol. In contrast, the temperature and enthalpy of the broad component increases, and the cooperativity decreases markedly over this same range of cholesterol concentrations. An apparent increase in cooperativity of the overall {DPPC} endotherm at 7 mol% cholesterol is shown to arise because of a convergence in the transition temperatures of the sharp and broad components of the {DSC} endotherms. Some of our experimental findings, particularly the absence of any evidence for the existence of a triple point near 7.5 mol% cholesterol, do not accord with a recently proposed {DPPC/cholesterol} phase diagram derived from {DSC} and {2H-NMR} data (see Vist, {M.R.} and Davis, {J.H.} (1990) Biochemistry 29, 451-464). In addition, we examined the effect of cholesterol on phosphatidylcholines {(PCs)} of different chain lengths and confirm that a eutectic point does not exist for any of these {PC/cholesterol} mixtures. We then propose a new, more complete {DPPC/cholesterol} phase diagram based on our high-sensitivity {DSC} data as well as some recent spectroscopic data on {PC/cholesterol} mixtures and explore some of its biological implications.

M. Bloom, E. Evans, O. G. Mouritsen (1991): Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective
Type: article by Quarterly Reviews of Biophysics.
link: http://www.ncbi.nlm.nih.gov/pubmed/1749824

M. G. J. Ford, I. G. Mills, B. J. Peter, Y. Vallis, G. J. K. Praefcke, P. R. Evans, H. T. McMahon (2002): Curvature of clathrin-coated pits driven by epsin
Type: article by Nature.
doi: 10.1038/nature01020
link: http://www.ncbi.nlm.nih.gov/pubmed/12353027
Abstract:

Clathrin-mediated endocytosis involves cargo selection and membrane budding into vesicles with the aid of a protein coat. Formation of invaginated pits on the plasma membrane and subsequent budding of vesicles is an energetically demanding process that involves the cooperation of clathrin with many different proteins. Here we investigate the role of the brain-enriched protein epsin 1 in this process. Epsin is targeted to areas of endocytosis by binding the membrane lipid phosphatidylinositol-4,5-bisphosphate {(PtdIns(4,5)P(2)).} We show here that epsin 1 directly modifies membrane curvature on binding to {PtdIns(4,5)P(2)} in conjunction with clathrin polymerization. We have discovered that formation of an amphipathic alpha-helix in epsin is coupled to {PtdIns(4,5)P(2)} binding. Mutation of residues on the hydrophobic region of this helix abolishes the ability to curve membranes. We propose that this helix is inserted into one leaflet of the lipid bilayer, inducing curvature. On lipid monolayers epsin alone is sufficient to facilitate the formation of clathrin-coated invaginations.

W. Knoll, G. Schmidt, K. Ibel, E. Sackmann (1985): {SANS-study} of lateral phase separation in {DMPC-cholesterol} mixed membranes
Type: article by Biochemistry.

S. Hübner, A. D. Couvillon, J. A. Käs, V. A. Bankaitis, R. Vegners, C. L. Carpenter, P. A. Janmey (1998): Enhancement of phosphoinositide 3-kinase {(PI} 3-kinase) activity by membrane curvature and inositol-phospholipid-binding peptides
Type: article by European Journal of Biochemistry / {FEBS}.
link: http://www.ncbi.nlm.nih.gov/pubmed/9874255
Abstract:

The phosphorylation of phosphatidylinositol {(PtdIns)} on the 3' position of the inositol ring by phosphoinositide 3-kinase {(PI} 3-kinase) is shown to depend strongly on the curvature of liposomes containing a mixture of phosphatidylcholine {(PtdCho)} and {PtdIns.} Vesicles with an average diameter of 50 nm are phosphorylated 100 times faster than chemically identical vesicles with an average diameter greater than 300 nm. The low reactivity of large vesicles is not due to the difference in vesicle number for large and small vesicles at constant total lipid, nor to occlusion of lipid surfaces in multilammelar structures, and can be reversed by addition of low ({textless} 1:100) molar ratios of either the {PtdIns} transfer protein sec14p or a ten-residue peptide derived from the inositol-phospholipid-binding site of gelsolin. Similar measurements using {PI} 4-kinase showed a weak dependence on vesicle size. The strong dependence of {PI} 3-kinase function on membrane curvature suggests possible localization of {PI} 3-kinase activity at sites where clustering of receptors, for example, may locally deform the membrane, and suggests that once {PI} 3-kinase is localized and activated at surface sites, the reaction may become self-accelerating.

D. R. Gaskell (1996): In: Cahn {RW,} Hassen P, editors. Physical Metallurgy
Type: book by Elsevier Science {BV}.

H. S. Seung, D. R. Nelson (1988): Defects in flexible membranes with crystalline order
Type: article by Physical Review. A.
link: http://www.ncbi.nlm.nih.gov/pubmed/9900464

K. Jacobson, O. G Mouritsen, R. G. Anderson (2007): Lipid rafts: at a crossroad between cell biology and physics
Type: article by Nature cell biology.

S. Komura, H. Shirotori, P. D. Olmsted, D. Andelman (2004): Lateral phase separation in mixtures of lipids and cholesterol
Type: article by Europhysics Letters.
link: http://adsabs.harvard.edu/abs/2004EL.....67..321K
Abstract:

In an effort to understand "rafts" in biological membranes, we propose

phenomenological models for saturated and unsaturated lipid mixtures, and lipid-cholesterol mixtures. We consider simple couplings between the local composition and internal membrane structure, and their influence on transitions between liquid and gel membrane phases. Assuming that the gel transition temperature of the saturated lipid is shifted by the presence of the unsaturated lipid, and that cholesterol acts as an external field on the chain melting transition, a variety of phase diagrams are obtained. The phase diagrams for binary mixtures of saturated/unsaturated lipids and lipid/cholesterol are in semi-quantitative agreement with the experiments. Our results also apply to regions in the ternary phase diagram of lipid/lipid/cholesterol systems.

J. C. Owicki, H. M. McConnell (1979): Theory of protein-lipid and protein-protein interactions in bilayer membranes
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 76
link: http://www.pnas.org/content/76/10/4750.abstract
Abstract:

A model for protein-lipid interactions in bilayer membranes where the proteins are very dilute is extended to higher protein concentration, where appreciable lipid-mediated protein-protein interactions occur. It is found that proteins may change the lipid phase transition temperature and that they weaken the phase transition. There exists a critical protein concentration above which the sharp lipid phase transition is abolished. The model also qualitatively reproduces several experimental observations on the physical behavior of bilayers formed from mixtures of cholesterol and phosphatidylcholines.

W. T. Góźdź, G. Gompper (1999): Shapes and shape transformations of two-component membranes of complex topology
Type: article by Physical Review E.
doi: 10.1103/PhysRevE.59.4305
link: http://link.aps.org/abstract/PRE/v59/p4305
Abstract:

The properties of two-component membranes, which form doubly periodic surfaces of complex topology, are studied in the strong-segregation limit. The membrane is described within the framework of curvature elasticity; the two components are distinguished by their spontaneous curvatures in this case. Four different domain morphologies are considered for a square lattice of passages: rings of component α inside the passage and caplets of component α outside the passage, as well as rings and caplets of component β. The dependences of the shape of the membrane and of the shape of the domain boundary are calculated as a function of composition. On the basis of a calculation of the curvature energy we conjecture the existence of doubly periodic, piecewise constant-mean-curvature surfaces. For small and intermediate line tensions, we predict several phase transitions between the investigated morphologies. We also discuss briefly the existence and shapes of vesicles of piecewise constant mean curvature.

G. G. Putzel, M. Schick (2008): Phenomenological Model and Phase Behavior of Saturated and Unsaturated Lipids and Cholesterol
Type: article by Biophysical Journal.

M. M. Perry, A. B. Gilbert (1979): Yolk transport in the ovarian follicle of the hen {(Gallus} domesticus): lipoprotein-like particles at the periphery of the oocyte in the rapid growth phase
Type: article by J Cell Sci.
link: http://jcs.biologists.org/cgi/content/abstract/39/1/257

J. Riegler, H. Möhwald (1986): Elastic Interactions of Photosynthetic Reaction Center Proteins Affecting Phase Transitions and Protein Distributions
Type: article by Biophysical Journal.

K. G. Rothberg, J. E. Heuser, W. C. Donzell, Y. S. Ying, J. R. Glenney, R. G. Anderson (1992): Caveolin, a protein component of caveolae membrane coats
Type: article by Cell.
link: http://www.ncbi.nlm.nih.gov/pubmed/1739974
Abstract:

Caveolae have been implicated in the transcytosis of macromolecules across endothelial cells and in the receptor-mediated uptake of 5-methyltetrahydrofolate. Structural studies indicate that caveolae are decorated on their cytoplasmic surface by a unique array of filaments or strands that form striated coatings. To understand how these nonclathrin-coated pits function, we performed structural analysis of the striated coat and searched for the molecular component(s) of the coat material. The coat cannot be removed by washing with high salt; however, exposure of membranes to cholesterol-binding drugs caused invaginated caveolae to flatten and the striated coat to disassemble. Antibodies directed against a 22 kd substrate for v-src tyrosine kinase in virus-transformed chick embryo fibroblasts decorated the filaments, suggesting that this molecule is a component of the coat. We have named the molecule caveolin. Caveolae represent a third type of coated membrane specialization that is involved in molecular transport.

E. A. Guggenheim (1985): Thermodynamics - An advanced treatment for chemists and physicists (7th edition)
Type: book by North Holland.
link: http://adsabs.harvard.edu/abs/1985anh..book.....G

Kapitel 13

M. Tanaka, E. Sackmann (2005): Polymer-supported membranes as models of the cell surface
Type: article by Nature.
doi: 10.1038/nature04164
link: http://dx.doi.org/10.1038/nature04164

G. I. Bell, M. Dembo, P. Bongrand (1984): Cell adhesion. Competition between nonspecific repulsion and specific bonding
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(84)84252-6
link: http://www.ncbi.nlm.nih.gov/pubmed/6743742
Abstract:

We develop a thermodynamic calculus for the modeling of cell adhesion. By means of this approach, we are able to compute the end results of competition between the formation of specific macromolecular bridges and nonspecific repulsion arising from electrostatic forces and osmotic (steric stabilization) forces. Using this calculus also allows us to derive in a straightforward manner the effects of cell deformability, the Young's modulus for stretching of bridges, diffusional mobility of receptors, heterogeneity of receptors, variation in receptor number, and the strength of receptor-receptor binding. The major insight that results from our analysis concerns the existence and characteristics of two phase transitions corresponding, respectively, to the onset of stable cell adhesion and to the onset of maximum cell-cell or cell-substrate contact. We are also able to make detailed predictions of the equilibrium contact area, equilibrium number of bridges, and the cell-cell or cell-substrate separation distance. We illustrate how our approach can be used to improve the analysis of experimental data, by means of two concrete examples.

A.-S. Smith, U. Seifert (2005): Force-induced de-adhesion of specifically bound vesicles: strong adhesion in competition with tether extraction
Type: article by Langmuir: The {ACS} Journal of Surfaces and Colloids.
doi: 10.1021/la051303f
link: http://www.ncbi.nlm.nih.gov/pubmed/16285811
Abstract:

A theoretical study of the thermodynamic equilibrium between force-induced tether formation and the adhesion of vesicles mediated by specific ligand-receptor interactions has been performed. The formation of bonds between mobile ligands in the vesicle and immobile receptors on the substrate is examined within a thermodynamic approximation. The shape of a vesicle pulled with a point force is calculated within a continuous approach. The two approaches are merged self-consistently by the use of the effective adhesion potential produced by the collective action of the bonds. As a result, the shapes of the vesicle and the tether, as well as the number of formed bonds in the contact zone, are determined as a function of the force, and approximate analytic expressions for them are provided. The de-adhesion process is characterized by the construction of a phase diagram that is a function of the density of the ligands in the vesicle, the surface coverage by receptors, the ligand-receptor binding affinity, and the reduced volume of the vesicle. In all cases, the phase diagram contains three regions separated by two nonintersecting lines of critical forces. The first is the line of onset forces associated with a second-order shape transition from a spherical cap to a tethered vesicle. The second line is attributed to the detachment forces at which a first-order unbinding transition from a tethered shape to a free vesicle occurs.

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.7, Elastizitätstheorie: {BD} 7
Type: book by Deutsch {(Harri)}.

P. G. de Gennes (1985): Wetting: statics and dynamics
Type: article by Reviews of Modern Physics.
link: http://adsabs.harvard.edu/abs/1985RvMP...57..827D
Abstract:

The wetting of solids by liquids is connected to physical chemistry

(wettability), to statistical physics (pinning of the contact line, wetting transitions, etc.), to long-range forces (van der Waals, double layers), and to fluid dynamics. The present review represents an attempt towards a unified picture with special emphasis on certain features of "dry spreading": (a) the final state of a spreading droplet need not be a monomolecular film; (b) the spreading drop is surrounded by a precursor film, where most of the available free energy is spent; and (c) polymer melts may slip on the solid and belong to a separate dynamical class, conceptually related to the spreading of superfluids.

A.-S. Smith, K. Sengupta, S. Goennenwein, U. Seifert, E. Sackmann (2008): Force-induced growth of adhesion domains is controlled by receptor mobility
Type: article by Proceedings of the National Academy of Sciences.
doi: 10.1073/pnas.0801706105
link: http://www.pnas.org/content/105/19/6906.abstract
Abstract:

In living cells, adhesion structures have the astonishing ability to grow and strengthen under force. Despite the rising evidence of the importance of this phenomenon, little is known about the underlying mechanism. Here, we show that force-induced adhesion-strengthening can occur purely because of the thermodynamic response to the elastic deformation of the membrane, even in the absence of the actively regulated cytoskeleton of the cell, which was hitherto deemed necessary. We impose {pN-forces} on two fluid membranes, locally pre-adhered by {RGD-integrin} binding. One of the binding partners is always mobile whereas the mobility of the other can be switched on or off. Immediate passive strengthening of adhesion structures occurs in both cases. When both binding partners are mobile, strengthening is aided by lateral movement of intact bonds as a transient response to force-induced membrane-deformation. By extending our microinterferometric technique to the suboptical regime, we show that the adhesion, as well as the resistance to force-induced de-adhesion, is greatly enhanced when both, rather than only one, of the binding partners are mobile. We formulate a theory that explains our observations by linking the macroscopic shape deformation with the microscopic formation of bonds, which further elucidates the importance of receptor mobility. We propose this fast passive response to be the first-recognition that triggers signaling events leading to mechanosensing in living cells.

T. A. Springer (1994): Traffic signals for lymphocyte recirculation and leukocyte emigration: the multistep paradigm
Type: article by Cell.
link: http://www.ncbi.nlm.nih.gov/pubmed/7507411

A. Albersdörfer, T. Feder, E. Sackmann (1997): Adhesion-induced domain formation by interplay of long-range repulsion and short-range attraction force: a model membrane study
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(97)78065-2
link: http://www.ncbi.nlm.nih.gov/pubmed/9199789
Abstract:

We study the role of the interplay of specific and universal forces for the adhesion of giant vesicles on solid supported membranes. To model the situation of cell adhesion, we incorporated lipopolymers (phospholipids with polyethyleneoxide headgroups) as artificial glycocalix, whereas attractive lock-and-key forces are mimicked by incorporating biotinylated lipids into both membranes and by mediating the strong coupling through streptavidin. Adhesion is studied by quantitative reflection interference contrast microscopy {(RICM),} which enables visualization of the contact zone and reconstruction of the height profile of the membrane beyond the contact line (outside the contact zone) up to a height of 1 micron. We demonstrate that adhesion is accompanied by lateral phase separation, leading to the formation of domains of tight adhesion (adhesion plaques) separated by areas of weak adhesion exhibiting pronounced flickering. By analyzing the height profile S(x) near the contact line in terms of the tension equilibrium {(Young} equation) and the moment equilibrium, respectively, the adhesion energy and membrane tension can be approximately measured locally. We show that the adhesion energy is about three orders of magnitude larger for the adhesion plaques than for the weekly adhering regions. The adhesion is studied as a function of the excess area of the vesicle generated by temperature variation. A very remarkable finding is that increased excess area is not always stored in the contact area, but leads to the formation of microbuds (diameter approximately 2 microns).

R. Bruinsma, A. Behrisch, E. Sackmann (2000): Adhesive switching of membranes: Experiment and theory
Type: article by Physical Review E.
doi: 10.1103/PhysRevE.61.4253
link: http://link.aps.org/abstract/PRE/v61/p4253
Abstract:

We report on a study of a model bioadhesion system: giant vesicles in contact with a supported lipid bilayer. Embedded in both membranes are very low concentrations of homophilic recognition molecules (contact site A receptors) competing with higher concentrations of repeller molecules: polyethylene glycol {(PEG)} lipids. These repellers mimic the inhibiting effect of the cell glycocalyx on adhesion. The effective adhesive interaction between the two membranes is probed by interferometric analysis of thermal fluctuations. We find two competing states of adhesion: initial weak adhesion is followed by slower aggregation of the adhesion molecules into small, tightly bound clusters that coexist with the regions of weak adhesion. We interpret our results in terms of a double-well intermembrane potential, and we present a theoretical analysis of the intermembrane interaction in the presence of mobile repeller molecules at a fixed chemical potential that shows that the interaction potential indeed should have just such a double-well shape. At a fixed repeller concentration we recover a conventional purely repulsive potential. We discuss the implications of our findings in terms of a general amplification mechanism of the action of sparse adhesion molecules by a nonspecific double-well potential. We also discuss the important role of the Helfrich undulation force for the proposed scenario.

P. L. Townes, J. Holtfreter (1955): Directed movements and selective adhesion of embryonic amphibian cells./. exp
Type: article

H. Lodish, A. Berk, C. A. Kaiser, M. Krieger, M. P. Scott, A. Bretscher (2007): Molecular Cell Biology
Type: book by Palgrave Macmillan.

S. F. Gilbert, S. R. Singer (2006): Developmental Biology
Type: book by Palgrave Macmillan.

C. R. Monks, B. A. Freiberg, H. Kupfer, N. Sciaky, A. Kupfer (1998): Three-dimensional segregation of supramolecular activation clusters in T cells
Type: article by Nature.
doi: 10.1038/25764
link: http://www.ncbi.nlm.nih.gov/pubmed/9738502
Abstract:

Activation of T cells by antigen-presenting cells {(APCs)} depends on the complex integration of signals that are delivered by multiple antigen receptors. Most receptor-proximal activation events in T cells were identified using multivalent anti-receptor antibodies, eliminating the need to use the more complex {APCs.} As the physiological membrane-associated ligands on the {APC} and the activating antibodies probably trigger the same biochemical pathways, it is unknown why the antibodies, even at saturating concentrations, fail to trigger some of the physiological T-cell responses. Here we study, at the level of the single cell, the responses of T cells to native ligands. We used a digital imaging system and analysed the three-dimensional distribution of receptors and intracellular proteins that cluster at the contacts between T cells and {APCs} during antigen-specific interactions. Surprisingly, instead of showing uniform oligomerization, these proteins clustered into segregated three-dimensional domains within the cell contacts. The antigen-specific formation of these new, spatially segregated supramolecular activation clusters may generate appropriate physiological responses and may explain the high sensitivity of the T cells to antigen.

D. R. Critchley, A. R. Gingras (2008): Talin at a glance
Type: article by Journal of Cell Science.
doi: 10.1242/jcs.018085
link: http://www.ncbi.nlm.nih.gov/pubmed/18434644

M. Gunzer, A. Schäfer, S. Borgmann, S. Grabbe, K. S. Zänker, E. B. Bröcker, E. Kämpgen, P. Friedl (2000): Antigen presentation in extracellular matrix: interactions of T cells with dendritic cells are dynamic, short lived, and sequential
Type: article by Immunity.
link: http://www.ncbi.nlm.nih.gov/pubmed/11021530
Abstract:

Cognate interactions of naive T cells with antigen-presenting dendritic cells require physical cell-cell contacts leading to signal induction and T cell activation. Using a three-dimensional collagen matrix videomicroscopy model for ovalbumin peptide-specific activation of murine and oxidative mitogenesis of human T cells, we show that T cells maintain vigorous migration upon cognate interactions to {DC} (dendritic cell), continuously crawl across the {DC} surface, and rapidly detach (median within 6-12 min). These dynamic and short-lived encounters favor sequential contacts with the same or other {DC} and trigger calcium influx, upregulation of activation markers, T blast formation, and proliferation. We conclude that a tissue environment supports the accumulation of sequential signals, implicating a numeric or "digital" control mechanism for an ongoing primary immune response.

C. S. Shelley, N. Da Silva, J. M. Teodoridis (2001): During U937 monocytic differentiation repression of the {CD43} gene promoter is mediated by the single-stranded {DNA} binding protein Pur alpha
Type: article by British Journal of Haematology.
link: http://www.ncbi.nlm.nih.gov/pubmed/11722429
Abstract:

Human {CD43} is an abundant, heavily glycosylated molecule expressed exclusively on the surface of leucocytes. When leucocytes are at rest, {CD43} acts to prevent intercellular interaction but during leucocyte differentiation such cell-cell interaction is facilitated by {CD43.} This change in the function of {CD43} is mediated in part by a reduction in its level of expression. Previous studies have implicated proteolytic cleavage events at the cell surface in causing such reduction. Here, we report that, in an in vitro model of leucocyte differentiation, {CD43} {mRNA} levels were also subject to reduction. Specifically, we demonstrated that within 48 h of the cell line U937 being induced to differentiate along the monocytic pathway, {CD43} {mRNA} levels were reduced by 69%. This decline coincided with a decrease in the activity of the {CD43} gene promoter mediated by the single-stranded {DNA} binding protein Pur alpha. Previously, we have demonstrated that Pur alpha mediates induction of the {CD11c} beta 2 integrin promoter during U937 differentiation. Consequently, Pur alpha represents a potential means by which the induction of pro-adhesive molecules and the repression of anti-adhesive molecules is co-ordinated during leucocyte differentiation.

S. Komura, D. Andelman (2000): Adhesion-induced lateral phase separation in membranes
Type: article by The European Physical Journal E.

Z. Guttenberg, B. Lorz, E. Sackmann, A. Boulbitch (2001): First-order transition between adhesion states in a system mimicking cell-tissue interaction
Type: article by Europhysics Letters.
link: http://adsabs.harvard.edu/abs/2001EL.....54..826G
Abstract:

We establish a model of cell-tissue interaction consisting of vesicles

carrying lipopolymers (to mimic the glycocalix) and mobile specific ligands of the blood platelet integrin {alphaIIbbeta3} covering the substrate. We find the phase diagram with a first-order transition between a gravity-controlled weak state of the vesicle-substrate adhesion and a strong-adhesion state governed by receptor-ligand interaction. Adhesion energy ɛadh is measured as a function of ligand and repeller concentration by interferometric contour analysis on the basis of a new refined model of soft shell adhesion (accounting for the membrane bending and stretching at the adhesion rim of the ellipsoidal vesicle). At ligand densities comparable to integrin density, ɛadh decreases sharply. Increasing the repeller content weakens the adhesion strength.

J. W. Cahn (1977): Critical point wetting
Type: article by The Journal of Chemical Physics.
doi: 10.1063/1.434402
link: http://link.aip.org/link/?JCP/66/3667/1

U. Seifert, R. Lipowsky (1995): Morphology of vesicles
Type: article by Handbook of biological physics.

M. L. Dustin, D. R. Colman (2002): Neural and Immunological Synaptic Relations
Type: article by Science.
doi: 10.1126/science.1076386
link: http://www.sciencemag.org/cgi/content/abstract/298/5594/785

K. Choudhuri, D. Wiseman, M. H. Brown, K. Gould, P. A. van der Merwe (2005): T-cell receptor triggering is critically dependent on the dimensions of its {peptide-MHC} ligand
Type: article by Nature.
doi: 10.1038/nature03843
link: http://dx.doi.org/10.1038/nature03843

T. H. Watts, H. E. Gaub, H. M. McConnell (1986): T-cell-mediated association of peptide antigen and major histocompatibility complex protein detected by energy transfer in an evanescent wave-field
Type: article by Nature.
doi: 10.1038/320179a0
link: http://dx.doi.org/10.1038/320179a0

A. Lambacher, P. Fromherz (1996): Fluorescence interference-contrast microscopy on oxidized silicon using a monomolecular dye layer
Type: article by Applied Physics A: Materials Science & Processing.
doi: 10.1007/BF01567871
link: http://dx.doi.org/10.1007/BF01567871
Abstract:

A silicon chip is covered by a monomolecular film of a fluorescence dye with silicon dioxide used as a spacer. The fluorescence depends on the distance of the dye from the silicon. The modulation of the intensity is described quantitatively by an optical theory which accounts for interference of the exciting light and of the emitted light. The effect is used to obtain a microscopic picture of the surface profile with a precision of a few Angströms. The perspectives for an application in wet systems such as neuron-silicon junctions and lipid membranes on silicon are pointed out.

D. Zagury, J. Bernard, N. Thierness, M. Feldman, G. Berke (1975): Isolation and characterization of individual functionally reactive cytotoxic T lymphocytes: conjugation, killing and recycling at the single cell level
Type: article by European Journal of Immunology.
doi: 10.1002/eji.1830051205
link: http://dx.doi.org/10.1002/eji.1830051205
Abstract:

Isolation and characterization of individual functionally reactive cytotoxic T lymphocytes have been achieved. Peritoneal exudate cytotoxic lymphocytes were obtained from {BALB/c} mice injected with {EL4} tumor cells. Lymphocyte tumor cell conjugation was promoted by centrifugation. Individual conjugates comprised of one lymphocyte bound to one tumor cell were isolated with a micropipette. The ultrastructure of isolated killer lymphocytes and the lysis of conjugated target cells were analyzed. The cytotoxic lymphocytes are small cells with an indented nucleus which is poor in peripheral chromatin and rich in rough nuclear sap. The cytoplasm contains one-membrane-bound lysosome-like granules and clusters of ribosomes, but no rough endoplasmatic reticulum. The Golgi apparatus is well developed. Direct evidence obtained at the single cell level shows that a single effector lymphocyte is required and sufficient for the destruction of a single target cell and that killer cells which have been responsible for the lysis of a given target cell can lyse a second and even a third time.

S. Goennenwein, M. Tanaka, B. Hu, L. Moroder, E. Sackmann (2003): Functional Incorporation of Integrins into Solid Supported Membranes on Ultrathin Films of Cellulose: Impact on Adhesion
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(03)74508-1

Kapitel 14

R. H. Adrian (1956): The effect of internal and external potassium concentration on the membrane potential of frog muscle
Type: article by The Journal of Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/13368111

P. C. Hiemenz, R. Rajagopalan (1997): Principles of Colloid and Surface Chemistry
Type: book by Marcel Dekker Inc.

E. Neher, B. Sakmann (1976): Single-channel currents recorded from membrane of denervated frog muscle fibres
Type: article by Nature.
link: http://www.ncbi.nlm.nih.gov/pubmed/1083489

J. Nicholls (2001): From Neuron to Brain: A Cellular and Molecular Approach to the Function of the Nervous System
Type: book by Palgrave Macmillan.

A. L. Hodgkin, A. F. Huxley (1952): Currents carried by sodium and potassium ions through the membrane of the giant axon of Loligo
Type: article by The Journal of Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/14946713

J. Jäckle (2007): The causal theory of the resting potential of cells
Type: article by Journal of Theoretical Biology.
doi: 10.1016/j.jtbi.2007.07.027
link: http://www.ncbi.nlm.nih.gov/pubmed/17904583
Abstract:

In this pedagogical article the causal theory of the resting potential of cells is presented, which for given extracellular ion concentrations predicts the intracellular ones simultaneously with the resting potential. In addition to the Na, K-pump, fixed charges on the membrane surfaces are taken into account. The equation determining the resting potential in the causal theory suggests a new explanation of the genesis of the resting potential. The usual criterion for an ion pump to be electrogenic is not relevant for the whole of the resting potential, and may therefore be misleading. The physical meaning of the {Goldman-Hodgkin-Katz} formula for the membrane potential as a diffusion potential is also explained and tested with numbers for the giant axon of the squid. A significant discrepancy between theory and experiment is found which calls for an experimental re-examination of the constitutive equations for passive potassium and sodium currents.

R. F. Rakowski, D. C. Gadsby, P. De Weer (1989): Stoichiometry and voltage dependence of the sodium pump in voltage-clamped, internally dialyzed squid giant axon
Type: article by The Journal of General Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/2544655
Abstract:

The stoichiometry and voltage dependence of the {Na/K} pump were studied in internally dialyzed, voltage-clamped squid giant axons by simultaneously measuring, at various membrane potentials, the changes in Na efflux (delta phi Na) and holding current (delta I) induced by dihydrodigitoxigenin {(H2DTG).} {H2DTG} stops the {Na/K} pump without directly affecting other current pathways: (a) it causes no delta I when the pump lacks Na, K, Mg, or {ATP,} and (b) ouabain causes no delta I or delta phi Na in the presence of saturating {H2DTG.} External K {(Ko)} activates Na efflux with {Michaelis-Menten} kinetics {(Km} = 0.45 +/- 0.06 {mM} {[SEM])} in Na-free seawater {(SW),} but with sigmoid kinetics in approximately 400 {mM} Na {SW} {(Hill} coefficient = 1.53 +/- 0.08, K1/2 = 3.92 +/- 0.29 {mM).} {H2DTG} inhibits less strongly {(Ki} = 6.1 +/- 0.3 {microM)} in 1 or 10 {mM} K Na-free {SW} than in 10 {mM} K, 390 {mM} Na {SW} (1.8 +/- 0.2 {microM).} Dialysis with 5 {mM} each {ATP,} phosphoenolpyruvate, and phosphoarginine reduced {Na/Na} exchange to at most 2% of the {H2DTG-sensitive} Na efflux. {H2DTG} sensitive but nonpump current caused by periaxonal K accumulation upon stopping the pump, was minimized by the K channel blockers 3,4-diaminopyridine (1 {mM),} tetraethylammonium (approximately 200 {mM),} and phenylpropyltriethylammonium (20-25 {mM)} whose adequacy was tested by varying {[K]o} (0-10 {mM)} with {H2DTG} present. Two ancillary clamp circuits suppressed stray current from the axon ends. Current and flux measured from the center pool derive from the same membrane area since, over the voltage range -60 to +20 {mV,} tetrodotoxin-sensitive current and Na efflux into Na-free {SW,} under K-free conditions, were equal. The stoichiometry and voltage dependence of pump {Na/K} exchange were examined at near-saturating {[ATP],} {[K]o} and {[Na]i} in both Na-free and 390 {mM} Na {SW.} The {H2DTG-sensitive} F delta phi Na/delta I ratio {(F} is Faraday's constant) of paired measurements corrected for membrane area match, was 2.86 +/- 0.09 (n = 8) at 0 {mV} and 3.05 +/- 0.13 (n = 6) at -60 to -90 {mV} in Na-free {SW,} and 2.72 +/- 0.09 (n = 7) at 0 {mV} and 2.91 +/- 0.21 (n = 4) at -60 {mV} in 390 {mM} Na {SW.} Its overall mean value was 2.87 +/- 0.07 (n = 25), which was not significantly different from the 3.0 expected of a 3 Na/2 K {pump.(ABSTRACT} {TRUNCATED} {AT} 400 {WORDS)}

A. L. Hodgkin, R. D. Keynes (1955): The potassium permeability of a giant nerve fibre
Type: article by The Journal of Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/14368575

A. L. Hodgkin, A. F. Huxley (1952): A quantitative description of ion currents and its applications to conduction and excitation in nerve membranes
Type: article by The Journal of Physiology.

D. E. Goldman (1943): {POTENTIAL,} {IMPEDANCE,} {AND} {RECTIFICATION} {IN} {MEMBRANES}
Type: article by The Journal of General Physiology.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2142582&rendertype=abstract
Abstract:

Impedance and potential measurements have been made on a number of artificial membranes. Impedance changes were determined as functions of current and of the composition of the environmental solutions. It was shown that rectification is present in asymmetrical systems and that it increases with the membrane potential. The behavior in pairs of solutions of the same salt at different concentrations has formed the basis for the studies although a few experiments with different salts at the same concentrations gave results consistent with the conclusions drawn. A theoretical picture has been presented based on the use of the general kinetic equations for ion motion under the influence of diffusion and electrical forces and on a consideration of possible membrane structures. The equations have been solved for two very simple cases; one based on the assumption of microscopic electroneutrality, and the other on the assumption of a constant electric field. The latter was found to give better results than the former in interpreting the data on potentials and rectification, showing agreement, however, of the right order of magnitude only. Although the indications are that a careful treatment of boundary conditions may result in better agreement with experiment, no attempt has been made to carry this through since the data now available are not sufficiently complete or reproducible. Applications of the second theoretical case to the squid giant axon have been made showing qualitative agreement with the rectification properties and very good agreement with the membrane potential data.

R. F. Schmidt, G. Thews, F. Lang (2000): Physiologie des Menschen
Type: book by Springer Berlin.

L. J. Mullins, K. Noda (1963): The Influence of {Sodium-Free} Solution on the membrane potential of frog muscle fibers
Type: article by The Journal of General Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/14060441

R. F. Thompson, M. Behncke Das Gehirn: Von der Nervenzelle zur Verhaltenssteuerung
Type: book by Spektrum Akademischer Verl..

A. L. Hodgkin, B. Katz (1949): The effect of sodium ions on the electrical activity of the giant axon of the squid
Type: article by The Journal of Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/16991839

Kapitel 15

P. Mueller, D. O. Rudin, H. T. Tien, W. C. WESCOTT (1962): Reconstitution of cell membrane structure in vitro and its transformation into an excitable system
Type: article by Nature.
link: http://www.ncbi.nlm.nih.gov/pubmed/14476933

L. C. Timpe, T. L. Schwarz, B. L. Tempel, D. M. Papazian, Y. N. Jan, L. Y. Jan (1988): Expression of functional potassium channels from Shaker {cDNA} in Xenopus oocytes
Type: article by Nature.
doi: 10.1038/331143a0
link: http://www.ncbi.nlm.nih.gov/pubmed/2448636
Abstract:

The Shaker gene of Drosophila melanogaster encodes a potassium-selective ion channel, the {'A'} channel, or one of its subunits. A single Shaker messenger {RNA} species suffices to direct the synthesis of functional A channels in Xenopus oocytes. Physiological characteristics of the A currents induced by two different {mRNA} species are compared.

E. Neher, B. Sakmann (1976): Single-channel currents recorded from membrane of denervated frog muscle fibres
Type: article by Nature.
link: http://www.ncbi.nlm.nih.gov/pubmed/1083489

E. Bamberg, P. Läuger (1973): Channel formation kinetics of gramicidin A in lipid bilayer membranes
Type: article by The Journal of Membrane Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/4131309

S. B. Hladky, D. A. Haydon (1972): Ion transfer across lipid membranes in the presence of gramicidin A. I. Studies of the unit conductance channel
Type: article by Biochimica Et Biophysica Acta.
link: http://www.ncbi.nlm.nih.gov/pubmed/5048999

J. Nicholls (2001): From Neuron to Brain: A Cellular and Molecular Approach to the Function of the Nervous System
Type: book by Palgrave Macmillan.

E. Neher, C. F. Stevens (1977): Conductance fluctuations and ionic pores in membranes
Type: article by Annual Review of Biophysics and Bioengineering.
doi: 10.1146/annurev.bb.06.060177.002021
link: http://www.ncbi.nlm.nih.gov/pubmed/68708

A. L. Hodgkin, A. F. Huxley (1952): Currents carried by sodium and potassium ions through the membrane of the giant axon of Loligo
Type: article by The Journal of Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/14946713

P. Fromherz (2001): Interfacing von Nervenzellen und Halbleiterchips
Type: article by Physikalische Blätter.

D. Colquhoun, B. Sakmann (1985): Fast events in single-channel currents activated by acetylcholine and its analogues at the frog muscle end-plate
Type: article by The Journal of Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/2419552
Abstract:

The fine structure of ion-channel activations by junctional nicotinic receptors in adult frog muscle fibres has been investigated. The agonists used were acetylcholine {(ACh),} carbachol {(CCh),} suberyldicholine {(SubCh)} and decan-1,10-dicarboxylic acid dicholine ester {(DecCh).} Individual activations (bursts) were interrupted by short closed periods; the distribution of their durations showed a major fast component ('short gaps') and a minor slower component ('intermediate gaps'). The mean duration of both short and intermediate gaps was dependent on the nature of the agonist. For short gaps the mean durations (microseconds) were: {ACh,} 20; {SubCh,} 43; {DecCh,} 71; {CCh,} 13. The mean number of short gaps per burst were: {ACh,} 1.9; {SubCh,} 4.1; {DecCh,} 2.0. The mean number of short gaps per burst, and the mean number per unit open time, were dependent on the nature of the agonist, but showed little dependence on agonist concentration or membrane potential for {ACh,} {SubCh} and {DecCh.} The short gaps in {CCh} increased in frequency with agonist concentration and were mainly produced by channel blockages by {CCh} itself. Partially open channels (subconductance states) were clearly resolved rarely (0.4% of gaps within bursts) but regularly. Conductances of 18% (most commonly) and 71% of the main value were found. However, most short gaps were probably full closures. The distribution of burst lengths had two components. The faster component represented mainly isolated short openings that were much more common at low agonist concentrations. The slower component represented bursts of longer openings. Except at very low concentrations more than 85% of activations were of this type, which corresponds to the 'channel lifetime' found by noise analysis. The frequency of channel openings increased slightly with hyperpolarization. The short gaps during activations were little affected when (a) the {[H+]o} or {[Ca2+]o} were reduced to 1/10th of normal, (b) when extracellular Ca2+ was replaced by Mg2+, (c) when the {[Cl-]i} was raised or (d) when, in one experiment on an isolated inside-out patch, the normal intracellular constituents were replaced by {KCl.} Reduction of {[Ca2+]O} to 1/10 of normal increased the single-channel conductance by 50%, and considerably increased the number of intermediate gaps. No temporal asymmetry was detectable in the bursts of openings. Positive correlations were found between the lengths of successive apparent open times at low {SubCh} concentrations, but no correlations between burst lengths were detectable. The component of brief openings behaves, at low concentrations, as though it originates from openings of singly occupied {channels.(ABSTRACT} {TRUNCATED} {AT} 400 {WORDS)}

F. Conti, E. Wanke (1975): Channel noise in nerve membranes and lipid bilayers
Type: article by Quarterly Reviews of Biophysics.
link: http://www.ncbi.nlm.nih.gov/pubmed/769042

J.-P. Changeux, J. Thiéry, Y. Tung, C. Kittel (1967): {ON} {THE} {COOPERATIVITY} {OF} {BIOLOGICAL} {MEMBRANES}
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/16591474

R. B. Rogart, L. L. Cribbs, L. K. Muglia, D. D. Kephart, M. W. Kaiser (1989): Molecular cloning of a putative tetrodotoxin-resistant rat heart Na+ channel isoform
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 86
link: http://www.pnas.org/content/86/20/8170.abstract
Abstract:

Voltage-gated Na+ channels in mammalian heart differ from those in nerve and skeletal muscle. One major difference is that tetrodotoxin {(TTX)-resistant} cardiac Na+ channels are blocked by 1-10 {microM} {TTX,} whereas {TTX-sensitive} nerve Na+ channels are blocked by nanomolar {TTX} concentrations. We constructed a {cDNA} library from 6-day-old rat hearts, where only low-affinity {[3H]saxitoxin} receptors, corresponding to {TTX-resistant} Na+ channels, were detected. We isolated several overlapping {cDNA} clones encompassing 7542 nucleotides and encoding the entire alpha subunit of a cardiac-specific Na+ channel isoform (designated rat heart I) as well as several rat brain I Na+ channel {cDNA} clones. The derived amino acid sequence of rat heart I was highly homologous to, but distinct from, previous Na+ channel clones. {RNase} protection studies showed that the corresponding {mRNA} species is abundant in newborn and adult rat hearts, but not detectable in brain or innervated skeletal muscle. The same {mRNA} species appears upon denervation of skeletal muscle, likely accounting for expression of new {TTX-resistant} Na+ channels. Thus, this cardiac-specific Na+ channel clone appears to encode a distinct {TTX-resistant} isoform and is another member of the mammalian Na+ channel multigene family, found in newborn heart and denervated skeletal muscles.

F. J. Sigworth, E. Neher (1980): Single Na+ channel currents observed in cultured rat muscle cells
Type: article by Nature.
link: http://www.ncbi.nlm.nih.gov/pubmed/6253802
Abstract:

The voltage- and time-dependent conductance of membrane Na+ channels is responsible for the propagation of action potentials in nerve and muscle cells. In voltage-step-clamp experiments on neurone preparations containing 10(4)-10(7) Na+ channels the membrane conductance shows smooth variations in time, but analysis of fluctuations and other eivdence suggest that the underlying single-channel conductance changes are stochastic, rapid transitions between 'closed' and 'open' states as seen in other channel types. We report here the first observations of currents through individual Na+ channels under physiological conditions using an improved version of the extracellular patch-clamp technique on cultured rat muscle cells. Our observations support earlier inferences about channel gating and show a single-channel conductance of approximately 18 {pS.}

C. M. Armstrong, F. Bezanilla (1977): Inactivation of the sodium channel. {II.} Gating current experiments
Type: article by The Journal of General Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/591912
Abstract:

Gating current {(Ig)} has been studied in relation to inactivation of Na channels. No component of Ig has the time course of inactivation; apparently little or no charge movement is associated with this step. Inactivation nonetheless affects Ig by immobilizing about two-thirds of gating charge. Immobilization can be followed by measuring {ON} charge movement during a pulse and comparing it to {OFF} charge after the pulse. The {OFF:ON} ratio is near 1 for a pulse so short that no inactivation occurs, and the ratio drops to about one-third with a time course that parallels inactivation. Other correlations between inactivation and immobilization are that: (a) they have the same voltage dependence; (b) charge movement recovers with the time coures of recovery from inactivation. We interpret this to mean that the immobilized charge returns slowly to "off" position with the time course of recovery from inactivation, and that the small current generated is lost in base-line noise. At -150 {mV} recover is very rapid, and the immobilized charge forms a distinct slow component of current as it returns to off position. After destruction of inactivation by pronase, there is no immobilization of charge. A model is presented in which inactivation gains its voltage dependence by coupling to the activation gate.

H. M. Fishman, H. R. Leuchtag, L. E. Moore (1983): Fluctuation and linear analysis of Na-current kinetics in squid axon
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(83)84353-7
link: http://www.ncbi.nlm.nih.gov/pubmed/6626670
Abstract:

The power spectrum of current fluctuations and the complex admittance of squid axon were determined in the frequency range 12.5 to 5,000 Hx during membrane voltage clamps to the same potentials in the same axon during internal perfusion with cesium. The complex admittance was determined rapidly and with high resolution by a fast Fourier transform computation of the current response, acquired after a steady state was attained, to a synthesized signal with predetermined spectral characteristics superposed as a continuous, repetitive, small perturbation on step voltage clamps. Linear conduction parameters were estimated directly from admittance data by fitting an admittance model, derived from the linearized {Hodgkin-Huxley} equations modified by replacing the membrane capacitance with a "constant-phase-angle" capacitance, to the data. The constant phase angle obtained was approximately 80 degrees. At depolarizations the phase of the admittance was 180 degrees, and the real part of the impedance locus was in the left-half complex plane for frequencies below 1 {kHz,} which indicates a steady-state negative Na conductance. The fits also yielded estimates of the natural frequencies of Na "activation" and "inactivation" processes. By fitting Na-current noise spectra with a double Lorentzian function, a lower and an upper corner frequency were obtained; these were compared with the two natural frequencies determined from admittance analysis at the corresponding potentials. The frequencies from fluctuation analyses ranged from 1.0 to 10.3 times higher than those from linear (admittance) analysis. This discrepancy is consistent with the concept that the fluctuations reflect a nonlinear rate process that cannot be fully characterized by linear perturbation analysis. Comparison of the real part of the admittance and the current noise spectrum shows that the Nyquist relation, which generally applies to equilibrium conductors, does not hold for the Na process in squid axon. The Na-channel conductance, gamma Na, was found to increase monotonically from 0.1 to 4.8 {pS} for depolarizations up to 50 {mV} from a holding potential of -60 {mV,} with no indication of a maximum value.

J. M. Berg, L. Stryer, J. L. Tymoczko (2007): Biochemie
Type: book by Spektrum Akademischer Verlag.

N. Unwin (2005): Refined structure of the nicotinic acetylcholine receptor at {4A} resolution
Type: article by Journal of Molecular Biology.
doi: 10.1016/j.jmb.2004.12.031
link: http://www.ncbi.nlm.nih.gov/pubmed/15701510
Abstract:

We present a refined model of the membrane-associated Torpedo acetylcholine {(ACh)} receptor at {4A} resolution. An improved experimental density map was obtained from 342 electron images of helical tubes, and the refined structure was derived to an R-factor of 36.7% {(R(free)} 37.9%) by standard crystallographic methods, after placing the densities corresponding to a single molecule into an artificial unit cell. The agreement between experimental and calculated phases along the helical layer-lines was used to monitor progress in the refinement and to give an independent measure of the accuracy. The atomic model allowed a detailed description of the whole receptor in the closed-channel form, including the ligand-binding and intracellular domains, which have not previously been interpreted at a chemical level. We confirm that the two ligand-binding alpha subunits have a different extended conformation from the three other subunits in the closed channel, and identify several interactions on both pairs of subunit interfaces, and within the alpha subunits, which may be responsible for their "distorted" structures. The {ACh-coordinating} amino acid side-chains of the alpha subunits are far apart in the closed channel, indicating that a localised rearrangement, involving closure of loops B and C around the bound {ACh} molecule, occurs upon activation. A comparison of the structure of the alpha subunit with that of {AChBP} having ligand present, suggests how the localised rearrangement overcomes the distortions and initiates the rotational movements associated with opening of the channel. Both vestibules of the channel are strongly electronegative, providing a cation-stabilising environment at either entrance of the membrane pore. Access to the pore on the intracellular side is further influenced by narrow lateral windows, which would be expected to screen out electrostatically ions of the wrong charge and size.


Kapitel 16

J. Nagumo, S. Arimoto (1962): An active pulse transmission line simulating nerve axon
Type: article by Proc. {IRE}.

A. C. Scott (1975): The electrophysics of a nerve fiber
Type: article by Reviews of Modern Physics.
link: http://adsabs.harvard.edu/abs/1975RvMP...47..487S
Abstract:

The "action potential" is a pulselike voltage wave which carries

information along a nerve fiber. Starting with fundamental concepts of biochemistry and electromagnetic theory, the derivation of the nonlinear diffusion equation which governs propagation of the action potential is reviewed. Our current understanding of this equation is discussed, paying particular attention to questions of interest in physics and applied mathematics.

K. F. Bonhoeffer (1953): Modelle der Nervenerregung
Type: article by Naturwissenschaften.
link: http://adsabs.harvard.edu/abs/1953NW.....40..301B

J. Nicholls (2001): From Neuron to Brain: A Cellular and Molecular Approach to the Function of the Nervous System
Type: book by Palgrave Macmillan.

J. M. Ritchie, R. B. Rogart (1977): Density of sodium channels in mammalian myelinated nerve fibers and nature of the axonal membrane under the myelin sheath
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/299947
Abstract:

The density of sodium channels in mammalian myelinated fibers has been estimated from measurements of the binding of {[3H]saxitoxin} to rabbit sciatic nerve. Binding both to intact and to homogenized nerve consists of a linear, nonspecific, component and a saturable component that represents binding to the sodium channel. The maximum saturable binding capacity in intact nerve is 19.9 +/- 1.9 fmol-mg wet-1; the equilibrium dissociation constant, Kt, is 3.4 +/- 2.0 {nM.} Homogenization makes little difference, the maximum binding capacity being 19.9 +/- 1.5 fmol-mg wet-1 with Kt = 1.3 +/- 0.7 {nM.} These values correspond to a density of about 700,000 sodium channels per node--i.e., about 12,000 per mum2 of nodal membrane. From the difference between the values of maximum saturable binding capacity in intact and homogenized preparation, given the statistical uncertainty of their estimate, it seems that the internodal membrane can have no more than about 25 channels per mum2. The significance of these findings for saltatory conduction and in demyelinating disease is discussed.

R. Fitzhugh (1962): Computation of impulse initiation and saltatory conduction in a myelinated nerve fiber
Type: article by Biophysical Journal.
link: http://www.ncbi.nlm.nih.gov/pubmed/13893367

A. F. Huxley, R. Stampfli (1949): Evidence for saltatory conduction in peripheral myelinated nerve fibres
Type: article by The Journal of Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/18144923

A. Hodgkin (1952): Quantitative description of membrane current and its application to conduction and excitation in nerve
Type: article by The Journal of Physiology.

H. G Schuster, W. Just (2005): Deterministic chaos an introduction
Type: book by {Wiley-VCH}.

G. Nicolis, I. Prigogine (1977): Self-organization in nonequilibrium systems: From dissipative structures to order through fluctuations
Type: book by Wiley, New York.

H. Haken (1977): Synergetics, an introduction: nonequilibrium phase transitions and self-organization in physics, chemistry, and biology
Type: book by Springer.

Kapitel 17

R. Adrian, L. Feldman, E. Jakobsson (1980): Frequency entrainment of squid axon membrane
Type: article by The Journal of Membrane Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/7441721
Abstract:

Sinusoidally varying stimulating currents were applied to space-clamped squid giant axon membranes in a double sucrose gap apparatus. Stimulus parameters varied were peak-to-peak current amplitude, frequency, and {DC} offset bias. In response to these stimuli, the membranes produced action potentials in varying patterns, according to variation of input stimulus parameters. For some stimulus parameters the output patterns were stable and obviously periodic with the periods being simple multiples of the input period; for other stimulus parameters no obvious periodicity was manifest in the output. The experimental results were compared with simulations using a computer model which was modified in several ways from the {Hodgkin-Huxley} model to make it more representative of our preparation. The model takes into account K+ accumulation in the periaxonal space, features of Na+ inactivation which are anomalous to the {Hodgkin-Huxley} model, sucrose gap hyperpolarization current, and membrane current noise. Many aspects of the experiments are successfully simulated but some are not, possibly because some very slow process present in the preparation is not included in the model.

F. Moss, S. Gielen (2001): Neuro-informatics and neural modelling
Type: book by North Holland.

A. T. Winfree (1977): Phase control of neural pacemakers
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/887919
Abstract:

An electrical stimulus resets the phase of a spontaneously rhythmic neuron. The "new phase" versus "old phase" curve shows either of two distinct topological characters, depending on the stimulus magnitude. These features, and a phase singularity implicit in them, are common to many stable oscillations deriving from continuous feedback between two or more biophysical quantities.

L. Glass, M. R. Guevara, A. Shrier, R. Perez (1983): Bifurcation and chaos in a periodically stimulated cardiac oscillator
Type: article by Physica D Nonlinear Phenomena.
link: http://adsabs.harvard.edu/abs/1983PhyD....7...89G
Abstract:

Periodic stimulation of an aggregate of spontaneously beating cultured

cardiac cells displays phase locking, period-doubling bifurcations and aperiodic ``chaotic dynamics at different values of the stimulation parameters. This behavior is analyzed by considering an experimentally determined one-dimensional Poincar� or first return map. A simplified version of the experimentally determined Poincar� map is proposed, and several features of the bifurcations of this map are described.

J. Keener, J. Sneyd (2008): Mathematical Physiology 1: Cellular Physiology
Type: book by Springer, Berlin.

L. A. Segel (1984): Modeling Dynamic Phenomena in Molecular and Cellular Biology
Type: book by Cambridge University Press.

R. F. Schmidt, G. Thews, F. Lang (2000): Physiologie des Menschen
Type: book by Springer Berlin.

Kapitel 18

B. Alberts, A. Johnson, P. Walter, J. Lewis, M. Raff, K. Roberts (2008): Molecular Biology of the Cell
Type: book by Taylor & Francis.

C. Semmrich, T. Storz, J. Glaser, R. Merkel, A. R. Bausch, K. Kroy (2007): Glass transition and rheological redundancy in F-actin solutions
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.0705513104
link: http://www.ncbi.nlm.nih.gov/pubmed/18077385
Abstract:

The unique mechanical performance of animal cells and tissues is attributed mostly to their internal biopolymer meshworks. Its perplexing universality and robustness against structural modifications by drugs and mutations is an enigma in cell biology and provides formidable challenges to materials science. Recent investigations could pinpoint highly universal patterns in the soft glassy rheology and nonlinear elasticity of cells and reconstituted networks. Here, we report observations of a glass transition in semidilute F-actin solutions, which could hold the key to a unified explanation of these phenomena. Combining suitable rheological protocols with high-precision dynamic light scattering, we can establish a remarkable rheological redundancy and trace it back to a highly universal exponential stretching of the single-polymer relaxation spectrum of a "glassy wormlike chain." By exploiting the ensuing generalized time-temperature superposition principle, the time domain accessible to microrheometry can be extended by several orders of magnitude, thus opening promising new metrological opportunities.

A. L. Bishop, A. Hall (2000): Rho {GTPases} and their effector proteins
Type: article by The Biochemical Journal.
link: http://www.ncbi.nlm.nih.gov/pubmed/10816416
Abstract:

Rho {GTPases} are molecular switches that regulate many essential cellular processes, including actin dynamics, gene transcription, cell-cycle progression and cell adhesion. About 30 potential effector proteins have been identified that interact with members of the Rho family, but it is still unclear which of these are responsible for the diverse biological effects of Rho {GTPases.} This review will discuss how Rho {GTPases} physically interact with, and regulate the activity of, multiple effector proteins and how specific effector proteins contribute to cellular responses. To date most progress has been made in the cytoskeleton field, and several biochemical links have now been established between {GTPases} and the assembly of filamentous actin. The main focus of this review will be Rho, Rac and Cdc42, the three best characterized mammalian Rho {GTPases,} though the genetic analysis of Rho {GTPases} in lower eukaryotes is making increasingly important contributions to this field.

G. Ladam, L. Vonna, E. Sackmann (2005): Protrusion force transmission of amoeboid cells crawling on soft biological tissue
Type: article by Acta Biomaterialia.
doi: 10.1016/j.actbio.2005.06.002
link: http://www.ncbi.nlm.nih.gov/pubmed/16701829
Abstract:

We applied a colloidal force microscopy technique to measure the spreading and retraction forces generated by protrusions (pseudopodia) of vegetative amoeboid cells {(Dictyostelium} discoideum) adhering on soft tissue analogues composed of 2-mm thick hydrogels of hyaluronic acid exhibiting Young's moduli between 10 and 200 Pa. Local shear deformations of the polymer films evoked by magnetic tweezers and by cellular protrusions were determined by analyzing the deflections of colloidal beads randomly deposited on the surface of the polymer cushions, which enabled us to measure forces generated by advancing ("pushing" forces) and retracting ("pulling" forces) protrusions in a direct way. We found that the maximum amplitudes generated by the advancing protrusions (pushes) decrease with increasing stiffness of the {HA} substrate while the amplitudes of the retractions do not show such a dependence. The maximum forces transmitted by the advancing and retracting protrusions increase with increasing stiffness of the {HA} films (from 0.02 to 1 {nN} for the case of pushing). The protrusions spread or retract with constant velocities which are higher for retractions (100 nm s(-1)) than for spreadings (50 nm s(-1)) and are not significantly influenced by the substrate rigidity. We provide evidence that elastic equilibrium during protrusion formation and retraction is maintained by local elastic dipole fields generated at the rim of the protrusions. A model of protrusion force transmission by coupling of growing actin gel in the cytoplasm of the protrusions to cell surface receptors through talin clutches is proposed.

D. R. Kovar, T. D. Pollard (2004): Insertional assembly of actin filament barbed ends in association with formins produces piconewton forces
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.0405902101
link: http://www.pnas.org/content/101/41/14725.abstract
Abstract:

Formins are large multidomain proteins required for assembly of actin cables that contribute to the polarity and division of animal and fungal cells. ormin omology-1 {(FH1)} domains bind profilin, and highly conserved {FH2} domains nucleate actin filaments. We characterized the effects of two formins, budding yeast Bni1p and fission yeast Cdc12p, on actin assembly. We used evanescent wave fluorescence microscopy to observe assembly of actin filaments () nucleated by soluble formin {FH1FH2} domains and () associated with formin {FH1FH2} domains immobilized on microscope slides. {Bni1p(FH1FH2)p} and {Cdc12p(FH1FH2)p} nucleated new actin filaments or captured the barbed ends of preformed actin filaments that grew by insertion of subunits between the immobilized formin and the barbed end of the filament. Both formins remained bound to growing actin filament barbed ends for {textgreater}1,000 sec. Elongation of a filament between an immobilized formin and a second anchor point buckled filament segments as short as 0.7 μm, demonstrating that polymerization of single actin filaments produces forces of {textgreater}1 piconewton, close to the theoretical maximum. After buckling, further growth produced long loops that did not supercoil, suggesting that formins do not stair step along the two subunits exposed on the growing barbed end. In agreement, Arp2/3 complex branched filaments did not rotate as they grew from formins attached to the slide surface. Formins are not mechanistically identical because barbed end elongation from {Cdc12(FH1FH2)p,} but not {Bni1(FH1FH2)p,} requires profilin. However, profilin increased the rate of {Bni1(FH1FH2)p-mediated} barbed end elongation from 75% to 100% of full-speed.

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.7, Elastizitätstheorie: {BD} 7
Type: book by Deutsch {(Harri)}.

S. Romero, C. Le Clainche, D. Didry, C. Egile, D. Pantaloni, M.-F. Carlier (2004): Formin is a processive motor that requires profilin to accelerate actin assembly and associated {ATP} hydrolysis
Type: article by Cell.
doi: 10.1016/j.cell.2004.09.039
link: http://www.ncbi.nlm.nih.gov/pubmed/15507212
Abstract:

Motile and morphogenetic cellular processes are driven by site-directed assembly of actin filaments. Formins, proteins characterized by formin homology domains {FH1} and {FH2,} are initiators of actin assembly. How formins simply bind to filament barbed ends in rapid equilibrium or find free energy to become a processive motor of filament assembly remains enigmatic. Here we demonstrate that the {FH1-FH2} domain accelerates hydrolysis of {ATP} coupled to profilin-actin polymerization and uses the derived free energy for processive polymerization, increasing 15-fold the rate constant for profilin-actin association to barbed ends. Profilin is required for and takes part in the processive function. Single filaments grow at least 10 microm long from formin bound beads without detaching. Transitory formin-associated processes are generated by poisoning of the processive cycle by barbed-end capping proteins. We successfully reconstitute formin-induced motility in vitro, demonstrating that this mechanism accounts for the puzzlingly rapid formin-induced actin processes observed in vivo.

P. J. Sammak, G. G. Borisy (1988): Direct observation of microtubule dynamics in living cells
Type: article by Nature.
doi: 10.1038/332724a0
link: http://www.ncbi.nlm.nih.gov/pubmed/3357537
Abstract:

The study of cell locomotion is fundamental to such diverse processes as embryonic development, wound healing and metastasis. Since microtubules play a role in establishing the leading lamellum and maintaining cell polarity, it is important to understand their dynamic behaviour. In vitro, subunits exchange with polymer by treadmilling and by dynamic instability. Disassembly events can be complete (catastrophic) or incomplete (tempered). In vivo, microtubules are in dynamic equilibrium with subunits with a half-time for turnover of 4-20 min. Microtubules grow by elongation of their ends and are replaced one by one with turnover being most rapid at the periphery. Although previous results are consistent with dynamic instability, we sought to directly test the mechanism of turnover. Direct observations of fluorescent microtubules in the fibroblast lamellum show that individual microtubules undergo rounds of assembly and disassembly from the same end. Reorganization of the microtubule network occurs by a tempered mode of dynamic instability.

D. Bray (2000): Cell Movement: From Molecules to Motility
Type: book by Garland Publishing Inc.

C. F. Schmidt, M. Baermann, G. Isenberg, E. Sackmann (1989): Chain dynamics, mesh size, and diffusive transport in networks of polymerized actin: a quasielastic light scattering and microfluorescence study
Type: article by Macromolecules.
doi: 10.1021/ma00199a023
link: http://dx.doi.org/10.1021/ma00199a023

H. Lodish, A. Berk, C. A. Kaiser, M. Krieger, M. P. Scott, A. Bretscher (2007): Molecular Cell Biology
Type: book by Palgrave Macmillan.

H. P. Erickson, E. T. O'Brien (1992): Microtubule dynamic instability and {GTP} hydrolysis
Type: article by Annual Review of Biophysics and Biomolecular Structure.
doi: 10.1146/annurev.bb.21.060192.001045
link: http://www.ncbi.nlm.nih.gov/pubmed/1525467

S. F. Gilbert, S. R. Singer (2006): Developmental Biology
Type: book by Palgrave Macmillan.

E. D. Korn, M. F. Carlier, D. Pantaloni (1987): Actin polymerization and {ATP} hydrolysis
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/3672117
Abstract:

F-actin is the major component of muscle thin filaments and, more generally, of the microfilaments of the dynamic, multifunctional cytoskeletal systems of nonmuscle eukaryotic cells. Polymeric F-actin is formed by reversible noncovalent self-association of monomeric G-actin. To understand the dynamics of microfilament systems in cells, the dynamics of polymerization of pure actin must be understood. The following model has emerged from recent work. During the polymerization process, adenosine 5'-triphosphate {(ATP)} that is bound to G-actin is hydrolyzed to adenosine 5'-diphosphate {(ADP)} that is bound to F-actin. The hydrolysis reaction occurs on the F-actin subsequent to the polymerization reaction in two steps: cleavage of {ATP} followed by the slower release of inorganic phosphate {(Pi).} As a result, at high rates of filament growth a transient cap of {ATP-actin} subunits exists at the ends of elongating filaments, and at steady state a stabilizing cap of {ADP.Pi-actin} subunits exists at the barbed ends of filaments. Cleavage of {ATP} results in a highly stable filament with bound {ADP.Pi,} and release of Pi destabilizes the filament. Thus these two steps of the hydrolytic reaction provide potential mechanisms for regulating the monomer-polymer transition.

E. M. Mandelkow, E. Mandelkow, R. A. Milligan (1991): Microtubule dynamics and microtubule caps: a time-resolved cryo-electron microscopy study
Type: article by The Journal of Cell Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/1874792
Abstract:

Microtubules display the unique property of dynamic instability characterized by phase changes between growth and shrinkage, even in constant environmental conditions. The phases can be synchronized, leading to bulk oscillations of microtubules. To study the structural basis of dynamic instability we have examined growing, shrinking, and oscillating microtubules by time-resolved {cryo-EM.} In particular we have addressed three questions which are currently a matter of debate: (a) What is the relationship between microtubules, tubulin subunits, and tubulin oligomers in microtubule dynamics?; (b) How do microtubules shrink? By release of subunits or via oligomers?; and (c) Is there a conformational change at microtubule ends during the transitions from growth to shrinkage and vice versa? The results show that (a) oscillating microtubules coexist with a substantial fraction of oligomers, even at a maximum of microtubule assembly; (b) microtubules disassemble primarily into oligomers; and (c) the ends of growing microtubules have straight protofilaments, shrinking microtubules have protofilaments coiled inside out. This is interpreted as a transition from a tense to a relaxed conformation which could be used to perform work, as suggested by some models of poleward chromosome movement during anaphase.

R. K. Meyer, U. Aebi (1990): Bundling of actin filaments by alpha-actinin depends on its molecular length
Type: article by The Journal of Cell Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/2351691
Abstract:

Cross-linking of actin filaments {(F-actin)} into bundles and networks was investigated with three different isoforms of the dumbbell-shaped alpha-actinin homodimer under identical reaction conditions. These were isolated from chicken gizzard smooth muscle, Acanthamoeba, and Dictyostelium, respectively. Examination in the electron microscope revealed that each isoform was able to cross-link F-actin into networks. In addition, F-actin bundles were obtained with chicken gizzard and Acanthamoeba alpha-actinin, but not Dictyostelium alpha-actinin under conditions where actin by itself polymerized into disperse filaments. This F-actin bundle formation critically depended on the proper molar ratio of alpha-actinin to actin, and hence F-actin bundles immediately disappeared when free alpha-actinin was withdrawn from the surrounding medium. The apparent dissociation constants {(Kds)} at half-saturation of the actin binding sites were 0.4 {microM} at 22 degrees C and 1.2 {microM} at 37 degrees C for chicken gizzard, and 2.7 {microM} at 22 degrees C for both Acanthamoeba and Dictyostelium alpha-actinin. Chicken gizzard and Dictyostelium alpha-actinin predominantly cross-linked actin filaments in an antiparallel fashion, whereas Acanthamoeba alpha-actinin cross-linked actin filaments preferentially in a parallel fashion. The average molecular length of free alpha-actinin was 37 nm for glycerol-sprayed/rotary metal-shadowed and 35 nm for negatively stained chicken gizzard; 46 and 44 nm, respectively, for Acanthamoeba; and 34 and 31 nm, respectively, for Dictyostelium alpha-actinin. In negatively stained preparations we also evaluated the average molecular length of alpha-actinin when bound to actin filaments: 36 nm for chicken gizzard and 35 nm for Acanthamoeba alpha-actinin, a molecular length roughly coinciding with the crossover repeat of the two-stranded F-actin helix (i.e., 36 nm), but only 28 nm for Dictyostelium alpha-actinin. Furthermore, the minimal spacing between cross-linking alpha-actinin molecules along actin filaments was close to 36 nm for both smooth muscle and Acanthamoeba alpha-actinin, but only 31 nm for Dictyostelium alpha-actinin. This observation suggests that the molecular length of the alpha-actinin homodimer may determine its spacing along the actin filament, and hence F-actin bundle formation may require "tight" (i.e., one molecule after the other) and "untwisted" (i.e., the long axis of the molecule being parallel to the actin filament axis) packing of alpha-actinin molecules along the actin filaments.

S. Rubino, J. V. Small (1987): The cytoskeleton of {spreadingDictyostelium} amoebae
Type: article by Protoplasma.
doi: 10.1007/BF01276319
link: http://dx.doi.org/10.1007/BF01276319
Abstract:

Summary The cytoarchitectural elements {ofDictyostelium} discoideum amoeba have been visualized by light and electron microscopy in cells prepared with mixtures of glutaraldehyde and {Triton-X-100.} After negative staining, the peripheral regions of spreading amoebae show a complex meshwork of actin filaments, the majority of which were less than 0.25 microns in length. Multiple branch points, end to side abutments and cross-overs were characteristic features of the actin meshworks. Filopodia extending from the cell periphery consisted of bundles of actin filaments that penetrated into and merged with the actin meshworks in the spreading lamellae. Microtubules emanating from the nucleus associated body penetrated to differing extents into the actin meshworks, sometimes extending close to the cell {periphery.Dictyostelium} cytoskeletons preparted as described here should prove useful for further studies on the locomotory mechanism.

F. Gerbal, P. Chaikin, Y. Rabin, J. Prost (2000): An elastic analysis of Listeria monocytogenes propulsion
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(00)76473-3
link: http://www.ncbi.nlm.nih.gov/pubmed/11053107
Abstract:

The bacterium Listeria monocytogenes uses the energy of the actin polymerization to propel itself through infected tissues. In steady state, it continuously adds new polymerized filaments to its surface, pushing on its tail, which is made from previously cross-linked actin filaments. In this paper we introduce an elastic model to describe how the addition of actin filaments to the tail results in the propulsive force on the bacterium. Filament growth on the bacterial surface produces stresses that are relieved at the back of the bacterium as it moves forward. The model leads to a natural competition between growth from the sides and growth from the back of the bacterium, with different velocities and strengths for each. This competition can lead to the periodic motion observed in a Listeria mutant.

F. Oosawa, M. Kasai (1962): A theory of linear and helical aggregations of macromolecules
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/14482095

T. P. Loisel, R. Boujemaa, D. Pantaloni, M. F. Carlier (1999): Reconstitution of actin-based motility of Listeria and Shigella using pure proteins
Type: article by Nature.
doi: 10.1038/44183
link: http://www.ncbi.nlm.nih.gov/pubmed/10524632
Abstract:

Actin polymerization is essential for cell locomotion and is thought to generate the force responsible for cellular protrusions. The Arp2/3 complex is required to stimulate actin assembly at the leading edge in response to signalling. The bacteria Listeria and Shigella bypass the signalling pathway and harness the Arp2/3 complex to induce actin assembly and to propel themselves in living cells. However, the Arp2/3 complex alone is insufficient to promote movement. Here we have used pure components of the actin cytoskeleton to reconstitute sustained movement in Listeria and Shigella in vitro. Actin-based propulsion is driven by the free energy released by {ATP} hydrolysis linked to actin polymerization, and does not require myosin. In addition to actin and activated Arp2/3 complex, actin depolymerizing factor {(ADF,} or cofilin) and capping protein are also required for motility as they maintain a high steady-state level of G-actin, which controls the rate of unidirectional growth of actin filaments at the surface of the bacterium. The movement is more effective when profilin, alpha-actinin and {VASP} (for Listeria) are also included. These results have implications for our understanding of the mechanism of actin-based motility in cells.

A. Mogilner, G. Oster (1996): Cell motility driven by actin polymerization
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(96)79496-1
link: http://www.ncbi.nlm.nih.gov/pubmed/8968574
Abstract:

Certain kinds of cellular movements are apparently driven by actin polymerization. Examples include the lamellipodia of spreading and migrating embryonic cells, and the bacterium Listeria monocytogenes, that propels itself through its host's cytoplasm by constructing behind it a polymerized tail of cross-linked actin filaments. Peskin et al. (1993) formulated a model to explain how a polymerizing filament could rectify the Brownian motion of an object so as to produce unidirectional force {(Peskin,} C., G. Odell, and G. Oster. 1993. Cellular motions and thermal fluctuations: the Brownian ratchet. Biophys. J. 65:316-324). Their {"Brownian} ratchet" model assumed that the filament was stiff and that thermal fluctuations affected only the "load," i.e., the object being pushed. However, under many conditions of biological interest, the thermal fluctuations of the load are insufficient to produce the observed motions. Here we shall show that the thermal motions of the polymerizing filaments can produce a directed force. This "elastic Brownian ratchet" can explain quantitatively the propulsion of Listeria and the protrusive mechanics of lamellipodia. The model also explains how the polymerization process nucleates the orthogonal structure of the actin network in lamellipodia.

M. Schindl, E. Wallraff, B. Deubzer, W. Witke, G. Gerisch, E. Sackmann (1995): Cell-substrate interactions and locomotion of Dictyostelium wild-type and mutants defective in three cytoskeletal proteins: a study using quantitative reflection interference contrast microscopy
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(95)80294-8
link: http://www.ncbi.nlm.nih.gov/pubmed/7756537
Abstract:

Reflection interference contrast microscopy combined with digital image processing was applied to study the motion of Dictyostelium discoideum cells in their pre-aggregative state on substrata of different adhesiveness (glass, albumin-covered glass, and freshly cleaved mica). The temporal variations of the size and shape of the cell/substratum contact area and the time course of advancement of pseudopods protruding in contact with the substratum were analyzed. The major goal was to study differences between the locomotion of wild-type cells and strains of triple mutants deficient in two F-actin cross-linking proteins (alpha-actinin and the {120-kDa} gelation factor) and one F-actin fragmenting protein (severin). The size of contact area, {AC,} of both wild-type and mutant cells fluctuates between minimum and maximum values on the order of minutes, pointing toward an intrinsic switching mechanism associated with the mechanochemical control system. The fluctuation amplitudes are much larger on freshly cleaved mica than on glass. Wild-type and mutant cells exhibit remarkable differences on mica but not on glass. These differences comprise the population median of {AC} and alterations in pseudopod protrusion. {AC} is smaller by a factor of two or more for all mutants. Pseudopods protrude slower and shorter in the mutants. It is concluded that cell shape and pseudopods are destabilized by defects in the actin-skeleton, which can be overcompensated by strongly adhesive substrata. Several features of amoeboid cell locomotion on substrata can be understood on the basis of the minimum bending energy concept of soft adhering shells and by assuming that adhesion induces local alterations of the composite membrane consisting of the protein/lipid bilayer on the cell surface and the underlying actin-cortex.

B. Vulevic, J. J. Correia (1997): Thermodynamic and structural analysis of microtubule assembly: the role of {GTP} hydrolysis
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(97)78782-4
link: http://www.ncbi.nlm.nih.gov/pubmed/9138581
Abstract:

Different models have been proposed that link the tubulin heterodimer nucleotide content and the role of {GTP} hydrolysis with microtubule assembly and dynamics. Here we compare the thermodynamics of microtubule assembly as a function of nucleotide content by van't Hoff analysis. The thermodynamic parameters of tubulin assembly in 30-100 {mM} {piperazine-N,N'-bis(2-ethanesulfonic} acid), 1 {mM} {MgSO4,} 2 {mM} {EGTA,} {pH} 6.9, in the presence of a weakly hydrolyzable analog, {GMPCPP,} the dinucleotide analog {GMPCP} plus 2 M glycerol, and {GTP} plus 2 M glycerol were obtained together with data for {taxol-GTP/GDP} tubulin assembly {(GMPCPP} and {GMPCP} are the {GTP} and {GDP} nucleotide analogs where the alpha beta oxygen has been replaced by a methylene, {-CH2-).} All of the processes studied are characterized by a positive enthalpy, a positive entropy, and a large, negative heat capacity change. {GMPCP-induced} assembly has the largest negative heat capacity change and {GMPCPP} has the second largest, whereas {GTP/2} M glycerol- and taxol-induced assembly have more positive values, respectively. A large, negative heat capacity is most consistent with the burial of water-accessible hydrophobic surface area, which gives rise to the release of bound water. The heat capacity changes observed with {GTP/2} M glycerol-induced and with taxol-induced assembly are very similar, -790 +/- 190 cal/mol/k, and correspond to the burial of 3330 +/- 820 A2 of nonpolar surface area. This value is shown to be very similar to an estimate of the buried nonpolar surface in a reconstructed microtubule lattice. Polymerization data from {GMPCP-} and {GMPCPP-induced} assembly are consistent with buried nonpolar surface areas that are 3 and 6 times larger. A linear enthalpy-entropy and enthalpy-free energy plot for tubulin polymerization reactions verifies that enthalpy-entropy compensation for this system is based upon true biochemical correlation, most likely corresponding to a dominant hydrophobic effect. Entropy analysis suggests that assembly with {GTP/2} M glycerol and with taxol is consistent with conformational rearrangements in 3-6% of the total amino acids in the heterodimer. In addition, taxol binding contributes to the thermodynamics of the overall process by reducing the delta H degree and delta S degree for microtubule assembly. In the presence of {GMPCPP} or {GMPCP,} tubulin subunits associate with extensive conformational rearrangement, corresponding to 10% and 26% of the total amino acids in the heterodimer, respectively, which gives rise to a large loss of configurational entropy. An alternative, and probably preferable, interpretation of these data is that, especially with {GMPCP-tubulin,} additional isomerization or protonation events are induced by the presence of the methylene moiety and linked to microtubule assembly. Structural analysis shows that {GTP} hydrolysis is not required for sheet closure into a microtubule cylinder, but only increases the probability of this event occurring. Sheet extensions and sheet polymers appear to have a similar average length under various conditions, suggesting that the minimum cooperative unit for closure of sheets into a microtubule cylinder is approximately 400 nm long. Because of their low level of occurrence, sheets are not expected to significantly affect the thermodynamics of assembly.

R. D. Vale, T. Kreis (1999): Guidebook to the Cytoskeletal and Motor Proteins
Type: book by Oxford Univ Pr.

D. R. Critchley, A. R. Gingras (2008): Talin at a glance
Type: article by Journal of Cell Science.
doi: 10.1242/jcs.018085
link: http://www.ncbi.nlm.nih.gov/pubmed/18434644

M. Gunzer, A. Schäfer, S. Borgmann, S. Grabbe, K. S. Zänker, E. B. Bröcker, E. Kämpgen, P. Friedl (2000): Antigen presentation in extracellular matrix: interactions of T cells with dendritic cells are dynamic, short lived, and sequential
Type: article by Immunity.
link: http://www.ncbi.nlm.nih.gov/pubmed/11021530
Abstract:

Cognate interactions of naive T cells with antigen-presenting dendritic cells require physical cell-cell contacts leading to signal induction and T cell activation. Using a three-dimensional collagen matrix videomicroscopy model for ovalbumin peptide-specific activation of murine and oxidative mitogenesis of human T cells, we show that T cells maintain vigorous migration upon cognate interactions to {DC} (dendritic cell), continuously crawl across the {DC} surface, and rapidly detach (median within 6-12 min). These dynamic and short-lived encounters favor sequential contacts with the same or other {DC} and trigger calcium influx, upregulation of activation markers, T blast formation, and proliferation. We conclude that a tissue environment supports the accumulation of sequential signals, implicating a numeric or "digital" control mechanism for an ongoing primary immune response.

R. F. Schmidt, G. Thews, F. Lang (2000): Physiologie des Menschen
Type: book by Springer Berlin.

R. Foisner, G. Wiche (1987): Structure and hydrodynamic properties of plectin molecules
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/3430617
Abstract:

Plectin is a cytoskeletal, high molecular weight protein of widespread and abundant occurrence in cultured cells and tissues. To study its molecular structure, the protein was purified from rat glioma C6 cells and subjected to chemical and biophysical analyses. Plectin's polypeptide chains have an apparent molecular weight of 300,000, as shown by one-dimensional sodium dodecyl sulfate/polyacrylamide electrophoresis. Cross-linking of non-denatured plectin in solution with dimethyl suberimidate and electrophoretic analyses on sodium dodecyl sulfate/agarose gels revealed that the predominant soluble plectin species was a molecule of 1200 X 10(3) Mr consisting of four 300 X 10(3) Mr polypeptide chains. Hydrodynamic properties of plectin in solution were obtained by sedimentation velocity centrifugation and high-pressure liquid chromatography analysis yielding a sedimentation coefficient of 10 S and a Stokes radius of 27 nm. The high f/fmin ratio of 4.0 indicated a very elongated shape of plectin molecules and an axial ratio of about 50. Shadowing and negative staining electron microscopy of plectin molecules revealed multiple domains: a rigid rod of 184 nm in length and 2 nm in diameter, and two globular heads of 9 nm diameter at each end of the rod. Circular dichroism spectra suggested a composition of 30% alpha-helix, 9% beta-structure and 61% random coil or aperiodic structure. The rod-like shape, the alpha-helix content as well as the thermal transition within a midpoint of 45 degrees C and the transition enthalpy (168 {kJ/mol)} of secondary structure suggested a double-stranded, alpha-helical coiled coil rod domain. Based on the available data, we favor a model of native plectin as a dumb-bell-like association of four 300 X 10(3) Mr polypeptide chains. Electron microscopy and turbidity measurements showed that plectin molecules self-associate into various oligomeric states in solutions of nearly physiological ionic strength. These interactions apparently involved the globular end domains of the molecule. Given its rigidity and elongated shape, and its tendency towards self-association, plectin may well be an interlinking element of the cytoskeleton that may also form a network of its own.

L. Song, S. M. Nadkarni, H. U. Bödeker, C. Beta, A. Bae, C. Franck, W.-J. Rappel, W. F. Loomis, E. Bodenschatz (2006): Dictyostelium discoideum chemotaxis: Threshold for directed motion
Type: article by European Journal of Cell Biology.
doi: 10.1016/j.ejcb.2006.01.012

T. M. Svitkina, E. A. Bulanova, O. Y. Chaga, D. M. Vignjevic, S. Kojima, J. M. Vasiliev, G. G. Borisy (2003): Mechanism of filopodia initiation by reorganization of a dendritic network
Type: article by Journal of Cell Biology.
doi: 10.1083/jcb.200210174
link: http://jcb.rupress.org/cgi/content/abstract/160/3/409
Abstract:

Afilopodium protrudes by elongation of bundled actin filaments in its core. However, the mechanism of filopodia initiation remains unknown. Using live-cell imaging with {GFP-tagged} proteins and correlative electron microscopy, we performed a kinetic-structural analysis of filopodial initiation in {B16F1} melanoma cells. Filopodial bundles arose not by a specific nucleation event, but by reorganization of the lamellipodial dendritic network analogous to fusion of established filopodia but occurring at the level of individual filaments. Subsets of independently nucleated lamellipodial filaments elongated and gradually associated with each other at their barbed ends, leading to formation of cone-shaped structures that we term {{Lambda}-precursors.} An early marker of initiation was the gradual coalescence of {GFP-vasodilator-stimulated} phosphoprotein {(GFP-VASP)} fluorescence at the leading edge into discrete foci. The {GFP-VASP} foci were associated with {{Lambda}-precursors,} whereas Arp2/3 was not. Subsequent recruitment of fascin to the clustered barbed ends of {{Lambda}-precursors} initiated filament bundling and completed formation of the nascent filopodium. We propose a convergent elongation model of filopodia initiation, stipulating that filaments within the lamellipodial dendritic network acquire privileged status by binding a set of molecules (including {VASP)} to their barbed ends, which protect them from capping and mediate association of barbed ends with each other.

M. Etzrodt, H. C. F. Ishikawa, J. Dalous, A. Müller-Taubenberger, T. Bretschneider, G. Gerisch (2006): Time-resolved responses to chemoattractant, characteristic of the front and tail of Dictyostelium cells
Type: article by {FEBS} Letters.

L. Vonna, A. Wiedemann, M. Aepfelbacher, E. Sackmann (2007): Micromechanics of filopodia mediated capture of pathogens by macrophages
Type: article by European Biophysics Journal.
doi: 10.1007/s00249-006-0118-y
link: http://dx.doi.org/10.1007/s00249-006-0118-y
Abstract:

Abstract The biological function of filopodia has been extensively studied while only little work has been done on their mechanical

properties. In the present study, we apply magnetic microbeads to explore the capturing and initial step of phagocytosis of pathogens by macrophages through filopodia. Microbeads were covered by the bacterial coat protein invasin which is known to trigger the invasion of the intestine by the bacteria Yersinia enterocolitica. These mimetics of bacteria were placed in the vicinity of J774 mouse macrophages exhibiting long filopodia. The specific adhesion of beads to the tip of a filopodium induced the retraction of the protrusion resulting in the dragging of the bead towards the cell body. The dynamics of the retraction process was analyzed by following the in-plane motion of the bead. We estimated the minimal force developed by filopodia and compared the results with previous magnetic tweezer studies of mechanical force induced growth of protrusions {(Vonna} et al. 2003). We show that very thin filopodia can generate astonishingly large retraction forces over large distances ({textgreater}10 μm) and can act as an efficient mechanical tool to detach pathogens adhering on surfaces.

C. Le Clainche, M.-F. Carlier (2008): Regulation of Actin Assembly Associated With Protrusion and Adhesion in Cell Migration
Type: article by Physiological Reviews.
doi: 10.1152/physrev.00021.2007
link: http://physrev.physiology.org/cgi/content/abstract/88/2/489
Abstract:

To migrate, a cell first extends protrusions such as lamellipodia and filopodia, forms adhesions, and finally retracts its tail. The actin cytoskeleton plays a major role in this process. The first part of this review (sect. {II)} describes the formation of the lamellipodial and filopodial actin networks. In lamellipodia, the {WASP-Arp2/3} pathways generate a branched filament array. This polarized dendritic actin array is maintained in rapid treadmilling by the concerted action of {ADF,} profilin, and capping proteins. In filopodia, formins catalyze the processive assembly of nonbranched actin filaments. Cell matrix adhesions mechanically couple actin filaments to the substrate to convert the treadmilling into protrusion and the actomyosin contraction into traction of the cell body and retraction of the tail. The second part of this review (sect. {III)} focuses on the function and the regulation of major proteins (vinculin, talin, tensin, and {alpha}-actinin) that control the nucleation, the binding, and the barbed-end growth of actin filaments in adhesions.

D. Heinrich, E. Sackmann (2006): Active mechanical stabilization of the viscoplastic intracellular space of Dictyostelia cells by microtubule–actin crosstalk
Type: article by Acta Biomaterialia.
doi: 10.1016/j.actbio.2006.05.014

A. Schirenbeck, T. Bretschneider, R. Arasada, M. Schleicher, J. Faix (2005): The Diaphanous-related formin {dDia2} is required for the formation and maintenance of filopodia
Type: article by Nat Cell Biol.
doi: 10.1038/ncb1266
link: http://dx.doi.org/10.1038/ncb1266

R. D. Mullins, J. A. Heuser, T. D. Pollard (1998): The interaction of Arp2/3 complex with actin: Nucleation, high affinity pointed end capping, and formation of branching networks of filaments
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 95
link: http://www.pnas.org/content/95/11/6181.abstract
Abstract:

The Arp2/3 complex is a stable assembly of seven protein subunits including two actin-related proteins {(Arp2} and Arp3) and five novel proteins. Previous work showed that this complex binds to the sides of actin filaments and is concentrated at the leading edges of motile cells. Here, we show that Arp2/3 complex purified from caps the pointed ends of actin filaments with high affinity. Arp2/3 complex inhibits both monomer addition and dissociation at the pointed ends of actin filaments with apparent nanomolar affinity and increases the critical concentration for polymerization at the pointed end from 0.6 to 1.0 {μM.} The high affinity of Arp2/3 complex for pointed ends and its abundance in amoebae suggest that all actin filament pointed ends are capped by Arp2/3 complex. Arp2/3 complex also nucleates formation of actin filaments that elongate only from their barbed ends. From kinetic analysis, the nucleation mechanism appears to involve stabilization of polymerization intermediates (probably actin dimers). In electron micrographs of quick-frozen, deep-etched samples, we see Arp2/3 bound to sides and pointed ends of actin filaments and examples of Arp2/3 complex attaching pointed ends of filaments to sides of other filaments. In these cases, the angle of attachment is a remarkably constant 70 ± 7°. From these biochemical properties, we propose a model for how Arp2/3 complex controls the assembly of a branching network of actin filaments at the leading edge of motile cells.

K. Rottner, B. Behrendt, J. V. Small, J. Wehland (1999): {VASP} dynamics during lamellipodia protrusion
Type: article by Nature Cell Biology.
doi: 10.1038/13040
link: http://www.ncbi.nlm.nih.gov/pubmed/10559946

K. Doubrovinski, K. Kruse (2008): Cytoskeletal waves in the absence of molecular motors
Type: article by {EPL} {(Europhysics} Letters).
link: http://www.iop.org/EJ/abstract/0295-5075/83/1/18003
Abstract:

Waves are a ubiquitous phenomenon in the cytoskeleton of cells

crawling or spreading on a substrate. In theoretical analysis, cytoskeletal waves have been attributed to the action of molecular motors that actively cross-link cytoskeletal filaments. Motivated by recent observations of cytoskeletal waves in human neutrophils, we develop a description of treadmilling filaments in the presence of nucleating proteins that are active when bound to the membrane adjacent to the substrate. If these proteins bind cooperatively to the membrane, we find traveling waves even in the absence of molecular motors. In a confined domain the system can organize into a pair of counter-rotating spirals that emit planar waves.

Kapitel 19

R. D. Vale (2003): Myosin V motor proteins: marching stepwise towards a mechanism
Type: article by The Journal of Cell Biology.
doi: 10.1083/jcb.200308093
link: http://www.ncbi.nlm.nih.gov/pubmed/14610051
Abstract:

Mammalian myosin V motors transport cargo processively along actin filaments. Recent biophysical and structural studies have led to a detailed understanding of the mechanism of myosin V, making it perhaps the best understood cytoskeletal motor. In addition to describing the mechanism, this review will illustrate how "dynamic" single molecule measurements can synergize with "static" protein structural studies to produce amazingly clear information on the workings of a nanometer-scale machine.

T. Hasson, R. E. Cheney (2001): Mechanisms of motor protein reversal
Type: article by Current Opinion in Cell Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/11163130
Abstract:

Members of the kinesin superfamily of microtubule-based motors and the myosin superfamily of actin-based motors that move 'backwards' have been identified. As the core catalytic domains of myosins and kinesins are similar in structure, this raises the intriguing questions of how direction reversal is accomplished and whether kinesins and myosins share mechanisms for switching their motors into reverse.

T. L. Hill (1974): Theoretical formalism for the sliding filament model of contraction of striated muscle. Part I
Type: article by Progress in Biophysics and Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/4617248

T. Duke, H. Flyvberg, P. Jülicher, P. Ormos, F. David (2000): Physics of bio-molecules and cells
Type: article by Nato Advanced Study Institute, Les Houches Session {LXXV} 2000.

H. Lodish, A. Berk, C. A. Kaiser, M. Krieger, M. P. Scott, A. Bretscher (2007): Molecular Cell Biology
Type: book by Palgrave Macmillan.

F. Jülicher, A. Ajdari, J. Prost (1997): Modeling molecular motors
Type: article by Reviews of Modern Physics.
link: http://adsabs.harvard.edu/abs/1997RvMP...69.1269J
Abstract:

The authors present general considerations and simple models for the

operation of isothermal motors at small scales, in asymmetric environments. Their work is inspired by recent observations on the behavior of molecular motors in the biological realm, where chemical energy is converted into mechanical energy. A generic Onsager-like description of the linear (close to equilibrium) regime is presented, which exhibits structural differences from the usual Carnot engines. Turning to more explicit models for a single motor, the authors show the importance of the time scales involved and of the spatial dependence of the motor's chemical activity. Considering the situation in which a large collection of such motors operates together. The authors exhibit new features among which are dynamical phase transitions formally similar to paramagnetic-ferromagnetic and liquid-vapor transitions.

J. L. McGrath (2005): Dynein motility: four heads are better than two
Type: article by Current Biology: {CB}.
doi: 10.1016/j.cub.2005.11.021
link: http://www.ncbi.nlm.nih.gov/pubmed/16332531
Abstract:

Cytoplasmic dynein is a microtubule-based motor protein that transports membranes in cells. The movement driven by a single dynein molecule in vitro is not as robust as dynein-driven movements in cells. A new study suggests that transport by multiple dyneins is more similar to cellular motions.

M. Rief, R. S. Rock, A. D. Mehta, M. S. Mooseker, R. E. Cheney, J. A. Spudich (2000): {Myosin-V} stepping kinetics: A molecular model for processivity
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 97
link: http://www.pnas.org/content/97/17/9482.abstract
Abstract:

{Myosin-V} is a molecular motor that moves processively along its actin track. We have used a feedback-enhanced optical trap to examine the stepping kinetics of this movement. By analyzing the distribution of time periods separating discrete ≈36-nm mechanical steps, we characterize the number and duration of rate-limiting biochemical transitions preceding each such step. These data show that {myosin-V} is a tightly coupled motor whose cycle time is limited by {ADP} release. On the basis of these results, we propose a model for {myosin-V} processivity.

C. Veigel, F. Wang, M. L. Bartoo, J. R. Sellers, J. E. Molloy (2002): The gated gait of the processive molecular motor, myosin V
Type: article by Nature Cell Biology.
doi: 10.1038/ncb732
link: http://www.ncbi.nlm.nih.gov/pubmed/11740494
Abstract:

Class V myosins are actin-based molecular motors involved in vesicular and organellar transport. Single myosin V molecules move processively along F-actin, taking several 36-nm steps for each diffusional encounter. Here we have measured the mechanical interactions between mouse brain myosin V and rabbit skeletal F-actin. The working stroke produced by a myosin V head is approximately 25 nm, consisting of two separate mechanical phases (20 + 5 nm). We show that there are preferred myosin binding positions (target zones) every 36 nm along the actin filament, and propose that the 36-nm steps of the double-headed motor are a combination of the working stroke (25 nm) of the bound head and a biased, thermally driven diffusive movement (11 nm) of the free head onto the next target zone. The second phase of the working stroke (5 nm) acts as a gate - like an escapement in a clock, coordinating the {ATPase} cycles of the two myosin V heads. This mechanism increases processivity and enables a single myosin V molecule to travel distances of several hundred nanometres along the actin filament.

J. Howard (2005): Mechanics of Motor Proteins and the Cytoskeleton
Type: book by Palgrave Macmillan.

R. Mallik, B. C. Carter, S. A. Lex, S. J. King, S. P. Gross (2004): Cytoplasmic dynein functions as a gear in response to load
Type: article by Nature.
doi: 10.1038/nature02293
link: http://www.ncbi.nlm.nih.gov/pubmed/14961123
Abstract:

Cytoskeletal molecular motors belonging to the kinesin and dynein families transport cargos (for example, messenger {RNA,} endosomes, virus) on polymerized linear structures called microtubules in the cell. These 'nanomachines' use energy obtained from {ATP} hydrolysis to generate force, and move in a step-like manner on microtubules. Dynein has a complex and fundamentally different structure from other motor families. Thus, understanding dynein's force generation can yield new insight into the architecture and function of nanomachines. Here, we use an optical trap to quantify motion of polystyrene beads driven along microtubules by single cytoplasmic dynein motors. Under no load, dynein moves predominantly with a mixture of 24-nm and 32-nm steps. When moving against load applied by an optical trap, dynein can decrease step size to 8 nm and produce force up to 1.1 {pN.} This correlation between step size and force production is consistent with a molecular gear mechanism. The ability to take smaller but more powerful strokes under load--that is, to shift gears--depends on the availability of {ATP.} We propose a model whereby the gear is downshifted through load-induced binding of {ATP} at secondary sites in the dynein head.

S. A. Burgess, M. L. Walker, H. Sakakibara, P. L. Knight, K. Oiwa (2003): Dynein structure and power stroke
Type: article by Nature.
doi: 10.1038/nature01377
link: http://www.ncbi.nlm.nih.gov/pubmed/12610617
Abstract:

Dynein {ATPases} are microtubule motors that are critical to diverse processes such as vesicle transport and the beating of sperm tails; however, their mechanism of force generation is unknown. Each dynein comprises a head, from which a stalk and a stem emerge. Here we use electron microscopy and image processing to reveal new structural details of dynein c, an isoform from Chlamydomonas reinhardtii flagella, at the start and end of its power stroke. Both stem and stalk are flexible, and the stem connects to the head by means of a linker approximately 10 nm long that we propose lies across the head. With both {ADP} and vanadate bound, the stem and stalk emerge from the head 10 nm apart. However, without nucleotide they emerge much closer together owing to a change in linker orientation, and the coiled-coil stalk becomes stiffer. The net result is a shortening of the molecule coupled to an approximately 15-nm displacement of the tip of the stalk. These changes indicate a mechanism for the dynein power stroke.

E. M. De La Cruz, E. M. Ostap (2004): Relating biochemistry and function in the myosin superfamily
Type: article by Current Opinion in Cell Biology.
doi: 10.1016/j.ceb.2003.11.011
link: http://www.ncbi.nlm.nih.gov/pubmed/15037306
Abstract:

All characterized myosins share a common {ATPase} mechanism. However, detailed kinetic analyses suggest that modulation of the rate and equilibrium constants that define the {ATPase} cycle confers specific properties to these motor proteins, suiting them to specific physiological tasks. Understanding the kinetic mechanisms allows potential cellular functions of the different myosin classes and isoforms to be better defined.

B. Maier, M. Koomey, M. P. Sheetz (2004): A force-dependent switch reverses type {IV} pilus retraction
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.0402305101
link: http://www.ncbi.nlm.nih.gov/pubmed/15256598
Abstract:

Type {IV} pilus dynamics is important for virulence, motility, and {DNA} transfer in a wide variety of prokaryotes. The type {IV} pilus system constitutes a very robust and powerful molecular machine that transports pilus polymers as well as {DNA} through the bacterial cell envelope. In Neisseria gonorrhoeae, pilus retraction is a highly irreversible process that depends on {PilT,} an {AAA} {ATPase} family member. However, when levels of {PilT} are reduced, the application of high external forces {(F} = 110 +/- 10 {pN)} induces processive pilus elongation. At forces of {textgreater}50 {pN,} single pili elongate at a rate of v = 350 +/- 50 nm/s. For forces of {textless}50 {pN,} elongation velocity depends strongly on force and relaxation causes immediate retraction. Both pilus retraction and force-induced elongation can be modeled by chemical kinetics with same step length for the rate-limiting translocation step. The model implies that a force-dependent molecular switch can induce pilus elongation by reversing the retraction mechanism.

Kapitel 20

L. Tskhovrebova, J. Trinick (2004): Properties of titin immunoglobulin and fibronectin-3 domains
Type: article by The Journal of Biological Chemistry.
doi: 10.1074/jbc.R400023200
link: http://www.ncbi.nlm.nih.gov/pubmed/15322090

H. P. Erickson (1997): Stretching single protein molecules: titin is a weird spring
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/9173540

T. L. Hill (1974): Theoretical formalism for the sliding filament model of contraction of striated muscle. Part I
Type: article by Progress in Biophysics and Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/4617248

K. A. Edman, N. A. Curtin (2001): Synchronous oscillations of length and stiffness during loaded shortening of frog muscle fibres
Type: article by The Journal of Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/11454972
Abstract:

1. A study was made of the damped oscillations in fibre length that are observed when isolated muscle fibres from the frog are released during the plateau of an isometric tetanus to shorten against a constant load (force clamp recording) near the isometric level (temperature, 1.0-11.0 degrees C; initial sarcomere length, 2.25 microm). 2. The oscillatory length changes of the whole fibre were associated with similar length changes of marked consecutive segments along the fibre. The segmental length changes were initially in synchrony with the whole-fibre movements but became gradually more disordered. At the same time the length oscillation of the whole fibre was progressively damped. 3. The fast length step that normally occurs at the outset of the load-clamp manoeuvre was essential for initiating the oscillatory behaviour. Accordingly, no length oscillation occurred when the load clamp was arranged to start as soon as the selected tension level was reached during the rising phase of the tetanus. 4. The instantaneous stiffness was measured as the change in force that occurred in response to a high-frequency (2-4 {kHz)} length oscillation of the fibre. During the load-clamp manoeuvre, when the tension was kept constant, the stiffness underwent periodic changes that correlated well in time with the damped oscillatory changes in fibre length. However, there was a phase shift between the stiffness oscillation and the oscillation of shortening velocity, the latter being in the lead of the stiffness response by 21.4 +/- 0.8 ms (n = 19) at 1.8 +/- 0.1 degrees C. 5. A mechanism is proposed to explain the oscillatory behaviour of the muscle fibre based on the idea that the quick length step at the outset of the load clamp leads to synchronous activity of the myosin cross-bridges along the length of the fibre.

F. Jülicher, A. Ajdari, J. Prost (1997): Modeling molecular motors
Type: article by Reviews of Modern Physics.
link: http://adsabs.harvard.edu/abs/1997RvMP...69.1269J
Abstract:

The authors present general considerations and simple models for the

operation of isothermal motors at small scales, in asymmetric environments. Their work is inspired by recent observations on the behavior of molecular motors in the biological realm, where chemical energy is converted into mechanical energy. A generic Onsager-like description of the linear (close to equilibrium) regime is presented, which exhibits structural differences from the usual Carnot engines. Turning to more explicit models for a single motor, the authors show the importance of the time scales involved and of the spatial dependence of the motor's chemical activity. Considering the situation in which a large collection of such motors operates together. The authors exhibit new features among which are dynamical phase transitions formally similar to paramagnetic-ferromagnetic and liquid-vapor transitions.

M. Rief, M. Gautel, F. Oesterhelt, J. M. Fernandez, H. E. Gaub (1997): Reversible Unfolding of Individual Titin Immunoglobulin Domains by {AFM}
Type: article by Science.
doi: 10.1126/science.276.5315.1109
link: http://www.sciencemag.org/cgi/content/abstract/276/5315/1109

K. K. Holmes (1983): Die molekulare Physiologie von Kontraktilität und Motilität
Type: incollection

R. F. Schmidt, G. Thews, F. Lang (2000): Physiologie des Menschen
Type: book by Springer Berlin.

T. A. Duke (1999): Molecular model of muscle contraction
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/10077586
Abstract:

A quantitative stochastic model of the mechanochemical cycle of myosin, the protein that drives muscle contraction, is proposed. It is based on three premises: (i) the myosin head incorporates a lever arm, whose equilibrium position adjusts as each of the products of {ATP} hydrolysis dissociates from the nucleotide pocket; (ii) the chemical reaction rates are modified according to the work done in moving the arm; and (iii) the compliance of myosin's elastic element is designed to permit many molecules to work together efficiently. The model has a minimal number of parameters and provides an explanation, at the molecular level, of many of the mechanical and thermodynamic properties of steadily shortening muscle. In particular, the inflexion in the force-velocity curve at a force approaching the isometric load is reproduced. Moreover, the model indicates that when large numbers of myosin molecules act collectively, their chemical cycles can be synchronized, and that this leads to stepwise motion of the thin filament. The oscillatory transient response of muscle to abrupt changes of load is interpreted in this light.

E. M. Puchner, A. Alexandrovich, A. L. Kho, U. Hensen, L. V. Schäfer, B. Brandmeier, F. Gräter, H. Grubmüller, H. E. Gaub, M. Gautel (2008): Mechanoenzymatics of titin kinase
Type: article by Proceedings of the National Academy of Sciences.
doi: 10.1073/pnas.0805034105
link: http://www.pnas.org/content/105/36/13385.abstract
Abstract:

Biological responses to mechanical stress require strain-sensing molecules, whose mechanically induced conformational changes are relayed to signaling cascades mediating changes in cell and tissue properties. In vertebrate muscle, the giant elastic protein titin is involved in strain sensing via its C-terminal kinase domain {(TK)} at the sarcomeric M-band and contributes to the adaptation of muscle in response to changes in mechanical strain. {TK} is regulated in a unique dual autoinhibition mechanism by a C-terminal regulatory tail, blocking the {ATP} binding site, and tyrosine autoinhibition of the catalytic base. For access to the {ATP} binding site and phosphorylation of the autoinhibitory tyrosine, the C-terminal autoinhibitory tail needs to be removed. Here, we use {AFM-based} single-molecule force spectroscopy, molecular dynamics simulations, and enzymatics to study the conformational changes during strain-induced activation of human {TK.} We show that mechanical strain activates {ATP} binding before unfolding of the structural titin domains, and that {TK} can thus act as a biological force sensor. Furthermore, we identify the steps in which the autoinhibition of {TK} is mechanically relieved at low forces, leading to binding of the cosubstrate {ATP} and priming the enzyme for subsequent autophosphorylation and substrate turnover.

Kapitel 21

H. C. Berg (2003): The rotary motor of bacterial flagella
Type: article by Annual Review of Biochemistry.
doi: 10.1146/annurev.biochem.72.121801.161737
link: http://www.ncbi.nlm.nih.gov/pubmed/12500982
Abstract:

Flagellated bacteria, such as Escherichia coli, swim by rotating thin helical filaments, each driven at its base by a reversible rotary motor, powered by an ion flux. A motor is about 45 nm in diameter and is assembled from about 20 different kinds of parts. It develops maximum torque at stall but can spin several hundred Hz. Its direction of rotation is controlled by a sensory system that enables cells to accumulate in regions deemed more favorable. We know a great deal about motor structure, genetics, assembly, and function, but we do not really understand how it works. We need more crystal structures. All of this is reviewed, but the emphasis is on function.

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.7, Elastizitätstheorie: {BD} 7
Type: book by Deutsch {(Harri)}.

S. Asakura, T. Iino (1972): Polymorphism of Salmonella flagella as investigated by means of in vitro copolymerization of flagellins derived from various strains
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/5015400

H. C. Berg, L. Turner (1993): Torque generated by the flagellar motor of Escherichia coli
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(93)81278-5
link: http://www.ncbi.nlm.nih.gov/pubmed/8298044
Abstract:

Cells of the bacterium Escherichia coli were tethered and spun in a high-frequency rotating electric field at a series of discrete field strengths. This was done first at low field strengths, then at field strengths generating speeds high enough to disrupt motor function, and finally at low field strengths. Comparison of the initial and final speed versus applied-torque plots yielded relative motor torque. For backward rotation, motor torque rose steeply at speeds close to zero, peaking, on average, at about 2.2 times the stall torque. For forward rotation, motor torque remained approximately constant up to speeds of about 60% of the zero-torque speed. Then the torque dropped linearly with speed, crossed zero, and reached a minimum, on average, at about -1.7 times the stall torque. The zero-torque speed increased with temperature (about 90 Hz at 11 degrees C, 140 Hz at 16 degrees C, and 290 Hz at 23 degrees C), while other parameters remained approximately constant. Sometimes the motor slipped at either extreme (delivered constant torque over a range of speeds), but eventually it broke. Similar results were obtained whether motors broke catastrophically (suddenly and completely) or progressively or were de-energized by brief treatment with an uncoupler. These results are consistent with a tightly coupled ratchet mechanism, provided that elastic deformation of force-generating elements is limited by a stop and that mechanical components yield at high applied torques.

R. Kamiya, S. Asakura, K. Wakabayashi, K. Namba (1979): Transition of bacterial flagella from helical to straight forms with different subunit arrangements
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/41952

P. Cluzel, M. Surette, S. Leibler (2000): An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/10698740
Abstract:

Understanding biology at the single-cell level requires simultaneous measurements of biochemical parameters and behavioral characteristics in individual cells. Here, the output of individual flagellar motors in Escherichia coli was measured as a function of the intracellular concentration of the chemotactic signaling protein. The concentration of this molecule, fused to green fluorescent protein, was monitored with fluorescence correlation spectroscopy. Motors from different bacteria exhibited an identical steep input-output relation, suggesting that they actively contribute to signal amplification in chemotaxis. This experimental approach can be extended to quantitative in vivo studies of other biochemical networks.

R. B. Bourret, J. F. Hess, K. A. Borkovich, A. A. Pakula, M. I. Simon (1989): Protein phosphorylation in chemotaxis and two-component regulatory systems of bacteria
Type: article by The Journal of Biological Chemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/2540171
Abstract:

Two-component regulatory systems appear to be widespread in bacteria. Phosphorylation has been demonstrated in three of the known systems and correlated with in vivo function in two cases {(Che} and Ntr). Although phosphorylation of sensor and regulator proteins has so far been observed exclusively in vitro, transient protein phosphorylation could provide a basis for the mechanism of signal transduction in these bacterial systems. There is currently insufficient evidence, however, to establish the precise functional relationship(s) between the conserved sensor and regulator sequences, phosphorylation, and the detailed mechanism involved in signal transduction via the sensor and regulator proteins.

C. R. Calladine (1976): Design requirements for the construction of bacterial flagella
Type: article by Journal of Theoretical Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/785102

W. S. Ryu, R. M. Berry, H. C. Berg (2000): Torque-generating units of the flagellar motor of Escherichia coli have a high duty ratio
Type: article by Nature.
doi: 10.1038/35000233
link: http://www.ncbi.nlm.nih.gov/pubmed/10667798
Abstract:

Rotation of the bacterial flagellar motor is driven by an ensemble of torque-generating units containing the proteins {MotA} and {MotB.} Here, by inducing expression of {MotA} in {motA-} cells under conditions of low viscous load, we show that the limiting speed of the motor is independent of the number of units: at vanishing load, one unit turns the motor as rapidly as many. This result indicates that each unit may remain attached to the rotor for most of its mechanochemical cycle, that is, that it has a high duty ratio. Thus, torque generators behave more like kinesin, the protein that moves vesicles along microtubules, than myosin, the protein that powers muscle. However, their translation rates, stepping frequencies and power outputs are much higher, being greater than 30 microm s(-1), 12 {kHz} and 1.5 x 10(5) {pN} nm s(-1), respectively.

G. Fuhr, R. Glaser, R. Hagedorn (1986): Rotation of dielectrics in a rotating electric high-frequency field. Model experiments and theoretical explanation of the rotation effect of living cells
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(86)83649-9
link: http://www.ncbi.nlm.nih.gov/pubmed/3955177
Abstract:

Model experiments are carried out to clarify the mechanism of rotation of living cells in a rotating electric field. According to classical investigations of the rotation of macroscopic bodies in external fields, the rotation of spherical glass vessels or metal cylinder filled with electrolyte solutions was investigated. The relation of the calculations of Lertes (1921a,b) to the recent paper of Arnold and Zimmerman (1982) and our new derivations lead to equations explaining the rotation of objects. The results are compared with measurements using mesophyll protoplasts and data from the literature.

S. Kojima, D. F. Blair (2001): Conformational change in the stator of the bacterial flagellar motor
Type: article by Biochemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/11669642
Abstract:

{MotA} and {MotB} are integral membrane proteins of Escherichia coli that form the stator of the proton-fueled flagellar rotary motor. The motor contains several {MotA/MotB} complexes, which function independently to conduct protons across the cytoplasmic membrane and couple proton flow to rotation. {MotB} contains a conserved aspartic acid residue, Asp32, that is critical for rotation. We have proposed that the protons energizing the motor interact with Asp32 of {MotB} to induce conformational changes in the stator that drive movement of the rotor. To test for conformational changes, we examined the protease susceptibility of {MotA} in membrane-bound complexes with either wild-type {MotB} or {MotB} mutated at residue 32. Small, uncharged replacements of Asp32 in {MotB} {(D32N,} {D32A,} {D32G,} {D32S,} or {D32C)} caused a significant change in the conformation of {MotA,} as evidenced by a change in the pattern of proteolytic fragments. The conformational change does not require any flagellar proteins besides {MotA} and {MotB,} as it was still seen in a strain that expresses no other flagellar genes. It affects a cytoplasmic domain of {MotA} that contains residues known to interact with the rotor, consistent with a role in the generation of torque. Influences of key residues of {MotA} on conformation were also examined. Pro173 of {MotA,} known to be important for rotation, is a significant determinant of conformation: Dominant Pro173 mutations, but not recessive ones, altered the proteolysis pattern of {MotA} and also prevented the conformational change induced by Asp32 replacements. Arg90 and Glu98, residues of {MotA} that engage in electrostatic interactions with the rotor, appear not to be strong determinants of conformation of the {MotA/MotB} complex in membranes. We note sequence similarity between {MotA} and {ExbB,} a cytoplasmic-membrane protein that energizes outer-membrane transport in Gram-negative bacteria. {ExbB} and associated proteins might also employ a mechanism involving proton-driven conformational change.

M. Mickler, T. Hugel (2008): Molekulare Motoren und künstliche Nanomaschinen. Energiewandlung in Polymeren
Type: article by Physik in unserer Zeit.
link: http://adsabs.harvard.edu/abs/2008PhuZ...39...14M

B. Maier, M. Koomey, M. P. Sheetz (2004): A force-dependent switch reverses type {IV} pilus retraction
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.0402305101
link: http://www.ncbi.nlm.nih.gov/pubmed/15256598
Abstract:

Type {IV} pilus dynamics is important for virulence, motility, and {DNA} transfer in a wide variety of prokaryotes. The type {IV} pilus system constitutes a very robust and powerful molecular machine that transports pilus polymers as well as {DNA} through the bacterial cell envelope. In Neisseria gonorrhoeae, pilus retraction is a highly irreversible process that depends on {PilT,} an {AAA} {ATPase} family member. However, when levels of {PilT} are reduced, the application of high external forces {(F} = 110 +/- 10 {pN)} induces processive pilus elongation. At forces of {textgreater}50 {pN,} single pili elongate at a rate of v = 350 +/- 50 nm/s. For forces of {textless}50 {pN,} elongation velocity depends strongly on force and relaxation causes immediate retraction. Both pilus retraction and force-induced elongation can be modeled by chemical kinetics with same step length for the rate-limiting translocation step. The model implies that a force-dependent molecular switch can induce pilus elongation by reversing the retraction mechanism.

Kapitel 22

S. Gueron, K. Levit-Gurevich, N. Liron, J. J. Blum (1997): Cilia internal mechanism and metachronal coordination as the result of hydrodynamical coupling
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/9177158
Abstract:

We present a simple but realistic model for the internal bend-generating mechanism of cilia, using parameters obtained from the analysis of data of the beat of a single cilium, and incorporate it into a recently developed dynamical model. Comparing the results to experimental data for two-dimensional beats, we demonstrate that the model captures the essential features of the motion, including many properties that are not built in explicitly. The beat pattern and frequency change in response to increased viscosity and the presence of neighboring cilia in a realistic fashion. Using the model, we are able to investigate multicilia configurations such as rows of cilia and two-dimensional arrays of cilia. When two adjacent model cilia start beating at different phase, they synchronize within two cycles, as observed in experiments in which two flagella beating out of phase are brought close together. Examination of various multicilia configurations shows that metachronal patterns (i. e., beats with a constant phase difference between neighboring cilia) evolve autonomously. This provides modeling evidence in support of the conjecture that metachronism may occur as a self-organized phenomenon due to hydrodynamical interactions between the cilia.

J. Gray, G. J. Hancock (1955): The Propulsion of {Sea-Urchin} Spermatozoa
Type: article by The Journal of Experimental Biology.
link: http://jeb.biologists.org/cgi/content/abstract/32/4/802
Abstract:

1. The general theory of flagellar propulsion is discussed and an expression obtained whereby the propulsive speed of a spermatozoon can be expressed in terms of the amplitude, wave-length and frequency of the waves passing down the tail of a spermatozoon of Psammechinus miliaris.2. The expression obtained is applicable to waves of relatively large amplitude, and allowance is made for the presence of an inert head.3. The calculated propulsive speed is almost identical with that derived from observational data. Unless the head of a spermatozoon is very much larger than that of Psammechinus, its presence makes relatively little difference to the propulsive speed. Most of the energy of the cell is used up in overcoming the tangential drag of the tail.4. Although the amplitude may change as a wave passes along the tail, the propulsive properties of the latter may be expected to be closely similar to those of a tail generating waves of the same average amplitude.

E. M. Purcell (1977): Life at low Reynolds number
Type: article by American Journal of Physics.
doi: 10.1119/1.10903
link: http://link.aip.org/link/?AJP/45/3/1
Abstract:

This is a reprint (slightly edited) of a paper of the same title that appeared in the book Physics and Our World: A Symposium in Honor of Victor F. Weisskopf, published by the American Institute of Physics (1976). The personal tone of the original talk has been preserved in the paper, which was itself a slightly edited transcript of a tape. The figures reproduce transparencies used in the talk. The demonstration involved a tall rectangular transparent vessel of corn syrup, projected by an overhead projector turned on its side. Some essential hand waving could not be reproduced.

A. Vilfan, F. Jülicher (2006): Hydrodynamic flow patterns and synchronization of beating cilia
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/16486996
Abstract:

We calculate the hydrodynamic flow field generated far from a cilium which is attached to a surface and beats periodically. In the case of two beating cilia, hydrodynamic interactions can lead to synchronization of the cilia, which are nonlinear oscillators. We present a state diagram where synchronized states occur as a function of the distance of cilia and the relative orientation of their beat. Synchronized states occur with different relative phases. In addition, asynchronous solutions exist. Our work could be relevant for the synchronized motion of cilia generating hydrodynamic flows on the surface of cells.

E. W. Knight-Jones (1954): Relations between Metachronism and the Direction of Ciliary Beat in Metazoa
Type: article by Quarterly Journal of Microscopical Science.
link: http://jcs.biologists.org/cgi/content/abstract/s3-95/32/503
Abstract:

In various ciliated epithelia one can distinguish either symplectic, antiplectic, dexioplectic, or laeoplectic metachronal waves, according to whether the effective beat of their cilia is with, against, to the right of, or to the left of, the direction of movement of the waves. In a given epithelium the relation between the direction of the waves and the direction of beat is {constant.Symplectic} waves are probably associated with the transport of large particles, or viscous masses of mucus; antiplectic and diaplectic waves are better suited for creating water currents. It is unusual to find both dexioplectic and laeoplectic waves in the same animal; indeed, it is the rule for only one of these two types of metachronism to occur throughout a given systematic group. Dexioplectic waves are found in Protochordata, primitive Spiralia, the velum of Eulamellibranchiata, Phoronidea, Brachiopoda, Bdelloidea, and Melicertida; laeoplectic waves are found in Chaetopterus, Mollusca generally, Bryozoa, and Ploima. The incidence of dexioplectic and laeoplectic metachronism is not influenced by morphological reversals of symmetry such as the situs inversus. The relation between the direction of beat and the direction of the waves is therefore probably determined by cytological or stereochemical factors, rather than by gross morphology.

K. E. Summers, I. R. Gibbons (1971): Adenosine triphosphate-induced sliding of tubules in trypsin-treated flagella of sea-urchin sperm
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/5289252
Abstract:

Axonemes isolated from the sperm of the sea urchin, Tripneustes gratilla, were briefly digested with trypsin. The digested axonemes retained their typical structure of a cylinder of nine doublet-tubules surrounding a pair of single tubules. The digestion modified the axonemes so that the subsequent addition of 0.1 {mM} {ATP} caused them to disintegrate actively into individual tubules and groups. The nucleotide specificity and divalent-cation requirements of this disintegration reaction paralleled those of flagellar motility, suggesting that the underlying mechanisms were closely related. Observations by dark-field microscopy showed that the disintegration resulted from active sliding between groups of the outer doublet-tubules, together with a tendency for the partially disintegrated axoneme to coil into a helix. Our evidence supports the hypothesis that the propagated bending waves of live-sperm tails are the result of {ATP-induced} shearing forces between outer tubules which, when resisted by the native structure, lead to localized sliding and generate an active bending moment.

J. Blake (1972): A Model for the {Micro-Structure} in Ciliated Organisms
Type: article by Journal of Fluid Mechanics Digital Archive.
doi: 10.1017/S0022112072001612
link: http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=384836

D. Bray (2000): Cell Movement: From Molecules to Motility
Type: book by Garland Publishing Inc.

H. Lodish, A. Berk, C. A. Kaiser, M. Krieger, M. P. Scott, A. Bretscher (2007): Molecular Cell Biology
Type: book by Palgrave Macmillan.

G. Taylor (1951): Analysis of the Swimming of Microscopic Organisms
Type: article by Proceedings of the Royal Society of London. Series A, Mathematical and Physical Sciences.
link: http://www.jstor.org/stable/98828
Abstract:

Large objects which propel themselves in air or water make use of inertia in the surrounding fluid. The propulsive organ pushes the fluid backwards, while the resistance of the body gives the fluid a forward momentum. The forward and backward momenta exactly balance, but the propulsive organ and the resistance can be thought about as acting separately. This conception cannot be transferred to problems of propulsion in microscopic bodies for which the stresses due to viscosity may be many thousands of times as great as those due to inertia. No case of self-propulsion in a viscous fluid due to purely viscous forces seems to have been discussed. The motion of a fluid near a sheet down which waves of lateral displacement are propagated is described. It is found that the sheet moves forwards at a rate 2π 2b2/λ 2 times the velocity of propagation of the waves. Here b is the amplitude and λ the wave-length. This analysis seems to explain how a propulsive tail can move a body through a viscous fluid without relying on reaction due to inertia. The energy dissipation and stress in the tail are also calculated. The work is extended to explore the reaction between the tails of two neighbouring small organisms with propulsive tails. It is found that if the waves down neighbouring tails are in phase very much less energy is dissipated in the fluid between them than when the waves are in opposite phase. It is also found that when the phase of the wave in one tail lags behind that in the other there is a strong reaction, due to the viscous stress in the fluid between them, which tends to force the two wave trains into phase. It is in fact observed that the tails of spermatozoa wave in unison when they are close to one another and pointing the same way.

Kapitel 23

B. Alberts, A. Johnson, P. Walter, J. Lewis, M. Raff, K. Roberts (2008): Molecular Biology of the Cell
Type: book by Taylor & Francis.

E. D. Hay (1992): Cell Biology of Extracellular Matrix
Type: book by {Springer-Verlag} Gmbh.

S. F. Gilbert, S. R. Singer (2006): Developmental Biology
Type: book by Palgrave Macmillan.

G. Michal (1999): {Biochemie-Atlas;} Biochemical Pathways, German ed.
Type: book by Spektrum Akademischer Verlag.

M. Gao, D. Craig, O. Lequin, I. D. Campbell, V. Vogel, K. Schulten (2003): Structure and functional significance of mechanically unfolded fibronectin type {III1} intermediates
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.2334390100
link: http://www.pnas.org/content/100/25/14784.abstract
Abstract:

Fibronectin {(FN)} forms fibrillar networks coupling cells to the extracellular matrix. The formation of {FN} fibrils, fibrillogenesis, is a tightly regulated process involving the exposure of cryptic binding sites in individual {FN} type {III} {(FN-III)} repeats presumably exposed by mechanical tension. The {FN-III} module has been previously proposed to contain such cryptic sites that promote the assembly of extracellular matrix {FN} fibrils. We have combined {NMR} and steered molecular dynamics simulations to study the structure and mechanical unfolding pathway of {FN-III.} This study finds that {FN-III} consists of a β-sandwich structure that unfolds to a mechanically stable intermediate about four times the length of the native folded state. Considering previous experimental findings, our studies provide a structural model by which mechanical stretching of {FN-III} may induce fibrillogenesis through this partially unfolded intermediate.

Kapitel 24

M. Doi, S. F. Edwards (1988): The Theory of Polymer Dynamics
Type: book by Oxford University Press.

R. Cahn, W. Ludwig (1985): Theorie der Wärme.
Type: book by Springer, Berlin.

P. C. Hiemenz, R. Rajagopalan (1997): Principles of Colloid and Surface Chemistry
Type: book by Marcel Dekker Inc.

J. Wilhelm, E. Frey (1996): Radial Distribution Function of Semiflexible Polymers
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/10061990

I. Borukhov, R. F. Bruinsma, W. M. Gelbart, A. J. Liu (2001): Elastically driven linker aggregation between two semiflexible polyelectrolytes
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/11289885
Abstract:

The behavior of mobile linkers connecting two semiflexible charged polymers, such as polyvalent counterions connecting {DNA} or F-actin chains, is studied theoretically. The chain bending rigidity induces an effective repulsion between linkers at large distances while the interchain electrostatic repulsion leads to an effective short-range interlinker attraction. We find a rounded phase transition from a dilute linker gas where the chains form large loops between linkers to a dense disordered linker fluid connecting parallel chains. The onset of chain pairing occurs within the rounded transition.

J. M. Ziman (1979): Models of Disorder: The Theoretical Physics of Homogeneously Disordered Systems
Type: book by Cambridge University Press.

L. Onsager (1949): The Effects of Shape on the Interaction of Colloidal Particles
Type: article by New York Academy Sciences Annals.
link: http://adsabs.harvard.edu/abs/1949NYASA..51..627O

G. S. Manning (1969): Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions I. Colligative Properties
Type: article by Journal of Chemical Physics.
link: http://adsabs.harvard.edu/abs/1969JChPh..51..924M

T. L. Hill (1988): An Introduction to Statistical Thermodynamics
Type: book by Dover Pubn Inc..

F. Vollrath (1992): Die Seiden und Netze von Spinnen
Type: article by Spektrum der Wissenschaft.

P. G. De Gennes (1979): Scaling Concepts in Polymer Physics
Type: book by Cornell Univ Pr.

T. Odijk, A. C. Houwaart (1978): On the theory of the excluded-volume effect of a polyelectrolyte in a 1-1 electrolyte solution
Type: article by Journal of Polymer Science: Polymer Physics Edition.

L. D. Landau, E. M. Lifschitz (1987): Lehrbuch der theoretischen Physik, 10 Bde., Bd.5, Statistische Physik: {BD} 5
Type: book by Deutsch {(Harri)}.

M. Rubinstein, R. H. Colby (2003): Polymer Physics
Type: book by Oxford University Press.

O. Kratky, G. Porod (1949): Röntgenuntersuchung Gelöster Fadenmoleküle. Rec. Tra V
Type: book by Chim.

Kapitel 25

M. Doi, S. F. Edwards (1988): The Theory of Polymer Dynamics
Type: book by Oxford University Press.

F. C. MacKintosh, J. Käs, P. A. Janmey (1995): Elasticity of semiflexible biopolymer networks
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/10059905

J. Käs, H. Strey, J. X. Tang, D. Finger, R. Ezzell, E. Sackmann, P. A. Janmey (1996): F-actin, a model polymer for semiflexible chains in dilute, semidilute, and liquid crystalline solutions
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(96)79630-3
link: http://www.ncbi.nlm.nih.gov/pubmed/8789080
Abstract:

Single actin filaments were analyzed in solutions ranging from dilute (0.2 microgram/ml), where filaments interact only with solvent, to concentrations (4.0 mg/ml) at which F-actin forms a nematic phase. A persistence length of approximately 1.8 microns and an average length of approximately 22 microns {(Kaufmann} et al., 1992) identify actin as a model for studying the dynamics of semiflexible polymers. In dilute solutions the filaments exhibit thermal bending undulations in addition to diffusive motion. At higher semidilute concentrations (1.4 mg/ml) three-dimensional reconstructions of confocal images of fluorescently labeled filaments in a matrix of unlabeled F-actin reveal steric interactions between filaments, which account for the viscoelastic behavior of these solutions. The restricted undulations of these labeled chains reveal the virtual tube formed around a filament by the surrounding actin. The average tube diameter {textless}a{textgreater} scales with monomer concentration c as {textless}a{textgreater} varies; is directly proportional to c-(0.5 +/- 0.15). The diffusion of filaments in semidilute solutions (c = (0.1-2.0) mg/ml) is dominated by diffusion along the filament contour (reptation), and constraint release by remodeling of the surrounding filaments is rare. The self-diffusion coefficient D parallel along the tube decreases linearly with the chain length for semidilute solutions. For concentrations {textgreater} 2.5 mg/ml a transition occurs from an isotropic entangled phase to a coexistence between isotropic and nematic domains. Analysis of the molecular motions of filaments suggests that the filaments in the aligned domains are in thermal equilibrium and that the diffusion coefficient parallel to the director D parallel is nearly independent of filament length. We also report the novel direct observation of u-shaped defects, called hairpins, in the nematic domains.

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.7, Elastizitätstheorie: {BD} 7
Type: book by Deutsch {(Harri)}.

H. Isambert, P. Venier, A. C. Maggs, A. Fattoum, R. Kassab, D. Pantaloni, M. F. Carlier (1995): Flexibility of actin filaments derived from thermal fluctuations. Effect of bound nucleotide, phalloidin, and muscle regulatory proteins
Type: article by The Journal of Biological Chemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/7744781
Abstract:

Single actin filaments undergoing brownian movement in two dimensions were observed at 20 degrees C in fluorescence optical video microscopy. The persistence length {(Lp)} was derived from the analysis of either the cosine correlation function or the average transverse fluctuations of a series of recorded shapes of filaments assembled from rhodamine-action. Phalloidin-stabilized filaments had a persistence length of 18 +/- 1 micron, in agreement with recent observations. In the absence of phalloidin, rhodamine-labeled filaments could be observed under a variety of solution conditions once diluted in free unlabeled G-actin at the appropriate critical concentration. Such nonstabilized {F-ADP-actin} filaments had the same Lp of 9 +/- 0.5 microns, whether they had been assembled from {ATP-G-actin} or from {ADP-G-actin,} and independently of the tightly bound divalent metal ion. In the presence of {BeF3-,} which mimics the gamma-phosphate of {ATP,} {F-ADP-BeF3-actin} was appreciably more rigid, with Lp = 13.5 microns. Hence, newly formed {F-ADP-Pi-actin} filaments are more rigid than "old" {F-ADP-actin} filaments, a fact which has implications in actin-based motility processes. In the presence of skeletal tropomyosin and troponin, filaments were rigid {(Lp} = 20 +/- 1 micron) in the off state {(-Ca2+),} and flexible {(Lp} = 12 microns) in the on state {(+Ca2+),} consistent with the steric blocking model. In agreement with x-ray diffraction data, no appreciable difference was recorded between the off and on states using smooth muscle tropomyosin and caldesmon {(Lp} = 20 +/- 1 micron). In conclusion, this method allows accurate measurement of small ({textless} or = 15%) changes in mechanical properties of actin filaments in correlation with their biological functions.

M. A. Dichtl, E. Sackmann (1999): Colloidal probe study of short time local and long time reptational motion of semiflexible macromolecules in entangled networks
Type: article by New Journal of Physics.
link: http://adsabs.harvard.edu/abs/1999NJPh....1...18D

J. F. Marko, E. D. Siggia (1995): Stretching {DNA}
Type: article by Macromolecules.
doi: 10.1021/ma00130a008
link: http://dx.doi.org/10.1021/ma00130a008

T. Odijk (1983): The statistics and dynamics of confined or entangled stiff polymers
Type: article by Macromolecules.
doi: 10.1021/ma00242a015
link: http://dx.doi.org/10.1021/ma00242a015

H. Isambert, A. C. Maggs (1996): Dynamics and Rheology of Actin Solutions
Type: article by Macromolecules.
doi: 10.1021/ma946418x
link: http://dx.doi.org/10.1021/ma946418x
Abstract:

We describe the dynamic behavior of semidilute solutions of actin filaments (a semiflexible polymer), pointing out some of the rheological regimes present in this biologically important system. We deduce the macroscopic storage modulus and show that over a certain frequency range semiflexible polymers show a novel variation in the shear modulus; the mechanism should be distinguished from Rouse behavior in solutions of flexible polymers.

D. C. Morse (2001): Tube diameter in tightly entangled solutions of semiflexible polymers
Type: article by Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics.
link: http://www.ncbi.nlm.nih.gov/pubmed/11308652
Abstract:

A statistical mechanical treatment is given of the confinement of a wormlike polymer in an entangled solution to a tube, yielding quantitative predictions for the average tube diameter D(e) and macroscopic plateau modulus G, in the tightly entangled regime in which D(e) is much less than the persistence length L(p). Three approaches are pursued. A self-consistent binary collision approximation, which explicitly describes the topological constraints imposed by neighboring chains, yields predictions consistent with the scaling laws D(e)proportional to rho(-3/5) and G proportional to rho(7/5) proposed previously, where rho is the contour length per unit volume. An effective medium approximation, which treats the network as a continuum with a modulus G, instead yields D(e) proportional to rho(-1/3) and G proportional to rho(4/3), which is found to be the correct scaling in the limit {rhoL(2)(p){textgreater}{textgreater}1.} An elastic network approximation treats the displacement of a test chain as the sum of a collective displacement of the network, which is treated as a continuum, plus a local displacement, which is treated in a binary collision approximation. Predictions are compared to measurements of both D(e) and G in actin protein filament {(F-actin)} solutions.

O. Lieleg, M. M. A. E. Claessens, C. Heussinger, E. Frey, A. R. Bausch (2007): Mechanics of bundled semiflexible polymer networks
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/17930985
Abstract:

While actin bundles are used by living cells for structural fortification, the microscopic origin of the elasticity of bundled networks is not understood. Here, we show that above a critical concentration of the actin binding protein fascin, a solution of actin filaments organizes into a pure network of bundles. While the elasticity of weakly cross-linked networks is dominated by the affine deformation of tubes, the network of bundles can be fully understood in terms of nonaffine bending undulations.

E. Frey (2001): {Schwerpunkt-Physikalische} Fragestellungen aus der Zellbiologie
Type: article by Physikalische Blatter.

M. Fixman, J. Kovac (1973): Polymer conformational statistics. {III.} Modified Gaussian models of stiff chains
Type: article by The Journal of Chemical Physics.
doi: 10.1063/1.1679396
link: http://link.aip.org/link/?JCP/58/1564/1

K. Kroy, E. Frey (1996): {Force-Extension} Relation and Plateau Modulus for Wormlike Chains
Type: article by Physical Review Letters.
doi: 10.1103/PhysRevLett.77.306
link: http://link.aps.org/abstract/PRL/v77/p306
Abstract:

We derive the linear force-extension relation of a wormlike chain of arbitrary stiffness including entropy elasticity, bending, and thermodynamic buckling. From this we infer the plateau modulus G0 of an isotropic entangled solution of wormlike chains. The entanglement length Le is expressed in terms of the characteristic network parameters for three different scaling regimes in the entangled phase. The entanglement transition and the concentration dependence of G0 are analyzed. Finally we compare our findings with experimental data.

Kapitel 26

H. Scher, M. Lax (1973): Stochastic Transport in a Disordered Solid. I. Theory
Type: article by Physical Review B.
link: http://adsabs.harvard.edu/abs/1973PhRvB...7.4491S
Abstract:

A general theory of stochastic transport in disordered systems has been

developed. The theory is based on a generalization of the {Montroll-Weiss} continuous-time random walk {(CTRW)} on a lattice. Starting from a general mobility formalism, specialized t�o hopping conduction, an exact expression for the conductivity sigma(omega) for the {CTRW} process is derived. The frequency dependence of sigma(omega) is determined by the Fourier transform of the zeroth and second spatial moments of the function psi(s--{textgreater},t), which is equal to the probability per unit time that the displacement and time between hops is s--{textgreater}, t. The conductivity corresponding to characteristically different types of hopping distributions is discussed, as well as the basic approximation in adopting a {CTRW} on a lattice to transport in disordered solids.

M. Doi, S. F. Edwards (1988): The Theory of Polymer Dynamics
Type: book by Oxford University Press.

B. Hinner, M. Tempel, E. Sackmann, K. Kroy, E. Frey (1998): Entanglement, Elasticity, and Viscous Relaxation of Actin Solutions
Type: article by Physical Review Letters.
link: http://adsabs.harvard.edu/abs/1998PhRvL..81.2614H
Abstract:

We have investigated the viscosity and the plateau modulus of actin

solutions with a magnetically driven rotating disk rheometer. For entangled solutions we observed a scaling of the plateau modulus versus concentration with a power of 7/5. The measured terminal relaxation time increases with a power 3/2 as a function of polymer length. We interpret the entanglement transition and the scaling of the plateau modulus in terms of the tube model for semiflexible polymers.

Y. C. Fung (1993): Biomechanics. Mechanical Properties of Living Tissues
Type: book by {Springer-Verlag} {GmbH}.

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.7, Elastizitätstheorie: {BD} 7
Type: book by Deutsch {(Harri)}.

C. F. Schmidt, M. Baermann, G. Isenberg, E. Sackmann (1989): Chain dynamics, mesh size, and diffusive transport in networks of polymerized actin: a quasielastic light scattering and microfluorescence study
Type: article by Macromolecules.
doi: 10.1021/ma00199a023
link: http://dx.doi.org/10.1021/ma00199a023

T. G. Mason, D. A. Weitz (1995): Optical measurements of frequency-dependent linear viscoelastic moduli of complex fluids
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/10058972

J. D. Ferry (1980): Viscoelastic Properties of Polymers
Type: book by John Wiley & Sons.

D. C. Morse (2001): Tube diameter in tightly entangled solutions of semiflexible polymers
Type: article by Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics.
link: http://www.ncbi.nlm.nih.gov/pubmed/11308652
Abstract:

A statistical mechanical treatment is given of the confinement of a wormlike polymer in an entangled solution to a tube, yielding quantitative predictions for the average tube diameter D(e) and macroscopic plateau modulus G, in the tightly entangled regime in which D(e) is much less than the persistence length L(p). Three approaches are pursued. A self-consistent binary collision approximation, which explicitly describes the topological constraints imposed by neighboring chains, yields predictions consistent with the scaling laws D(e)proportional to rho(-3/5) and G proportional to rho(7/5) proposed previously, where rho is the contour length per unit volume. An effective medium approximation, which treats the network as a continuum with a modulus G, instead yields D(e) proportional to rho(-1/3) and G proportional to rho(4/3), which is found to be the correct scaling in the limit {rhoL(2)(p){textgreater}{textgreater}1.} An elastic network approximation treats the displacement of a test chain as the sum of a collective displacement of the network, which is treated as a continuum, plus a local displacement, which is treated in a binary collision approximation. Predictions are compared to measurements of both D(e) and G in actin protein filament {(F-actin)} solutions.

F. G. Schmidt, F. Ziemann, E. Sackmann (1996): Shear field mapping in actin networks by using magnetic tweezers
Type: article by European Biophysics Journal: {EBJ}.
link: http://www.ncbi.nlm.nih.gov/pubmed/8766693
Abstract:

An improved magnetic bead microrheometer based on phase contrast microscopy allowing high resolution measurements of local deformations within macromolecular network is applied to study local viscoelastic properties of cross-linked actin networks. By embedding nonmagnetic colloidal beads as probes into the networks, the spatial variation of the strain field within cross-linked actin networks can be mapped. Moreover, the Poisson ratio and shear modulus can be measured locally.

J. C. Crocker, M. T. Valentine, E. R. Weeks, T. Gisler, P. D. Kaplan, A. G. Yodh, D. A. Weitz (2000): Two-point microrheology of inhomogeneous soft materials
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/10991424
Abstract:

We demonstrate a novel method for measuring the microrheology of soft viscoelastic media, based on cross correlating the thermal motion of pairs of embedded tracer particles. The method does not depend on the exact nature of the coupling between the tracers and the medium, and yields accurate rheological data for highly inhomogeneous materials. We demonstrate the accuracy of this method with a guar solution, for which other microscopic methods fail due to the polymer's mesoscopic inhomogeneity. Measurements in an F-actin solution suggest conventional microrheology measurements may not reflect the true bulk behavior.

D. C. Morse (1998): Viscoelasticity of Concentrated Isotropic Solutions of Semiflexible Polymers. 2. Linear Response
Type: article by Macromolecules.
doi: 10.1021/ma980304u
link: http://dx.doi.org/10.1021/ma980304u
Abstract:

Linear rheological properties of tightly-entangled isotropic solutions of semi-flexible polymers are calculated using a tube model, and qualitative predictions are given for the response of more dilute solutions. The linear complex modulus of a solution of long, tightly-entangled chains is dominated at low frequencies by a curvature contribution, analogous to the elastic stress of entangled flexible chains, that relaxes by reptation and gives rise to a broad elastic plateau. The modulus is dominated at higher frequencies by a larger tension contribution, whose frequency dependence is controlled at intermediate frequencies by the diffusion of excess length along the tube and at very high frequencies by the unhindered transverse motion of the chain within the tube. This high-frequency regime yields a complex modulus that varies as G*(omega) (iomega)3/4 with frequency omega. Solutions of shorter, rod-like chains also exhibit a slowly-decaying orientational contribution analogous to the elastic stress found in solutions of true rigid rods. The linear response of the flow birefringence and the effect of cross-links between chains are also discussed.

H. A. Barnes, J. F. Hutton, K. Walters (1989): An introduction to rheology, Rheology Series 3
Type: book by Elsevier, Amsterdam.

N. W. Tschoegl (1989): The phenomenological theory of linear viscoelastic behavior: an introduction
Type: book by Springer.

A. Caspi, R. Granek, M. Elbaum (2002): Diffusion and directed motion in cellular transport
Type: article by Physical Review E.
doi: 10.1103/PhysRevE.66.011916
link: http://link.aps.org/abstract/PRE/v66/e011916
Abstract:

We study the motion of a probe driven by microtubule-associated motors within a living eukaryotic cell. The measured mean square displacement, 〈x(t)2〉 of engulfed 2 and 3μm diameter microspheres shows enhanced diffusion scaling as t3/2 at short times, with a clear crossover to ordinary or subdiffusive scaling, i.e., tγ with γ less than or equal to 1, at long times. Using optical tweezers we tried to move the engulfed bead within the cell in order to relate the anomalous diffusion scaling to the density of the network in which the bead is embedded. Results show that the larger beads, 2 and 3μm diameter, must actively push the cytoskeleton filaments out of the way in order to move, whereas smaller beads of 1μm diameter can be “rattled” within a cage. The 1 μm beads also perform an enhanced diffusion but with a smaller and less consistent exponent 1.2{textless}γ{textless}1.45. We interpret the half-integer power observed with large beads based on two diverse phenomena widely studied in purified cytoskeleton filaments: (1) the motion of the intracellular probe results from random forces generated by motor proteins rather than thermal collisions for classical Brownian particles, and (2) thermal bending modes of these semiflexible polymers lead to anomalous subdiffusion of particles embedded in purified gel networks or attached to single filaments, with 〈x(t)2〉∼t3/4. In the case of small beads, there may also be a Brownian contribution to the motion that results in a smaller exponent.

Kapitel 27

B. Hinner, M. Tempel, E. Sackmann, K. Kroy, E. Frey (1998): Entanglement, Elasticity, and Viscous Relaxation of Actin Solutions
Type: article by Physical Review Letters.
link: http://adsabs.harvard.edu/abs/1998PhRvL..81.2614H
Abstract:

We have investigated the viscosity and the plateau modulus of actin

solutions with a magnetically driven rotating disk rheometer. For entangled solutions we observed a scaling of the plateau modulus versus concentration with a power of 7/5. The measured terminal relaxation time increases with a power 3/2 as a function of polymer length. We interpret the entanglement transition and the scaling of the plateau modulus in terms of the tube model for semiflexible polymers.

M. Tempel, G. Isenberg, E. Sackmann (1996): Temperature-induced sol-gel transition and microgel formation in alpha -actinin cross-linked actin networks: A rheological study
Type: article by Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics.
link: http://www.ncbi.nlm.nih.gov/pubmed/9965260

Y. C. Fung (1993): Biomechanics. Mechanical Properties of Living Tissues
Type: book by {Springer-Verlag} {GmbH}.

F. C. MacKintosh, J. Käs, P. A. Janmey (1995): Elasticity of semiflexible biopolymer networks
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/10059905

M. Elbaum, D. Kuchnir Fygenson, A. Libchaber (1996): Buckling microtubules in vesicles
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/10061186

L. Limozin, A. Roth, E. Sackmann (2005): Microviscoelastic moduli of biomimetic cell envelopes
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/16383873
Abstract:

Bioanalogue models of composite cell envelopes were designed by electrostatically driven self-assembly of actin shells inside giant vesicles. Viscoelastic relaxation moduli were measured between 0.03 and 20 s as a function of actin density by magnetic bead microrheometry. The shear relaxation spectra exhibited by the composite shells compare well with those of natural cell envelopes and bulk entangled actin networks. Absolute value of the shear modulus was measured for the first time by deformation field mapping. Shear and bending moduli agree well with values obtained by bead fluctuations analysis.

R. Tharmann, M. M. A. E. Claessens, A. R. Bausch (2007): Viscoelasticity of isotropically cross-linked actin networks
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/17359131
Abstract:

Despite their importance for the proper function of living cells, the physical properties of cross-linked actin networks remain poorly understood as the occurrence of heterogeneities hamper a quantitative physical description. The isotropic homogeneously cross-linked actin network presented here enables us to quantitatively relate the network response to a single filament model by determining the dominating length scale. The frequency dependence of the linear response and nonuniversal form of the nonlinear response reveal the importance of cross-linker unbinding events.

T. L. Hill (1988): An Introduction to Statistical Thermodynamics
Type: book by Dover Pubn Inc..

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.6, Hydrodynamik: {BD} 6
Type: book by Deutsch {(Harri)}.

D. C. Morse (2001): Tube diameter in tightly entangled solutions of semiflexible polymers
Type: article by Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics.
link: http://www.ncbi.nlm.nih.gov/pubmed/11308652
Abstract:

A statistical mechanical treatment is given of the confinement of a wormlike polymer in an entangled solution to a tube, yielding quantitative predictions for the average tube diameter D(e) and macroscopic plateau modulus G, in the tightly entangled regime in which D(e) is much less than the persistence length L(p). Three approaches are pursued. A self-consistent binary collision approximation, which explicitly describes the topological constraints imposed by neighboring chains, yields predictions consistent with the scaling laws D(e)proportional to rho(-3/5) and G proportional to rho(7/5) proposed previously, where rho is the contour length per unit volume. An effective medium approximation, which treats the network as a continuum with a modulus G, instead yields D(e) proportional to rho(-1/3) and G proportional to rho(4/3), which is found to be the correct scaling in the limit {rhoL(2)(p){textgreater}{textgreater}1.} An elastic network approximation treats the displacement of a test chain as the sum of a collective displacement of the network, which is treated as a continuum, plus a local displacement, which is treated in a binary collision approximation. Predictions are compared to measurements of both D(e) and G in actin protein filament {(F-actin)} solutions.

O. Lieleg, M. M. A. E. Claessens, C. Heussinger, E. Frey, A. R. Bausch (2007): Mechanics of bundled semiflexible polymer networks
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/17930985
Abstract:

While actin bundles are used by living cells for structural fortification, the microscopic origin of the elasticity of bundled networks is not understood. Here, we show that above a critical concentration of the actin binding protein fascin, a solution of actin filaments organizes into a pure network of bundles. While the elasticity of weakly cross-linked networks is dominated by the affine deformation of tubes, the network of bundles can be fully understood in terms of nonaffine bending undulations.

D. Stauffer, A. Bunde (1987): Introduction to Percolation Theory
Type: article by Physics Today.
link: http://adsabs.harvard.edu/abs/1987PhT....40j.122S

P. G. De Gennes (1979): Scaling Concepts in Polymer Physics
Type: book by Cornell Univ Pr.

E. W. Weiler (2000): Wie Pflanzen fühlen
Type: article by Spektrum der Wissenschaft.

R. H. Colby, J. R. Gillmor, M. Rubinstein (1993): Dynamics of near-critical polymer gels
Type: article by Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics.
link: http://www.ncbi.nlm.nih.gov/pubmed/9961028

F. J. Nédélec, T. Surrey, A. C. Maggs, S. Leibler (1997): Self-organization of microtubules and motors
Type: article by Nature.
doi: 10.1038/38532
link: http://www.ncbi.nlm.nih.gov/pubmed/9305848
Abstract:

Cellular structures are established and maintained through a dynamic interplay between assembly and regulatory processes. Self-organization of molecular components provides a variety of possible spatial structures: the regulatory machinery chooses the most appropriate to express a given cellular function. Here we study the extent and the characteristics of self-organization using microtubules and molecular motors as a model system. These components are known to participate in the formation of many cellular structures, such as the dynamic asters found in mitotic and meiotic spindles. Purified motors and microtubules have previously been observed to form asters in vitro. We have reproduced this result with a simple system consisting solely of multi-headed constructs of the motor protein kinesin and stabilized microtubules. We show that dynamic asters can also be obtained from a homogeneous solution of tubulin and motors. By varying the relative concentrations of the components, we obtain a variety of self-organized structures. Further, by studying this process in a constrained geometry of micro-fabricated glass chambers, we demonstrate that the same final structure can be reached through different assembly 'pathways.

P. Fratzl (2002): Von Knochen, Holz und Zähnen
Type: article by Physik Journal.
Abstract:

Biologische Materialien wie Holz, Knochen

oder Zähne sind im Laufe der Evolution von der Natur für ihre jeweilige Anwendung optimiert worden. Die Bauprinzipien dieser Gewebe, ihre Eigenschaften und ihre Funktion liefern für die Materialwissenschaft wichtige Erkenntnisse, die sich für „biomimetisches“ Design von neuartigen Werkstoffen einsetzen lassen. Anstatt viele (teure) Grundstoffe zu verwenden, kommt die Natur für den Großteil ihrer Materialien mit relativ wenigen Grundelementen aus, die gezielt strukturiert werden. Die meisten dieser Prinzipien sind noch unbekannt oder physikalisch unverstanden und bieten ein noch kaum erkundetes Betätigungsfeld für den Materialphysiker. Mögliche Anwendungen liegen in der Entwicklung von Werkstoffen für die Biomedizin (z. B. Knochenersatzmaterialien), aber auch für neuartige Sensoren oder intelligente Materialien.

T. Tanaka (1978): Collapse of Gels and the Critical Endpoint
Type: article by Physical Review Letters.
doi: 10.1103/PhysRevLett.40.820
link: http://link.aps.org/abstract/PRL/v40/p820
Abstract:

Collapse of polyacrylamide gels is observed upon changing temperature or fluid composition. It is explained in terms of mean-field theory based on the extension of Flory's formula for free energy of gels. Theory predicts, and I have observed, existence of a critical endpoint in the phase equilibria.

Kapitel 28

E. Tzima, M. Irani-Tehrani, W. B. Kiosses, E. Dejana, D. A. Schultz, B. Engelhardt, G. Cao, H. DeLisser, M. A. Schwartz (2005): A mechanosensory complex that mediates the endothelial cell response to fluid shear stress
Type: article by Nature.
doi: 10.1038/nature03952
link: http://www.ncbi.nlm.nih.gov/pubmed/16163360
Abstract:

Shear stress is a fundamental determinant of vascular homeostasis, regulating vascular remodelling, cardiac development and atherogenesis, but the mechanisms of transduction are poorly understood. Previous work showed that the conversion of integrins to a high-affinity state mediates a subset of shear responses, including cell alignment and gene expression. Here we investigate the pathway upstream of integrin activation. {PECAM-1} (which directly transmits mechanical force), vascular endothelial cell cadherin (which functions as an adaptor) and {VEGFR2} (which activates {phosphatidylinositol-3-OH} kinase) comprise a mechanosensory complex. Together, these receptors are sufficient to confer responsiveness to flow in heterologous cells. In support of the relevance of this pathway in vivo, {PECAM-1-knockout} mice do not activate {NF-kappaB} and downstream inflammatory genes in regions of disturbed flow. Therefore, this mechanosensing pathway is required for the earliest-known events in atherogenesis.

P. Andriopoulou, P. Navarro, A. Zanetti, M. G. Lampugnani, E. Dejana (1999): Histamine induces tyrosine phosphorylation of endothelial cell-to-cell adherens junctions
Type: article by Arteriosclerosis, Thrombosis, and Vascular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/10521356
Abstract:

Endothelial adherens junctions {(AJ)} promote intercellular adhesion and may contribute to the control of vascular permeability. These structures are formed by a transmembrane and cell-specific adhesive protein, vascular endothelial {(VE)-cadherin,} which is linked by its cytoplasmic tail to intracellular proteins called catenins (alpha-catenin, beta-catenin, and plakoglobin) and to the actin cytoskeleton. Little is known about the functional regulation of {AJ} in endothelial cells. In this study, we analyzed the effect of histamine on {AJ} organization in cultured endothelial cells. We first observed that histamine induced detectable intercellular gaps only in loosely-confluent cells, whereas this effect was strongly reduced or absent in long-confluent cultures. Despite this difference, in vitro permeability was augmented by histamine in both conditions. In resting conditions, tyrosine phosphorylation of {AJ} components and permeability values were higher in recently-confluent cells as compared with long-confluent cells. Histamine did not affect the phosphorylation state of {AJ} in recently-confluent cells but strongly increased this parameter in long-confluent cultures. In addition, in long-confluent cells, histamine caused dissociation of {VE-cadherin} from the actin cytoskeleton measured by a decrease of the amount of the molecule in the detergent-insoluble fraction of the cell extracts. Dibutyryl {cAMP} was able to prevent the effect of histamine on both tyrosine phosphorylation of {AJ} components and on endothelial permeability. The effect of histamine was specific for {VE-cadherin} because the phosphorylation state of neural {(N)-cadherin,} the other major endothelial cadherin, was unchanged by this agent. Hence {AJ} components are a target of histamine activation cascade; we suggest that induction of tyrosine phosphorylation of {VE-cadherin} and catenins contributes to the histamine effect on permeability, even in absence of frank intercellular gaps and cell retraction.

P. F. Davies, A. Robotewskyj, M. L. Griem (1994): Quantitative studies of endothelial cell adhesion. Directional remodeling of focal adhesion sites in response to flow forces
Type: article by The Journal of Clinical Investigation.
doi: 10.1172/JCI117197
link: http://www.ncbi.nlm.nih.gov/pubmed/8182135
Abstract:

Focal adhesion sites were observed in cultured endothelial cells by tandem scanning confocal microscopy and digitized image analysis, techniques that provide real-time images of adhesion site area and topography in living cells. Image subtraction demonstrated that in the presence of unidirectional steady laminar flow (shear stress [tau] = 10 dyn/cm2) a substantial fraction of focal adhesion sites remodeled in the direction of flow. In contrast, focal adhesions of control (no flow) cells remodeled without preferred direction. In confluent monolayers subjected to shear stresses of 10 dyn/cm2, cells began to realign in the direction of flow after 7-9 h. This was accompanied by redistribution of intracellular stress fibers, alignment of individual focal adhesion sites, and the coalescence of smaller sites resulting in fewer, but larger, focal adhesions per cell. Cell adhesion, repeatedly calculated in the same cells as a function of the areas of focal contact and the separation distances between membrane and substratum, varied by {textless} 10% during both short (30 min), or prolonged ({textless} or = 24 h), periods of exposure to flow. Consistent with these measurements, the gains and losses of focal adhesion area as each site remodeled were approximately equivalent. When the glass substratum was coated with gelatin, rates of remodeling were inhibited by 47% during flow (tau = 10 dyn/cm2). These studies: (a) reveal the dynamic nature of focal adhesion; (b) demonstrate that these sites at the ablumenal endothelial membrane are both acutely and chronically responsive to frictional shear stress forces applied to the opposite (lumenal) cell surface; and (c) suggest that components of the focal adhesion complex may be mechanically responsive elements coupled to the cytoskeleton.

G. Cinamon, V. Shinder, R. Alon (2001): Shear forces promote lymphocyte migration across vascular endothelium bearing apical chemokines
Type: article by Nature Immunology.
doi: 10.1038/88710
link: http://www.ncbi.nlm.nih.gov/pubmed/11376338
Abstract:

Leukocyte transendothelial migration {(TEM)} is thought to be a chemotactic process controlled by chemokine gradients across the endothelium. Using cytokine-activated human umbilical vascular endothelial cells {(HUVECs)} as a model of inflamed endothelium, we have shown that apical endothelial chemokines can trigger robust peripheral blood lymphocyte {(PBL)} migration across endothelial cells. Lymphocyte {TEM} was promoted by physiological shear stress applied continuously to migrating lymphocytes. Lymphocyte integrins, intact actin cytoskeleton and G(i) protein-mediated chemokine signaling, but not a chemotactic gradient, were mandatory for {TEM.} {PBL} {TEM} did not require intracellular free calcium or intact phosphatidyl inositol kinase activity in migrating lymphocytes. Thus, lymphocyte {TEM} is promoted by fluid shear-induced mechanical signals coupled to G(i) protein signals at apical endothelial zones.

T. A. Springer (1990): Adhesion receptors of the immune system
Type: article by Nature.
doi: 10.1038/346425a0
link: http://www.ncbi.nlm.nih.gov/pubmed/1974032
Abstract:

The adhesive interactions of cells with other cells and with the extracellular matrix are crucial to all developmental processes, but have a central role in the functions of the immune system throughout life. Three families of cell-surface molecules regulate the migration of lymphocytes and the interactions of activated cells during immune responses.

M. Essler, M. Amano, H. J. Kruse, K. Kaibuchi, P. C. Weber, M. Aepfelbacher (1998): Thrombin inactivates myosin light chain phosphatase via Rho and its target Rho kinase in human endothelial cells
Type: article by The Journal of Biological Chemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/9705325
Abstract:

The role of Rho {GTPase} and its downstream targets Rho kinase and myosin light chain phosphatase in thrombin-induced endothelial cell contraction was investigated. The specific Rho inactivator C3-transferase from Clostridium botulinum as well as microinjection of the isolated Rho-binding domain of Rho kinase or active myosin light chain phosphatase abolished thrombin-stimulated endothelial cell contraction. Conversely, microinjection of constitutively active {V14Rho,} constitutively active catalytic domain of Rho kinase, or treatment with the phosphatase inhibitor tautomycin caused contraction. These data are consistent with the notion that thrombin activates {Rho/Rho} kinase to inactivate myosin light chain phosphatase in endothelial cells. In fact, we demonstrate that thrombin transiently inactivated myosin light chain phosphatase, and this correlated with a peak in myosin light chain phosphorylation. C3-transferase abolished the decrease in myosin light chain phosphatase activity as well as the subsequent increase in myosin light chain phosphorylation and cell contraction. These data suggest that thrombin activates the {Rho/Rho} kinase pathway to inactivate myosin light chain phosphatase as part of a signaling network that controls myosin light chain phosphorylation/contraction in human endothelial cells.

T. A. Springer (1994): Traffic signals for lymphocyte recirculation and leukocyte emigration: the multistep paradigm
Type: article by Cell.
link: http://www.ncbi.nlm.nih.gov/pubmed/7507411

H. Lodish, A. Berk, C. A. Kaiser, M. Krieger, M. P. Scott, A. Bretscher (2007): Molecular Cell Biology
Type: book by Palgrave Macmillan.

W. Feneberg, M. Aepfelbacher, E. Sackmann (2004): Microviscoelasticity of the apical cell surface of human umbilical vein endothelial cells {(HUVEC)} within confluent monolayers
Type: article by Biophysical Journal.
doi: 10.1529/biophysj.103.037044
link: http://www.ncbi.nlm.nih.gov/pubmed/15298936
Abstract:

We studied the local viscoelasticity of the apical membrane of human umbilical vein endothelial cells within confluent layers by magnetic tweezers microrheometry. Magnetic beads are coupled to various integrins by coating with fibronectin or invasin. By analyzing the deflection of beads evoked by various force scenarios we demonstrate that the cell envelope behaves as a linear viscoelastic body if forces up to 2 {nN} are applied for short times ({textless}20 s) but can respond in an adaptive way if stress pulses are applied longer ({textgreater}30 s). The time-dependent shear relaxation modulus G(t) exhibits three time regimes: a fast response (t {textless} 0.05 s) where the relaxation modulus G(t) obeys a power law G(t) approximately t(-0.82+/-0.02); a plateau-like behavior (at 0.05 s {textless} t {textless} 0.15 s); and a slow flow-like response which is, however, partially reversible. Strain field mapping experiments with colloidal probes show that local forces induce a strain field exhibiting a range of zeta = 10 +/- 1 microm, but which could only be observed if nonmagnetic beads were coupled to the cell surface by invasin. By application of the theory of elasticity of planar bodies we estimated a surface shear modulus of 2.5 x10(-4) N/m. By assuming a thickness of the actin cortex of approximately 0.5 microm we estimate a Young modulus micro approximately 400 Pa for the apical membrane. The value agrees with a plateau modulus of an entangled or weakly cross-linked actin network of an actin concentration of 100 {microM} (mesh size 0.2 microm). This result together with our observation of a strong reduction of the shear modulus by the actin destabilizing agent latrunculin A suggests that the shear modulus measured by our technique is determined by the actin cortex. The effect of two ligands inducing actin stress fiber formation and centripetal contraction of cells (associated with the formation of gaps in the confluent cell monolayer) on the viscoelastic responses were studied: histamine and lysophosphatidic acid {(LPA).} Histamine evoked a dramatic increase of the cell stiffness by {textgreater}1 order of magnitude within {textless}30 s, which is attributed to a transient rise of the intracellular Ca(2+) level, since {DMSO} exerted a similar effect. The stiffening is accompanied by a concomitant rounding of the cells as observed by microinterferometry and relaxes partially in the timescale of 5 min, whereas gaps between cells close after approximately 30 min. {LPA} did not exert a remarkable and reproducible effect other than an occasional very weak transient increase of the shear stiffness, which shows that the gap formation activated by {LPA} is mediated by a different mechanism than that induced by histamine.

D. R. Critchley, A. R. Gingras (2008): Talin at a glance
Type: article by Journal of Cell Science.
doi: 10.1242/jcs.018085
link: http://www.ncbi.nlm.nih.gov/pubmed/18434644

T. Borbiev, A. D. Verin, S. Shi, F. Liu, J. G. Garcia (2001): Regulation of endothelial cell barrier function by calcium/calmodulin-dependent protein kinase {II}
Type: article by American Journal of Physiology. Lung Cellular and Molecular Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/11290523
Abstract:

Thrombin-induced endothelial cell barrier dysfunction is tightly linked to Ca(2+)-dependent cytoskeletal protein reorganization. In this study, we found that thrombin increased Ca(2+)/calmodulin-dependent protein kinase {II} {(CaM} kinase {II)} activities in a Ca(2+)- and time-dependent manner in bovine pulmonary endothelium with maximal activity at 5 min. Pretreatment with {KN-93,} a specific {CaM} kinase {II} inhibitor, attenuated both thrombin-induced increases in monolayer permeability to albumin and decreases in transendothelial electrical resistance {(TER).} We next explored potential thrombin-induced {CaM} kinase {II} cytoskeletal targets and found that thrombin causes translocation and significant phosphorylation of nonmuscle filamin {(ABP-280),} which was attenuated by {KN-93,} whereas thrombin-induced myosin light chain phosphorylation was unaffected. Furthermore, a cell-permeable N-myristoylated synthetic filamin peptide (containing the {COOH-terminal} {CaM} kinase {II} phosphorylation site) attenuated both thrombin-induced filamin phosphorylation and decreases in {TER.} Together, these studies indicate that {CaM} kinase {II} activation and filamin phosphorylation may participate in thrombin-induced cytoskeletal reorganization and endothelial barrier dysfunction.

R. F. Schmidt, G. Thews, F. Lang (2000): Physiologie des Menschen
Type: book by Springer Berlin.

V. Grabovsky, S. Feigelson, C. Chen, D. A. Bleijs, A. Peled, G. Cinamon, F. Baleux, F. Arenzana-Seisdedos, T. Lapidot, Y. van Kooyk, R. R. Lobb, R. Alon (2000): Subsecond Induction of {alpha}4 Integrin Clustering by Immobilized Chemokines Stimulates Leukocyte Tethering and Rolling on Endothelial Vascular Cell Adhesion Molecule 1 under Flow Conditions
Type: article by The Journal of Experimental Medicine.
doi: 10.1084/jem.192.4.495
link: http://jem.rupress.org/cgi/content/abstract/192/4/495
Abstract:

Leukocyte recruitment to target tissue is initiated by weak rolling attachments to vessel wall ligands followed by firm integrin-dependent arrest triggered by endothelial chemokines. We show here that immobilized chemokines can augment not only arrest but also earlier integrin-mediated capture (tethering) of lymphocytes on inflamed endothelium. Furthermore, when presented in juxtaposition to vascular cell adhesion molecule 1 {(VCAM-1),} the endothelial ligand for the integrin very late antigen 4 {(VLA-4,} {alpha}4{beta}1), chemokines rapidly augment reversible lymphocyte tethering and rolling adhesions on {VCAM-1.} Chemokines potentiate {VLA-4} tethering within {textless}0.1 s of contact through Gi protein signaling, the fastest inside-out integrin signaling events reported to date. Although {VLA-4} affinity is not altered upon chemokine signaling, subsecond {VLA-4} clustering at the leukocyte-substrate contact zone results in enhanced leukocyte avidity to {VCAM-1.} Endothelial chemokines thus regulate all steps in adhesive cascades that control leukocyte recruitment at specific vascular beds.

D.A. Hammer, S.M. Apte (1992): Simulation of cell rolling and adhesion on surfaces in shear flow: general results and analysis of selectin-mediated neutrophil adhesion
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(92)81577-1

J. Wegener, M. Sieber, H.-J. Galla (1996): Impedance analysis of epithelial and endothelial cell monolayers cultured on gold surfaces
Type: article by Journal of Biochemical and Biophysical Methods.

M. Poujade, E. Grasland-Mongrain, A. Hertzog, J. Jouanneau, P. Chavrier, B. Ladoux, A. Buguin, P. Silberzan (2007): Collective migration of an epithelial monolayer in response to a model wound
Type: article by Proceedings of the National Academy of Sciences.
doi: 10.1073/pnas.0705062104
link: http://www.pnas.org/content/104/41/15988.abstract
Abstract:

Using an original microfabrication-based technique, we experimentally study situations in which a virgin surface is presented to a confluent epithelium with no damage made to the cells. Although inspired by wound-healing experiments, the situation is markedly different from classical scratch wounding because it focuses on the influence of the free surface and uncouples it from the other possible contributions such as cell damage and/or permeabilization. Dealing with {Madin–Darby} canine kidney cells on various surfaces, we found that a sudden release of the available surface is sufficient to trigger collective motility. This migration is independent of the proliferation of the cells that mainly takes place on the fraction of the surface initially covered. We find that this motility is characterized by a duality between collective and individual behaviors. On the one hand, the velocity fields within the monolayer are very long range and involve many cells in a coordinated way. On the other hand, we have identified very active “leader cells” that precede a small cohort and destabilize the border by a fingering instability. The sides of the fingers reveal a pluricellular actin “belt” that may be at the origin of a mechanical signaling between the leader and the followers. Experiments performed with autocrine cells constitutively expressing hepatocyte growth factor {(HGF)} or in the presence of exogenous {HGF} show a higher average velocity of the border and no leader.

Kapitel 29

N. Q. Balaban, U. S. Schwarz, D. Riveline, P. Goichberg, G. Tzur, I. Sabanay, D. Mahalu, S. Safran, A. Bershadsky, L. Addadi, B. Geiger (2001): Force and focal adhesion assembly: a close relationship studied using elastic micropatterned substrates
Type: article by Nature Cell Biology.
doi: 10.1038/35074532
link: http://www.ncbi.nlm.nih.gov/pubmed/11331874
Abstract:

Mechanical forces play a major role in the regulation of cell adhesion and cytoskeletal organization. In order to explore the molecular mechanism underlying this regulation, we have investigated the relationship between local force applied by the cell to the substrate and the assembly of focal adhesions. A novel approach was developed for real-time, high-resolution measurements of forces applied by cells at single adhesion sites. This method combines micropatterning of elastomer substrates and fluorescence imaging of focal adhesions in live cells expressing {GFP-tagged} vinculin. Local forces are correlated with the orientation, total fluorescence intensity and area of the focal adhesions, indicating a constant stress of 5.5 +/- 2 {nNmicrom(-2).} The dynamics of the force-dependent modulation of focal adhesions were characterized by blocking actomyosin contractility and were found to be on a time scale of seconds. The results put clear constraints on the possible molecular mechanisms for the mechanosensory response of focal adhesions to applied force.

C. Semmrich, T. Storz, J. Glaser, R. Merkel, A. R. Bausch, K. Kroy (2007): Glass transition and rheological redundancy in F-actin solutions
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.0705513104
link: http://www.ncbi.nlm.nih.gov/pubmed/18077385
Abstract:

The unique mechanical performance of animal cells and tissues is attributed mostly to their internal biopolymer meshworks. Its perplexing universality and robustness against structural modifications by drugs and mutations is an enigma in cell biology and provides formidable challenges to materials science. Recent investigations could pinpoint highly universal patterns in the soft glassy rheology and nonlinear elasticity of cells and reconstituted networks. Here, we report observations of a glass transition in semidilute F-actin solutions, which could hold the key to a unified explanation of these phenomena. Combining suitable rheological protocols with high-precision dynamic light scattering, we can establish a remarkable rheological redundancy and trace it back to a highly universal exponential stretching of the single-polymer relaxation spectrum of a "glassy wormlike chain." By exploiting the ensuing generalized time-temperature superposition principle, the time domain accessible to microrheometry can be extended by several orders of magnitude, thus opening promising new metrological opportunities.

R. Merkel, N. Kirchgessner, C. M. Cesa, B. Hoffmann (2007): Cell force microscopy on elastic layers of finite thickness
Type: article by Biophysical Journal.
doi: 10.1529/biophysj.107.111328
link: http://www.ncbi.nlm.nih.gov/pubmed/17660320
Abstract:

Forces applied by cells to substrates can be measured using soft substrates with embedded displacement markers. Traction forces are retrieved from microscopic images by determining the displacements of these markers and fitting the generating forces. Here we show that using elastic films of 5-10-microm thickness one can improve the spatial resolution of the technique. To this end we derived explicit equations for the mechanical response of an elastic layer of finite thickness to point forces. Moreover, these equations allow highly accurate force measurements on eukaryotic cells on films where finite thickness effects are relevant (below approximately 60 microm).

S. W. Grill, K. Kruse, F. Jülicher (2005): Theory of mitotic spindle oscillations
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/15783531
Abstract:

During unequal cell division the mitotic spindle is positioned away from the center of the cell before cell cleavage. In many biological systems this repositioning is accompanied by oscillatory movements of the spindle. We present a theoretical description for mitotic spindle oscillations. We show that the cooperative attachment and detachment of cortical force generators to astral microtubules leads to spontaneous oscillations beyond a critical number of force generators. This mechanism can quantitatively describe the spindle oscillations observed during unequal division of the one cell stage Caenorhabditis elegans embryo.

J. P. Butler, I. M. Tolić-Nørrelykke, B. Fabry, J. J. Fredberg (2002): Traction fields, moments, and strain energy that cells exert on their surroundings
Type: article by American Journal of Physiology. Cell Physiology.
doi: 10.1152/ajpcell.00270.2001
link: http://www.ncbi.nlm.nih.gov/pubmed/11832345
Abstract:

Adherent cells exert tractions on their surroundings. These tractions can be measured by observing the displacements of beads embedded on a flexible gel substrate on which the cells are cultured. This paper presents an exact solution to the problem of computing the traction field from the observed displacement field. The solution rests on recasting the relationship between displacements and tractions into Fourier space, where the recovery of the traction field is especially simple. We present two subcases of the solution, depending on whether or not tractions outside the observed cell boundaries are set to be zero. The implementation is computationally efficient. We also give the solution for the traction field in a representative human airway smooth muscle cell contracted by treatment with histamine. Finally, we give explicit formulas for reducing the traction and displacement fields to contraction moments, the orientation of the principal axes of traction, and the strain energy imparted by the cell to the substrate.

S. Munevar (2001): Traction Force Microscopy of Migrating Normal and H-ras Transformed {3T3} Fibroblasts
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(01)76145-0
link: http://www.cell.com/biophysj/abstract/S0006-3495(01)76145-0
Abstract:

Mechanical interactions between cell and substrate are involved in vital cellular functions from migration to signal transduction. A newly developed technique, traction force microscopy, makes it possible to visualize the dynamic characteristics of mechanical forces exerted by fibroblasts, including the magnitude, direction, and shear. In the present study such analysis is applied to migrating normal and transformed {3T3} cells. For normal cells, the lamellipodium provides almost all the forces for forward locomotion. A zone of high shear separates the lamellipodium from the cell body, suggesting that they are mechanically distinct entities. Timing and distribution of tractions at the leading edge bear no apparent relationship to local protrusive activities. However, changes in the pattern of traction forces often precede changes in the direction of migration. These observations suggest a frontal towing mechanism for cell migration, where dynamic traction forces at the leading edge actively pull the cell body forward. For H-ras transformed cells, pockets of weak, transient traction scatter among small pseudopods and appear to act against one another. The shear pattern suggests multiple disorganized mechanical domains. The weak, poorly coordinated traction forces, coupled with weak cell-substrate adhesions, are likely responsible for the abnormal motile behavior of H-ras transformed cells.

D. E. Ingber (2000): Opposing views on tensegrity as a structural framework for understanding cell mechanics
Type: article by Journal of Applied Physiology {(Bethesda,} Md.: 1985).
link: http://www.ncbi.nlm.nih.gov/pubmed/11007610

A. C. Rowat, J. Lammerding, J. H. Ipsen (2006): Mechanical properties of the cell nucleus and the effect of emerin deficiency
Type: article by Biophysical Journal.
doi: 10.1529/biophysj.106.086454
link: http://www.ncbi.nlm.nih.gov/pubmed/16997877
Abstract:

Nuclear structure and mechanics are gaining recognition as important factors that affect gene expression, development, and differentiation in normal function and disease, yet the physical mechanisms that govern nuclear mechanical stability remain unclear. Here we examined the physical properties of the cell nucleus by imaging fluorescently labeled components of the inner nucleus (chromatin and nucleoli) and the nuclear envelope (lamins and membranes) in nuclei deformed by micropipette aspiration (confocal imaged microdeformation). We investigated nuclei, both isolated and in intact, living cells, and found that nuclear volume significantly decreased by 60-70% during aspiration. While nuclear membranes exhibited blebbing and fluid characteristics during aspiration, the nuclear lamina exhibited behavior of a solid-elastic shell. Under large deformations of {GFP-lamin} A-labeled nuclei, we observed a decay of fluorescence intensity into the tip of the deformed tongue that we interpreted in terms of nonlinear, two-dimensional elasticity theory. Here we applied this method to study nuclear envelope stability in disease and found that mouse embryo fibroblasts lacking the inner nuclear membrane protein, emerin, had a significantly decreased ratio of the area expansion to shear moduli {(K/mu)} compared to wild-type cells (2.1 +/- 0.2 versus 5.1 +/- 1.3). These data suggest that altered nuclear envelope elasticity caused by loss of emerin could contribute to increased nuclear fragility in {Emery-Dreifuss} muscular dystrophy patients with mutations in the emerin gene. Based on our experimental results and theoretical considerations, we present a model describing how the nucleus is stabilized in the pipette. Such a model is essential for interpreting the results of any micropipette study of the nucleus and porous materials in general.

J. Guck, R. Ananthakrishnan, H. Mahmood, T. J. Moon, C. C. Cunningham, J. Käs (2001): The optical stretcher: a novel laser tool to micromanipulate cells
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(01)75740-2
link: http://www.ncbi.nlm.nih.gov/pubmed/11463624
Abstract:

When a dielectric object is placed between two opposed, nonfocused laser beams, the total force acting on the object is zero but the surface forces are additive, thus leading to a stretching of the object along the axis of the beams. Using this principle, we have constructed a device, called an optical stretcher, that can be used to measure the viscoelastic properties of dielectric materials, including biologic materials such as cells, with the sensitivity necessary to distinguish even between different individual cytoskeletal phenotypes. We have successfully used the optical stretcher to deform human erythrocytes and mouse fibroblasts. In the optical stretcher, no focusing is required, thus radiation damage is minimized and the surface forces are not limited by the light power. The magnitude of the deforming forces in the optical stretcher thus bridges the gap between optical tweezers and atomic force microscopy for the study of biologic materials.

W. Feneberg, M. Aepfelbacher, E. Sackmann (2004): Microviscoelasticity of the apical cell surface of human umbilical vein endothelial cells {(HUVEC)} within confluent monolayers
Type: article by Biophysical Journal.
doi: 10.1529/biophysj.103.037044
link: http://www.ncbi.nlm.nih.gov/pubmed/15298936
Abstract:

We studied the local viscoelasticity of the apical membrane of human umbilical vein endothelial cells within confluent layers by magnetic tweezers microrheometry. Magnetic beads are coupled to various integrins by coating with fibronectin or invasin. By analyzing the deflection of beads evoked by various force scenarios we demonstrate that the cell envelope behaves as a linear viscoelastic body if forces up to 2 {nN} are applied for short times ({textless}20 s) but can respond in an adaptive way if stress pulses are applied longer ({textgreater}30 s). The time-dependent shear relaxation modulus G(t) exhibits three time regimes: a fast response (t {textless} 0.05 s) where the relaxation modulus G(t) obeys a power law G(t) approximately t(-0.82+/-0.02); a plateau-like behavior (at 0.05 s {textless} t {textless} 0.15 s); and a slow flow-like response which is, however, partially reversible. Strain field mapping experiments with colloidal probes show that local forces induce a strain field exhibiting a range of zeta = 10 +/- 1 microm, but which could only be observed if nonmagnetic beads were coupled to the cell surface by invasin. By application of the theory of elasticity of planar bodies we estimated a surface shear modulus of 2.5 x10(-4) N/m. By assuming a thickness of the actin cortex of approximately 0.5 microm we estimate a Young modulus micro approximately 400 Pa for the apical membrane. The value agrees with a plateau modulus of an entangled or weakly cross-linked actin network of an actin concentration of 100 {microM} (mesh size 0.2 microm). This result together with our observation of a strong reduction of the shear modulus by the actin destabilizing agent latrunculin A suggests that the shear modulus measured by our technique is determined by the actin cortex. The effect of two ligands inducing actin stress fiber formation and centripetal contraction of cells (associated with the formation of gaps in the confluent cell monolayer) on the viscoelastic responses were studied: histamine and lysophosphatidic acid {(LPA).} Histamine evoked a dramatic increase of the cell stiffness by {textgreater}1 order of magnitude within {textless}30 s, which is attributed to a transient rise of the intracellular Ca(2+) level, since {DMSO} exerted a similar effect. The stiffening is accompanied by a concomitant rounding of the cells as observed by microinterferometry and relaxes partially in the timescale of 5 min, whereas gaps between cells close after approximately 30 min. {LPA} did not exert a remarkable and reproducible effect other than an occasional very weak transient increase of the shear stiffness, which shows that the gap formation activated by {LPA} is mediated by a different mechanism than that induced by histamine.

A. K. Harris, D. Stopak, P. Wild (1981): Fibroblast traction as a mechanism for collagen morphogenesis
Type: article by Nature.
link: http://www.ncbi.nlm.nih.gov/pubmed/7207616
Abstract:

To make visible the traction forces exerted by individuals cells, we have previously developed a method of culturing them on thin distortable sheets of silicone rubber. We have now used this method to compare the forces exerted by various differentiated cell types and have examined the effects of cellular traction on re-precipitated collagen-matrices. We find that the strength of cellular traction differs greatly between cell types and this traction is paradoxically weakest in the most mobile and invasive cells (leukocytes and nerve growth cones). Untransformed fibroblasts exert forces very much larger than those actually needed for locomotion. This strong traction distorts collagen gels dramatically, creating patterns similar to tendons and organ capsules. We propose that this morphogenetic rearrangement of extracellular matrices is the primary function of fibroblast traction and explains its excessive strength.

P. Fernandez, L. Heymann, A. Ott, N. Aksel, P. A. Pullarkat (2007): Shear rheology of a cell monolayer
Type: article by New Journal of Physics.
link: http://adsabs.harvard.edu/abs/2007NJPh....9..419F
Abstract:

We report a systematic investigation of the mechanical properties of

fibroblast cells using a novel cell monolayer rheology {(CMR)} technique. The new technique provides quantitative rheological parameters averaged over {textasciitilde}106 cells making the experiments highly reproducible. Using this method, we are able to explore a broad range of cell responses not accessible using other present day techniques. We perform harmonic oscillation experiments and step shear or step stress experiments to reveal different viscoelastic regimes. The evolution of the live cells under externally imposed cyclic loading and unloading is also studied. Remarkably, the initially nonlinear response becomes linear at long timescales as well as at large amplitudes. Within the explored rates, nonlinear behaviour is only revealed by the effect of a nonzero average stress on the response to small, fast deformations. When the cell cytoskeletal crosslinks are made permanent using a fixing agent, the large amplitude linear response disappears and the cells exhibit a stress stiffening response instead. This result shows that the dynamic nature of the cross-links and/or filaments is responsible for the linear stress-strain response seen under large deformations. We rule out the involvement of myosin motors in this using the inhibitor drug blebbistatin. These experiments provide a broad framework for understanding the mechanical responses of the cortical actin cytoskeleton of fibroblasts to different imposed mechanical stimuli.

J. E. Gordon, D. C. Mattis (1985): The New Science of Strong Materials, or, Why You Don't Fall Through the Floor
Type: article by American Journal of Physics.
link: http://adsabs.harvard.edu/abs/1985AmJPh..53..508G

J. Rosenblatt, L. P. Cramer, B. Baum, K. M. McGee (2004): Myosin {II-dependent} cortical movement is required for centrosome separation and positioning during mitotic spindle assembly
Type: article by Cell.
link: http://www.ncbi.nlm.nih.gov/pubmed/15109496
Abstract:

The role of myosin {II} in mitosis is generally thought to be restricted to cytokinesis. We present surprising new evidence that cortical myosin {II} is also required for spindle assembly in cells. Drug- or {RNAi-mediated} disruption of myosin {II} in cells interferes with normal spindle assembly and positioning. Time-lapse movies reveal that these treatments block the separation and positioning of duplicated centrosomes after nuclear envelope breakdown {(NEBD),} thereby preventing the migration of the microtubule asters to opposite sides of chromosomes. Immobilization of cortical movement with tetravalent lectins produces similar spindle defects to myosin {II} disruption and suggests that myosin {II} activity is required within the cortex. Latex beads bound to the cell surface move in a myosin {II-dependent} manner in the direction of the separating asters. We propose that after {NEBD,} completion of centrosome separation and positioning around chromosomes depends on astral microtubule connections to a moving cell cortex.

C. Rotsch (2000): {Drug-Induced} Changes of Cytoskeletal Structure and Mechanics in Fibroblasts: An Atomic Force Microscopy Study
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(00)76614-8
link: http://www.cell.com/biophysj/abstract/S0006-3495(00)76614-8
Abstract:

The effect of various drugs affecting the integrity of different components of the cytoskeleton on the elasticity of two fibroblast cell lines was investigated by elasticity measurements with an atomic force microscope {(AFM).} Disaggregation of actin filaments always resulted in a distinct decrease in the cells average elastic modulus indicating the crucial importance of the actin network for the mechanical stability of living cells. Disruption or chemical stabilization of microtubules did not affect cell elasticity. For the f-actin-disrupting drugs different mechanisms of drug action were observed. Cytochalasins B and D and Latrunculin A disassembled stress fibers. For Cytochalasin D this was accompanied by an aggregation of actin within the cytosol. Jasplakinolide disaggregated actin filaments but did not disassemble stress fibers. Fibrous structures found in {AFM} images and elasticity maps of fibroblasts could be identified as stress fibers by correlation of {AFM} data and fluorescence images.

K. Terai, T. Takano-Yamamoto, Y. Ohba, K. Hiura, M. Sugimoto, M. Sato, H. Kawahata, N. Inaguma, Y. Kitamura, S. Nomura (1999): Role of osteopontin in bone remodeling caused by mechanical stress
Type: article by Journal of Bone and Mineral Research: The Official Journal of the American Society for Bone and Mineral Research.
link: http://www.ncbi.nlm.nih.gov/pubmed/10352091
Abstract:

Changes in the number and proportion of osteopontin {mRNA} {(Opn)} expressing osteocytes and osteoclasts caused by the mechanical stress applied during experimental tooth movement were examined in the present study. Opn expression was detected in the osteocytes on the pressure side at the early stage, and gradually spread to those on the tension side and also to the osteoblasts and bone-lining cells in the alveolar bone. Only 3.3% of the osteocytes located on the pressure side expressed Opn in the interradicular septum of control rats; in contrast, the value was increased to 87.5% at 48 h after the initiation of tooth movement. These results indicate that these cells responded to mechanical stress loaded on the bone with expression of the osteopontin gene. Following the increased expression of Opn in these cells, a 17-fold greater number of osteoclasts compared with the control and numerous resorption pits were observed on the pressure side of the alveolar bone. Injection of arginine-glycine-aspartic acid-serine peptide but not that of arginine-glycine-glutamic acid-serine peptide strongly inhibited the increase in the number of osteoclasts. Furthermore, an in vitro migration assay demonstrated the chemotactic activity of osteopontin {(OPN)} on the precursor of osteoclasts. Our study strongly suggests that {OPN} is an important factor triggering bone remodeling caused by mechanical stress.

I. B. Bischofs, U. S. Schwarz (2003): Cell organization in soft media due to active mechanosensing
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.1233544100
link: http://www.ncbi.nlm.nih.gov/pubmed/12883003
Abstract:

Adhering cells actively probe the mechanical properties of their environment and use the resulting information to position and orient themselves. We show that a large body of experimental observations can be consistently explained from one unifying principle, namely that cells strengthen contacts and cytoskeleton in the direction of large effective stiffness. Using linear elasticity theory to model the extracellular environment, we calculate optimal cell organization for several situations of interest and find excellent agreement with experiments for fibroblasts, both on elastic substrates and in collagen gels: cells orient in the direction of external tensile strain; they orient parallel and normal to free and clamped surfaces, respectively; and they interact elastically to form strings. Our method can be applied for rational design of tissue equivalents. Moreover, our results indicate that the concept of contact guidance has to be reevaluated. We also suggest that cell-matrix contacts are up-regulated by large effective stiffness in the environment because, in this way, build-up of force is more efficient.

D. Heinrich, E. Sackmann (2006): Active mechanical stabilization of the viscoplastic intracellular space of Dictyostelia cells by microtubule–actin crosstalk
Type: article by Acta Biomaterialia.
doi: 10.1016/j.actbio.2006.05.014

I. Kaverina, O. Krylyshkina, J. V. Small (2002): Regulation of substrate adhesion dynamics during cell motility
Type: article by The International Journal of Biochemistry & Cell Biology.
doi: 10.1016/S1357-2725(01)00171-6

A. Micoulet, J. P. Spatz, A. Ott (2005): Mechanical Response Analysis and Power Generation by {Single-Cell} Stretching
Type: article by {ChemPhysChem}.
doi: 10.1002/cphc.200400417
link: http://dx.doi.org/10.1002/cphc.200400417
Abstract:

To harvest useful information about cell response due to mechanical perturbations under physiological conditions, a cantilever-based technique was designed, which allowed precise application of arbitrary forces or deformation histories on a single cell in vitro. Essential requirements for these investigations are a mechanism for applying an automated cell force and an induced-deformation detection system based on fiber-optical force sensing and closed loop control. The required mechanical stability of the setup can persist for several hours since mechanical drifts due to thermal gradients can be eliminated sufficiently (these gradients are caused by local heating of the cell observation chamber to 37 {°C).} During mechanical characterization, the cell is visualized with an optical microscope, which enables the simultaneous observation of cell shape and intracellular morphological changes. Either the cell elongation is observed as a reaction against a constant load or the cell force is measured as a response to constant deformation. Passive viscoelastic deformation and active cell response can be discriminated. The active power generated during contraction is in the range of Pmax=10-16 Watts, which corresponds to 2500 {ATP} molecules s-1 at 10 {kBT/molecule.} The ratio of contractive to dissipative power is estimated to be in the range of 10-2. The highest forces supported by the cell suggest that about 104 molecular motors must be involved in contraction. This indicates an energy-conversion efficiency of approximately 0.5. Our findings propose that, in addition to the recruitment of cell-contractile elements upon mechanical stimulation, the cell cytoskeleton becomes increasingly crosslinked in response to a mechanical pull. Quantitative stress-strain data, such as those presented here, may be employed to test physical models that describe cellular responses to mechanical stimuli.

A. J. Engler, S. Sen, H. L. Sweeney, D. E. Discher (2006): Matrix Elasticity Directs Stem Cell Lineage Specification
Type: article by Cell.
doi: 10.1016/j.cell.2006.06.044

Kapitel 30

B. Alberts, A. Johnson, P. Walter, J. Lewis, M. Raff, K. Roberts (2008): Molecular Biology of the Cell
Type: book by Taylor & Francis.

W. Zinth, J. Wachtveitl (2005): The first picoseconds in bacterial photosynthesis--ultrafast electron transfer for the efficient conversion of light energy
Type: article by Chemphyschem: A European Journal of Chemical Physics and Physical Chemistry.
doi: 10.1002/cphc.200400458
link: http://www.ncbi.nlm.nih.gov/pubmed/15884069
Abstract:

In this Minireview, we describe the function of the bacterial reaction centre {(RC)} as the central photosynthetic energy-conversion unit by ultrafast spectroscopy combined with structural analysis, site-directed mutagenesis, pigment exchange and theoretical modelling. We show that primary energy conversion is a stepwise process in which an electron is transferred via neighbouring chromophores of the {RC.} A well-defined chromophore arrangement in a rigid protein matrix, combined with optimised energetics of the different electron carriers, allows a highly efficient charge-separation process. The individual molecular reactions at room temperature are well described by conventional electron-transfer theory.

E. Bausch, N. W. Woodbury (2004): Purple bacteria: electron acceptors and donors
Type: incollection

M. J. Gresser, J. A. Myers, P. D. Boyer (1982): Catalytic site cooperativity of beef heart mitochondrial F1 adenosine triphosphatase. Correlations of initial velocity, bound intermediate, and oxygen exchange measurements with an alternating three-site model
Type: article by The Journal of Biological Chemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/6214554

Y. Rondelez, G. Tresset, T. Nakashima, Y. Kato-Yamada, H. Fujita, S. Takeuchi, H. Noji (2005): Highly coupled {ATP} synthesis by {F1-ATPase} single molecules
Type: article by Nature.
doi: 10.1038/nature03277
link: http://www.ncbi.nlm.nih.gov/pubmed/15716957
Abstract:

{F1-ATPase} is the smallest known rotary motor, and it rotates in an anticlockwise direction as it hydrolyses {ATP.} Single-molecule experiments point towards three catalytic events per turn, in agreement with the molecular structure of the complex. The physiological function of F1 is {ATP} synthesis. In the ubiquitous {F0F1} complex, this energetically uphill reaction is driven by F0, the partner motor of F1, which forces the backward (clockwise) rotation of F1, leading to {ATP} synthesis. Here, we have devised an experiment combining single-molecule manipulation and microfabrication techniques to measure the yield of this mechanochemical transformation. Single F1 molecules were enclosed in femtolitre-sized hermetic chambers and rotated in a clockwise direction using magnetic tweezers. When the magnetic field was switched off, the F1 molecule underwent anticlockwise rotation at a speed proportional to the amount of synthesized {ATP.} At 10 Hz, the mechanochemical coupling efficiency was low for the alpha3beta3gamma subcomplex {(F1-epsilon)),} but reached up to 77% after reconstitution with the epsilon-subunit {(F1+epsilon)).} We provide here direct evidence that F1 is designed to tightly couple its catalytic reactions with the mechanical rotation. Our results suggest that the epsilon-subunit has an essential function during {ATP} synthesis.

X. Hu, A. Damjanović, T. Ritz, K. Schulten (1998): Architecture and mechanism of the light-harvesting apparatus of purple bacteria
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/9600895
Abstract:

Photosynthetic organisms fuel their metabolism with light energy and have developed for this purpose an efficient apparatus for harvesting sunlight. The atomic structure of the apparatus, as it evolved in purple bacteria, has been constructed through a combination of x-ray crystallography, electron microscopy, and modeling. The detailed structure and overall architecture reveals a hierarchical aggregate of pigments that utilizes, as shown through femtosecond spectroscopy and quantum physics, elegant and efficient mechanisms for primary light absorption and transfer of electronic excitation toward the photosynthetic reaction center.

J. Yano, J. Kern, K. Sauer, M. J. Latimer, Y. Pushkar, J. Biesiadka, B. Loll, W. Saenger, J. Messinger, A. Zouni, V. K. Yachandra (2006): Where water is oxidized to dioxygen: structure of the photosynthetic {Mn4Ca} cluster
Type: article by Science {(New} York, {N.Y.)}.
doi: 10.1126/science.1128186
link: http://www.ncbi.nlm.nih.gov/pubmed/17082458
Abstract:

The oxidation of water to dioxygen is catalyzed within photosystem {II} {(PSII)} by a {Mn(4)Ca} cluster, the structure of which remains elusive. Polarized extended x-ray absorption fine structure {(EXAFS)} measurements on {PSII} single crystals constrain the {Mn(4)Ca} cluster geometry to a set of three similar high-resolution structures. Combining polarized {EXAFS} and x-ray diffraction data, the cluster was placed within {PSII,} taking into account the overall trend of the electron density of the metal site and the putative ligands. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 angstrom-resolution x-ray structures or other previously proposed models.

C. R. D. Lancaster Purple bacteria: Photosynthetic reaction centers
Type: incollection

H. T. Witt (1979): Energy conversion in the functional membrane of photosynthesis. Analysis by light pulse and electric pulse methods. The central role of the electric field
Type: article by Biochimica Et Biophysica Acta.
link: http://www.ncbi.nlm.nih.gov/pubmed/35227

G. Renger, P. Kühn (2007): Reaction pattern and mechanism of light induced oxidative water splitting in photosynthesis
Type: article by Biochimica Et Biophysica Acta.
doi: 10.1016/j.bbabio.2006.12.004
link: http://www.ncbi.nlm.nih.gov/pubmed/17428439
Abstract:

This mini review is an attempt to briefly summarize our current knowledge on light driven oxidative water splitting in photosynthesis. The reaction leading to molecular oxygen and four protons via photosynthesis comprises thermodynamic and kinetic constraints that require a balanced fine tuning of the reaction coordinates. The mode of coupling between electron {(ET)} and proton transfer {(PT)} reactions is shown to be of key mechanistic relevance for the redox turnover of {Y(Z)} and the reactions within the {WOC.} The {WOC} is characterized by peculiar energetics of its oxidation steps in the {WOC.} In all oxygen evolving photosynthetic organisms the redox state S(1) is thermodynamically most stable and therefore this general feature is assumed to be of physiological relevance. Available information on the Gibbs energy differences between the individual redox states S(i+1) and S(i) and on the activation energies of their oxidative transitions are used to construct a general reaction coordinate of oxidative water splitting in photosystem {II} {(PS} {II).} Finally, an attempt is presented to cast our current state of knowledge into a mechanism of oxidative water splitting with special emphasis on the formation of the essential {O-O} bond and the active role of the protein environment in tuning the local proton activity that depends on time and redox state S(i). The {O-O} linkage is assumed to take place within a multistate equilibrium at the redox level of S(3), comprising both redox isomerism and proton tautomerism. It is proposed that one state, {S(3)(P),} attains an electronic configuration and nuclear geometry that corresponds with a hydrogen bonded peroxide which acts as the entatic state for the generation of complexed molecular oxygen through {S(3)(P)} oxidation by {Y(Z)(ox).}

G. Renger (1978): Photosynthese
Type: article by Biophysik. {Springer-Verlag}.

P. Gräber, A. Labahn (1992): Proton transport-coupled unisite catalysis by the {H(+)-ATPase} from chloroplasts
Type: article by Journal of Bioenergetics and Biomembranes.
link: http://www.ncbi.nlm.nih.gov/pubmed/1331040
Abstract:

Proton transport-coupled unisite catalysis was measured with the {H(+)-ATPase} from chloroplasts. The reaction was measured in the {ATP} hydrolysis direction under deenergized conditions and in the {ATP} synthesis direction under energized conditions. The equilibrium constant of the enzyme does not change upon energization, whereas the dissociation constants of substrates and products change by orders of magnitude. This indicates that the Gibbs free enthalpy derived from proton translocation is used to change binding affinities of substrates and products, and this results in synthesis of free {ATP.}

G. McDermott, S. M. Prince, A. A. Freer, A. M. Hawthornthwaite-Lawless, M. Z. Papiz, R. J. Cogdell, N. W. Isaacs (1995): Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria
Type: article by Nature.
link: http://adsabs.harvard.edu/abs/1995Natur.374..517M
Abstract:

The crystal structure of the light-harvesting antenna complex {(LH2)} from

Rhodopseudomonas acidophila strain 10050 shows that the active assembly consists of two concentric cylinders of helical protein subunits which enclose the pigment molecules. Eighteen bacteriochlorophyll a molecules sandwiched between the helices form a continuous overlapping ring, and a further nine are positioned between the outer helices with the bacteriochlorin rings perpendicular to the transmembrane helix axis. There is an elegant intertwining of the bacteriochlorophyll phytol chains with carotenoid, which spans the complex.

S. Schmidt, R. Reich, H. T. Witt (1971): Electrochromism of chlorophylls and carotenoids in multilayers and in chloroplasts
Type: article by Die Naturwissenschaften.
link: http://www.ncbi.nlm.nih.gov/pubmed/5110404

J. H. Golbeck Photosynthetic Reaction Centers: So little time, so much to do
Type: article

J. M. Berg, L. Stryer, J. L. Tymoczko (2007): Biochemie
Type: book by Spektrum Akademischer Verlag.

R. D. Sjolund, D. D. Smith (1974): Freeze-fracture studies of photosynthetically deficient "supergranal" chloroplasts in tissue cultures containing virus-like particles
Type: article by The Journal of Cell Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/4809243

M. Diez, B. Zimmermann, M. Börsch, M. König, E. Schweinberger, S. Steigmiller, R. Reuter, S. Felekyan, V. Kudryavtsev, C. A.M Seidel, others (2004): Proton-powered subunit rotation in single membrane-bound F 0 F {1-ATP} synthase
Type: article by Nature structural & molecular biology.

P. Gräber, H. T. Witt (1975): Direct measurement of the protons pumped into the inner phase of the functional membrane of photosynthesis per electron transfer
Type: article by {FEBS} Letters.
doi: 10.1016/0014-5793(75)80371-1

W. Junge (2004): Protons, Proteins and {ATP}
Type: article by Photosynthesis Research.
doi: 10.1023/B:PRES.0000030677.98474.74
link: http://dx.doi.org/10.1023/B:PRES.0000030677.98474.74
Abstract:

Abstract The machinery of life has been disclosed in the second half of the 20th century to a degree not in the least envisioned previously

by even the most daring players in this field. It has been extremely rewarding to start out from the fogs and to enjoy the brightness at the end of one's active career. Perhaps the most astounding lesson to learn is how conservative and modular is the construction of key devices. Oxidative and photophosphorylation are carried out by {ATP} synthase, which is unique in converting electrochemical, mechanical and chemical forms of energy within one nano-machine. This complex protein consists of more than 20 polypeptides of at least eight different kinds. Still, its activity survives in engineered chimerical constructs joining parts from organisms that underwent billions of years of separate evolution. The path of discovery of its structure and function is sketched here from a personal viewpoint. It has been a long way from before-structure-bioenergetics to the post-structural one (which now dominates the biology textbooks), but there is still a long way to go for a rigorous physical understanding. The author has been privileged to enjoy the friendship, cooperation and competition of excellent scientists from widely different backgrounds and expertise.

J. Deisenhofer, O. Epp, K. Miki, R. Huber, H. Michel (1985): Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3Å resolution
Type: article by Nature.
doi: 10.1038/318618a0
link: http://adsabs.harvard.edu/abs/1985Natur.318..618D

W. Junge, H. Lill, S. Engelbrecht (1997): {ATP} synthase: an electrochemical ransducer with rotatory mechanics
Type: article by Trends in Biochemical Sciences.
doi: 10.1016/S0968-0004(97)01129-8

B. Kok, B. Forbush, M. McGloin (1970): Cooperation of charges in photosynthetic O2 {evolution-I.} A linear four step mechanism
Type: article by Photochemistry and Photobiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/5456273

T. Ritz, A. Damjanovic, K. Schulten (2002): The Quantum Physics of Photosynthesis
Type: article by {ChemPhysChem}.
doi: 10.1002/1439-7641(20020315)3:3<243::AID-CPHC243>3.0.CO;2-Y
link: http://dx.doi.org/10.1002/1439-7641(20020315)3:3<243::AID-CPHC243>3.0.CO;2-Y
Abstract:

Biological cells contain nanoscale machineries that exhibit a unique combination of high efficiency, high adaptability to changing environmental conditions, and high reliability. Recent progress in obtaining atomically resolved structures provide an opportunity for an atomic-level explanation of the biological function of cellular machineries and the underlying physical mechanisms. A prime example in this regard is the apparatus with which purple bacteria harvest the light of the sun. Its highly symmetrical architecture and close interplay of biological functionality with quantum physical processes allow an illuminating demonstration of the fact that properties of living beings ultimately rely on and are determined by the laws of physics.

Kapitel 31

H. Kuhn (1986): Electron transfer mechanism in the reaction center of photosynthetic bacteria
Type: article by Physical Review. A.
link: http://www.ncbi.nlm.nih.gov/pubmed/9897660

R. A. Markus, N. Sutin (1985): Electron transfer in chemistry and biology
Type: article by Biochim Biophys Acta.

T. Förster (1948): Zwischenmolekulare Energiewanderung und Fluoreszenz
Type: article by Annalen der Physik.
link: http://adsabs.harvard.edu/abs/1948AnP...437...55F
Abstract:

In Weiterentwicklung früherer Theorien von J. und F. Perrin und

klassischphysikalischer überlegungen des Verfassers wird eine quantenmechanische Behandlung des Übergangs von Elektronenanregungsenergie zwischen gleichartigen Molek�len in Lösung gegeben. Der kritische Molekülabstand, unterhalb dessen der Übergang während der Anregungsdauer stattfindet, läßt sich aus den Absorptions- und Fluoreszenzspektren und der Anregungsdauer der Moleküle berechnen. Für Fluorescein und Chlorophyll a ergeben sich Werte von 50 bzw. 80 {�E,} entsprechend den mittleren Molekülabständen in Lösungen von 3,2 . 10-3 bzw. 7,7 . 10-4 {Molen/Liter.} Für die Bereiche oberhalb und unterhalb der kritischen Konzentration werden Formeln zur Berechnung der Energieabwanderung vom Primärmolekül angegeben, die mit den vorliegenden Messungen der Konzentrationsdepolarisation der Fluoreszenz gut Übereinstimmen. Die Anwendung auf analoge Energiewanderungsprobleme in Molekülkristallen und im Assimilationsapparat der Pflanze wird diskutiert.

H. Haken, H. C. Wolf (2006): Molekülphysik und Quantenchemie: Einführung in die experimentellen und theoretischen Grundlagen
Type: book by Springer, Berlin.

N. J. Turro (1978): Modern Molecular Photochemistry
Type: book by {Benjamin/Cummings} {Pub.Co.,U.S.}.

H. Kuhn (1982): Energieübertragungsmechanismen
Type: incollection

J. R. Lakowicz (2006): Principles of Fluorescence Spectroscopy
Type: book by Springer, Berlin.

W. Schmidt (2000): Optische Spektroskopie. Eine Einführung
Type: book by {Wiley-VCH}.

M. Born, R. Oppenheimer (1927): Zur Quantentheorie der Molekeln
Type: article by Annalen der Physik.

J. Jortner (1980): Dynamics of electron transfer in bacterial photosynthesis
Type: article by Biochimica Et Biophysica Acta.
link: http://www.ncbi.nlm.nih.gov/pubmed/7018575

H. Kuhn (1948): Elektronengasmodell zur quantitativen Deutung der Lichtabsorption von organischen Farbstoffen I
Type: article by Helvetica Chimica Acta.
doi: 10.1002/hlca.19480310602
link: http://dx.doi.org/10.1002/hlca.19480310602
Abstract:

Die Lage des Maximums der ersten (im Sichtbaren liegenden) Absorptionsbande von symmetrischen Cyaninfarbstoffen wird ermittelt unter Zugrundelegung eines Modells der Farbstoffmolekel, welches analog ist zu dem insbesondere von Sommerfeld als Modell f�r das Metall verwendeten Bild des freien Elektronengases. Die {pi-Elektronengas} der Polymethinkette werden als eindimensionales, freies Elektronengas betrachtet, welches sich der Polymethinkette entlang hinzieht.

J. B. Birks (1970): Photophysics of Aromatic Molecules
Type: book by John Wiley & Sons Ltd.

J. N. Murrell (1967): Elektronenspektren Organischer Moleküle.
Type: book by Bibliographisches Institut.

C. C. Moser, J. M. Keske, K. Warncke, R. S. Farid, P. L. Dutton (1992): Nature of biological electron transfer
Type: article by Nature.
doi: 10.1038/355796a0
link: http://www.ncbi.nlm.nih.gov/pubmed/1311417
Abstract:

Powerful first-order analysis of intraprotein electron transfer is developed from electron-transfer measurements both in biological and in chemical systems. A variation of 20 A in the distance between donors and acceptors in protein changes the electron-transfer rate by 10(12)-fold. Protein presents a uniform electronic barrier to electron tunnelling and a uniform nuclear characteristic frequency, properties similar to an organic glass. Selection of distance, free energy and reorganization energy are sufficient to define rate and directional specificity of biological electron transfer, meeting physiological requirements in diverse systems.

D. L. Dexter (1953): A Theory of Sensitized Luminescence in Solids
Type: article by Journal of Chemical Physics.
link: http://adsabs.harvard.edu/abs/1953JChPh..21..836D

A. Kawski On the estimation of excited-state dipole moments from solvatochromic shifts of absorption and fluorescence spectra
Type: article

G. W. Robinson, R. P. Frosch (1963): Electronic Excitation Transfer and Relaxation
Type: article by The Journal of Chemical Physics.
doi: 10.1063/1.1733823
link: http://link.aip.org/link/?JCP/38/1187/1

R. C. Hilborn (2002): Einstein coefficients, cross sections, f values, dipole moments, and all that
Type: article by physics/0202029.
link: http://arxiv.org/abs/physics/0202029
Abstract:

The relationships among various parameters describing the strength of optical transitions in atoms and molecules are reviewed. The application of these parameters to the description of the interaction between nearly monochromatic, directional light beams and atoms and molecules is given careful attention. Common pitfalls in relating these parameters are pointed out. This is a revised {(February,} 2002) version of a paper that originally appeared in Am. J. Phys. 50, 982-986 (1982).

T. Ritz, A. Damjanovic, K. Schulten (2002): The Quantum Physics of Photosynthesis
Type: article by {ChemPhysChem}.
doi: 10.1002/1439-7641(20020315)3:3<243::AID-CPHC243>3.0.CO;2-Y
link: http://dx.doi.org/10.1002/1439-7641(20020315)3:3<243::AID-CPHC243>3.0.CO;2-Y
Abstract:

Biological cells contain nanoscale machineries that exhibit a unique combination of high efficiency, high adaptability to changing environmental conditions, and high reliability. Recent progress in obtaining atomically resolved structures provide an opportunity for an atomic-level explanation of the biological function of cellular machineries and the underlying physical mechanisms. A prime example in this regard is the apparatus with which purple bacteria harvest the light of the sun. Its highly symmetrical architecture and close interplay of biological functionality with quantum physical processes allow an illuminating demonstration of the fact that properties of living beings ultimately rely on and are determined by the laws of physics.

A. J. Hoff, J. Deisenhofer (1997): Photophysics of photosynthesis. Structure and spectroscopy of reaction centers of purple bacteria
Type: article by Physics Reports.
doi: 10.1016/S0370-1573(97)00004-5

Kapitel 32

D. T. Kemp (1978): Stimulated acoustic emissions from within the human auditory system
Type: article by The Journal of the Acoustical Society of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/744838
Abstract:

A new auditory phenomenon has been identified in the acoustic impulse response of the human ear. Using a signal averaging technique, a study has been made of the response of the closed external acoustic meatus to acoustic impulses near to the threshold of audibility. Particular attention has been paid to the waveform of the response at post excitation times in excess of 5 ms. No previous worker appears to have extended observations into this region. The response observed after about 5 ms is not a simple extension of the initial response attributable to the middle ear. The oscillatory response decay time constant was found to change from approximately 1 ms to over 12 ms at about this time. The slowly decaying response component was present in all normal ears tested, but was not present in ears with cochlear deafness. This component of the response appears to have its origin in some nonlinear mechanism probably located in the cochlea, responding mechanically to auditory stimulation, and dependent upon the normal functioning of the cochlea transduction process. A cochlear reflection hypothesis received some support from these results.

H. Helmholtz (1954): On the Sensations of Tone
Type: book by Dover Pubns.

J. Nicholls (2001): From Neuron to Brain: A Cellular and Molecular Approach to the Function of the Nervous System
Type: book by Palgrave Macmillan.

L. Robles, M. A. Ruggero (2001): Mechanics of the mammalian cochlea
Type: article by Physiological Reviews.
link: http://www.ncbi.nlm.nih.gov/pubmed/11427697
Abstract:

In mammals, environmental sounds stimulate the auditory receptor, the cochlea, via vibrations of the stapes, the innermost of the middle ear ossicles. These vibrations produce displacement waves that travel on the elongated and spirally wound basilar membrane {(BM).} As they travel, waves grow in amplitude, reaching a maximum and then dying out. The location of maximum {BM} motion is a function of stimulus frequency, with high-frequency waves being localized to the "base" of the cochlea (near the stapes) and low-frequency waves approaching the "apex" of the cochlea. Thus each cochlear site has a characteristic frequency {(CF),} to which it responds maximally. {BM} vibrations produce motion of hair cell stereocilia, which gates stereociliar transduction channels leading to the generation of hair cell receptor potentials and the excitation of afferent auditory nerve fibers. At the base of the cochlea, {BM} motion exhibits a {CF-specific} and level-dependent compressive nonlinearity such that responses to low-level, {near-CF} stimuli are sensitive and sharply frequency-tuned and responses to intense stimuli are insensitive and poorly tuned. The high sensitivity and sharp-frequency tuning, as well as compression and other nonlinearities (two-tone suppression and intermodulation distortion), are highly labile, indicating the presence in normal cochleae of a positive feedback from the organ of Corti, the "cochlear amplifier." This mechanism involves forces generated by the outer hair cells and controlled, directly or indirectly, by their transduction currents. At the apex of the cochlea, nonlinearities appear to be less prominent than at the base, perhaps implying that the cochlear amplifier plays a lesser role in determining apical mechanical responses to sound. Whether at the base or the apex, the properties of {BM} vibration adequately account for most frequency-specific properties of the responses to sound of auditory nerve fibers.

G. Neuweiler (1982): Die Echoortung
Type: article by Biophysik, 2nd edn. Springer, Berlin Heidelberg New York.

W. S. Rhode (1971): Observations of the vibration of the basilar membrane in squirrel monkeys using the Mössbauer technique
Type: article by The Journal of the Acoustical Society of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/4994693

E. Zwicker, G. Manley (1982): challrezeption am Beispiel der Säugetiere und Menschen
Type: incollection

R. F. Schmidt, G. Thews, F. Lang (2000): Physiologie des Menschen
Type: book by Springer Berlin.


Kapitel 33

R. Skalak, Sh. Chien (1986): Handbook of Bioengineering
Type: book by {McGraw-Hill,} Maidenh..

G. von Bekesy (1989): Experiments in Hearing
Type: book by American Institute of Physics.

O. F. Ranke (1950): Theory of Operation of the Cochlea: A Contribution to the Hydrodynamics of the Cochlea
Type: article by The Journal of the Acoustical Society of America.
doi: 10.1121/1.1906688
link: http://link.aip.org/link/?JAS/22/772/1
Abstract:

This paper presents a short summary of calculations on the vibrations of the cochlear partition (basilar membrane). It is possible to determine the shape, velocity, and amplitude distribution of the traveling waves running from the stapes to the inner ear. Furthermore, it is shown that the calculated vibration pattern is in agreement with observations made on the human cochlea and on models of human inner ears. In particular, analogies between the waves in the inner ear and on the seashore are pointed out. These analogies show the importance of the velocities of propagation for the excitation of the hearing nerve cells.

L. Robles, M. A. Ruggero (2001): Mechanics of the mammalian cochlea
Type: article by Physiological Reviews.
link: http://www.ncbi.nlm.nih.gov/pubmed/11427697
Abstract:

In mammals, environmental sounds stimulate the auditory receptor, the cochlea, via vibrations of the stapes, the innermost of the middle ear ossicles. These vibrations produce displacement waves that travel on the elongated and spirally wound basilar membrane {(BM).} As they travel, waves grow in amplitude, reaching a maximum and then dying out. The location of maximum {BM} motion is a function of stimulus frequency, with high-frequency waves being localized to the "base" of the cochlea (near the stapes) and low-frequency waves approaching the "apex" of the cochlea. Thus each cochlear site has a characteristic frequency {(CF),} to which it responds maximally. {BM} vibrations produce motion of hair cell stereocilia, which gates stereociliar transduction channels leading to the generation of hair cell receptor potentials and the excitation of afferent auditory nerve fibers. At the base of the cochlea, {BM} motion exhibits a {CF-specific} and level-dependent compressive nonlinearity such that responses to low-level, {near-CF} stimuli are sensitive and sharply frequency-tuned and responses to intense stimuli are insensitive and poorly tuned. The high sensitivity and sharp-frequency tuning, as well as compression and other nonlinearities (two-tone suppression and intermodulation distortion), are highly labile, indicating the presence in normal cochleae of a positive feedback from the organ of Corti, the "cochlear amplifier." This mechanism involves forces generated by the outer hair cells and controlled, directly or indirectly, by their transduction currents. At the apex of the cochlea, nonlinearities appear to be less prominent than at the base, perhaps implying that the cochlear amplifier plays a lesser role in determining apical mechanical responses to sound. Whether at the base or the apex, the properties of {BM} vibration adequately account for most frequency-specific properties of the responses to sound of auditory nerve fibers.

J. Tonndorf (1960): Shearing Motion in Scala Media of Cochlear Models
Type: article by The Journal of the Acoustical Society of America.
doi: 10.1121/1.1908025
link: http://link.aip.org/link/?JAS/32/238/1
Abstract:

In 1953, Bekesy first reported the occurrence of shearing motion within the cochlear duct and furthermore the notion that it is this mode of motion which constitutes the adequate stimulus for the hair cells. There were two modes of shear motion: radially directed in the region proximal to the place of maximal amplitude of the traveling-wave pattern, and longitudinally directed distal to that {point.This} phenomenon was studied in cochlear models. The envelopes over both modes of shear motion were found to be much smaller than that over the traveling-wave pattern. A simple explanation presented itself. The direction of the shearing motion in each domain coincides with the dominant curvature produced by the traveling waves in that section of the cochlear {duct.Earlier,} it had been shown that under the effect of Bekesy's eddies, i.e., at higher driving amplitudes, the displacement pattern of the cochlear partition becomes asymmetrical. This asymmetry produces a dc-shift in both domains of shear motion: in an outward direction within the domain of radial shear and in an apical direction within the domain of longitudinal shear. However, when the round window was driven, both directions of the dc-components were reversed. The latter finding aided in establishing the causal relationship mentioned in the foregoing.

J. Zwislocki (1953): Review of Recent Mathematical Theories of Cochlear Dynamics
Type: article by The Journal of the Acoustical Society of America.
doi: 10.1121/1.1907170
link: http://link.aip.org/link/?JAS/25/743/1
Abstract:

An analysis of several theories of cochlear mechanics has been attempted on the basis of general hydrodynamic theory. The theories are divided into two classes according to the mathematical treatment. The first class assumes that transverse waves propagated along the cochlea are long in comparison to the cross-sectional dimension of the canal: all theories of this class can be deduced from one differential equation when the emphasis put on different factors. The second class assumes that the waves are relatively not long, and the mathematical treatment becomes a boundary problem to which no exact solution has yet been found. The analysis of the individual theories indicates a certain convergence of opinions, and it is clear that definite progress has been achieved toward an understanding of the dynamic behavior of the cochlea. In spite of this trend, however, no one of the theories seems entirely satisfactory.

J. B. Allen, M. M. Sondhi (1979): Cochlear macromechanics: time domain solutions
Type: article by The Journal of the Acoustical Society of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/489828
Abstract:

In this paper we report on a new method of solving a previous derived, two-dimensional model, integral equation for basilar membrane {(BM)} motion. The method uses a recursive algorithm for the solution of an initial-value problem in the time domain, combined with a fast Fourier transform {(FFT)} convolution in the space domain at each time step. Thus, the method capitalizes on the high speed and accuracy of the {FFT} yet allows the {BM} to have nonlinear mechanical properties. Using the new method we compute (linear) solutions for various choices of model parameters and compare the results to the experimental measurements of Rhode. {[J.} Acoust. Soc. Am. 49, 1218-1231 (1971)]. We also demonstrate the effect of including longitudinal stiffness along the {BM} and conclude that it is useful in matching the high-frequency slope as measured by Rhode.


Kapitel 34

T. Hasson, P. G. Gillespie, J. A. Garcia, R. B. MacDonald, Y. Zhao, A. G. Yee, M. S. Mooseker, D. P. Corey (1997): Unconventional myosins in inner-ear sensory epithelia
Type: article by The Journal of Cell Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/9182663
Abstract:

To understand how cells differentially use the dozens of myosin isozymes present in each genome, we examined the distribution of four unconventional myosin isozymes in the inner ear, a tissue that is particularly reliant on actin-rich structures and unconventional myosin isozymes. Of the four isozymes, each from a different class, three are expressed in the hair cells of amphibia and mammals. In stereocilia, constructed of cross-linked F-actin filaments, {myosin-Ibeta} is found mostly near stereociliary tips, {myosin-VI} is largely absent, and {myosin-VIIa} colocalizes with crosslinks that connect adjacent stereocilia. In the cuticular plate, a meshwork of actin filaments, {myosin-Ibeta} is excluded, {myosin-VI} is concentrated, and modest amounts of {myosin-VIIa} are present. These three myosin isozymes are excluded from other actin-rich domains, including the circumferential actin belt and the cortical actin network. A member of a fourth class, {myosin-V,} is not expressed in hair cells but is present at high levels in afferent nerve cells that innervate hair cells. Substantial amounts of {myosins-Ibeta,} {-VI,} and {-VIIa} are located in a pericuticular necklace that is largely free of F-actin, squeezed between (but not associated with) actin of the cuticular plate and the circumferential belt. Our localization results suggest specific functions for three hair-cell myosin isozymes. As suggested previously, {myosin-Ibeta} probably plays a role in adaptation; concentration of {myosin-VI} in cuticular plates and association with stereociliary rootlets suggest that this isozyme participates in rigidly anchoring stereocilia; and finally, colocalization with cross-links between adjacent stereocilia indicates that {myosin-VIIa} is required for the structural integrity of hair bundles.

G. A. Manley (2000): Cochlear mechanisms from a phylogenetic viewpoint
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.97.22.11736
link: http://www.ncbi.nlm.nih.gov/pubmed/11050203
Abstract:

The hearing organ of the inner ear was the last of the paired sense organs of amniotes to undergo formative evolution. As a mechanical sensory organ, the inner-ear hearing organ's function depends highly on its physical structure. Comparative studies suggest that the hearing organ of the earliest amniote vertebrates was small and simple, but possessed hair cells with a cochlear amplifier mechanism, electrical frequency tuning, and incipient micromechanical tuning. The separation of the different groups of amniotes from the stem reptiles occurred relatively early, with the ancestors of the mammals branching off first, approximately 320 million years ago. The evolution of the hearing organ in the three major lines of the descendents of the stem reptiles (e.g., mammals, birds-crocodiles, and lizards-snakes) thus occurred independently over long periods of time. Dramatic and parallel improvements in the middle ear initiated papillar elongation in all lineages, accompanied by increased numbers of sensory cells with enhanced micromechanical tuning and group-specific hair-cell specializations that resulted in unique morphological configurations. This review aims not only to compare structure and function across classification boundaries (the comparative approach), but also to assess how and to what extent fundamental mechanisms were influenced by selection pressures in times past (the phylogenetic viewpoint).

J. F. Ashmore (1987): A fast motile response in guinea-pig outer hair cells: the cellular basis of the cochlear amplifier
Type: article by The Journal of Physiology.
link: http://www.ncbi.nlm.nih.gov/pubmed/3656195
Abstract:

1. Outer hair cells from the cochlea of the guinea-pig were isolated and their motile properties studied in short-term culture by the whole-cell variant of the patch recording technique. 2. Cells elongated and shortened when subjected to voltage steps. Cells from both high- and low-frequency regions of the cochlea responded with an elongation when hyperpolarized and a shortening when depolarized. The longitudinal motion of the cell was measured by a differential photosensor capable of responding to motion frequencies 0-40 {kHz.} 3. Under voltage clamp the length change of the cell was graded with command voltage over a range +/- 2 microns (approximately 4% of the length) for cells from the apical turns of the cochlea. The mean sensitivity of the movement was 2.11 {nm/pA} injected current, or 19.8 {nm/mV} membrane polarization. 4. The kinetics of the cell length change during a voltage step were measured. Stimulated at their basal end, cells from the apical (low-frequency) cochlear turns responded with a latency of between 120 and 255 microseconds. The cells thereafter elongated exponentially by a process which could be characterized by three time constants, one with value 240 microseconds, and a second in the range 1.3-2.8 ms. A third time constant with a value 20-40 ms characterized a slower component which may represent osmotic changes. 5. Consistent with the linearity shown to voltage steps, sinusoidal stimulation of the cell generated movements which could be measured at frequencies above 1 {kHz.} The phase of the movement relative to the stimulus continued to grow with frequency, suggesting the presence of an absolute delay in the response of about 200 microseconds. 6. The electrically stimulated movements were insensitive to the ionic composition of the cell, manipulated by dialysis from the patch pipette. The responses occurred when the major cation was K+ or Na+ in the pipette. Loading the cell with {ATP-free} solutions or calcium buffers did not inhibit the response. 7. It is concluded that interaction between actin and myosin, although present in the cell, is unlikely to account for the cell motility. Instead, it is proposed that outer hair cell motility is associated with structures in the cell cortex. The implications for cochlear mechanics of such force generation in outer hair cells are discussed.

B. N. Evans, P. Dallos (1993): Stereocilia displacement induced somatic motility of cochlear outer hair cells
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/8378305
Abstract:

Outer hair cells, isolated from mammalian cochleas, are known to respond to electrical stimulation with elongation or contraction of the cell's cylindrical soma. It is assumed that such shape changes, when driven by the cell's receptor potential in vivo, are a part of the feedback process that underlies cochlear amplification. To date it has not been possible to demonstrate somatic shape changes upon normal mechanical stimulation of the cell--i.e., the deflection of its hair bundle. We show here that mechanically induced hair-bundle deflection produces somatic motility of the cell. Such motility is dependent upon a functioning forward transducer process and disappears upon interference with transduction. The motile response also reflects the hair bundle's known directional sensitivity. This demonstration of mechanically driven motility indicates that the cell may possess capabilities to affect its mechanical environment under control of its own receptor potential and, thereby, participate in a local cochlear feedback process.

M. C. Holley (1996): Outer hair cell motility
Type: article by Springer Handbook of Auditory Research.

G. Huang, J. Santos-Sacchi (1993): Mapping the distribution of the outer hair cell motility voltage sensor by electrical amputation
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(93)81248-7
link: http://www.ncbi.nlm.nih.gov/pubmed/8298046
Abstract:

The outer hair cell {(OHC)} possesses a nonlinear charge movement whose characteristics indicate that it represents the voltage sensor responsible for {OHC} mechanical activity. {OHC} mechanical activity is known to exist along a restricted extent of the cell's length. We have used a simultaneous partitioning microchamber and whole cell voltage clamp technique to electrically isolate sections of the {OHC} membrane and find that the nonlinear charge movement is also restricted along the cell's length. Apical and basal portions of the {OHC} are devoid of voltage sensors, corresponding to regions of the cell where the subsurface cisternae and/or the mechanical responses are absent. We conclude that the physical domain of the motility voltage sensor corresponds to that of the mechanical effector and speculate that sensor and effector reside within one intra membranous molecular species, perhaps an evolved nonconducting or poorly conducting voltage-dependent ion channel.

P. Martin, A. J. Hudspeth (2001): Compressive nonlinearity in the hair bundle's active response to mechanical stimulation
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.251530498
link: http://www.ncbi.nlm.nih.gov/pubmed/11724944
Abstract:

The auditory system's ability to interpret sounds over a wide range of amplitudes rests on the nonlinear responsiveness of the ear. Whether measured by basilar-membrane vibration, nerve-fiber activity, or perceived loudness, the ear is most sensitive to small signals and grows progressively less responsive as stimulation becomes stronger. Seeking a correlate of this behavior at the level of mechanoelectrical transduction, we examined the responses of hair bundles to direct mechanical stimulation. As reported by the motion of an attached glass fiber, an active hair bundle from the bullfrog's sacculus oscillates spontaneously. Sinusoidal movement of the fiber's base by as little as +/-1 nm, corresponding to the application at the bundle's top of a force of +/-0.3 {pN,} causes detectable phase-locking of the bundle's oscillations to the stimulus. Although entrainment increases as the stimulus grows, the amplitude of the hair-bundle movement does not rise until phase-locking is nearly complete. A bundle is most sensitive to stimulation at its frequency of spontaneous oscillation. Far from that frequency, the sensitivity of an active hair bundle resembles that of a passive bundle. Over most of its range, an active hair bundle's response grows as the one-third power of the stimulus amplitude; the bundle's sensitivity declines accordingly in proportion to the negative two-thirds power of the excitation. This scaling behavior, also found in the response of the mammalian basilar membrane to sound, signals the operation of an amplificatory process at the brink of an oscillatory instability, a Hopf bifurcation.

J. S. Oghalai, H. B. Zhao, J. W. Kutz, W. E. Brownell (2000): Voltage- and tension-dependent lipid mobility in the outer hair cell plasma membrane
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/10650000
Abstract:

The mechanism responsible for electromotility of outer hair cells in the ear is unknown but is thought to reside within the plasma membrane. Lipid lateral diffusion in the outer hair cell plasma membrane is a sigmoidal function of transmembrane potential and bathing media osmolality. Cell depolarization or hyposmotic challenge shorten the cell and reduce membrane fluidity by half. Changing the membrane tension with amphipathic drugs results in similar reductions. These dynamic changes in membrane fluidity represent the modulation of membrane tension by lipid-protein interactions. The voltage dependence may be associated with the force-generating motors that contribute to the exquisite sensitivity of mammalian hearing.

J. Zheng, W. Shen, D. Z. He, K. B. Long, L. D. Madison, P. Dallos (2000): Prestin is the motor protein of cochlear outer hair cells
Type: article by Nature.
doi: 10.1038/35012009
link: http://www.ncbi.nlm.nih.gov/pubmed/10821263
Abstract:

The outer and inner hair cells of the mammalian cochlea perform different functions. In response to changes in membrane potential, the cylindrical outer hair cell rapidly alters its length and stiffness. These mechanical changes, driven by putative molecular motors, are assumed to produce amplification of vibrations in the cochlea that are transduced by inner hair cells. Here we have identified an abundant complementary {DNA} from a gene, designated Prestin, which is specifically expressed in outer hair cells. Regions of the encoded protein show moderate sequence similarity to pendrin and related sulphate/anion transport proteins. Voltage-induced shape changes can be elicited in cultured human kidney cells that express prestin. The mechanical response of outer hair cells to voltage change is accompanied by a 'gating current', which is manifested as nonlinear capacitance. We also demonstrate this nonlinear capacitance in transfected kidney cells. We conclude that prestin is the motor protein of the cochlear outer hair cell.

J. Gao, X. Wang, X. Wu, S. Aguinaga, K. Huynh, S. Jia, K. Matsuda, M. Patel, J. Zheng, M. Cheatham, D. Z. He, P. Dallos, J. Zuo (2007): Prestin-based outer hair cell electromotility in knockin mice does not appear to adjust the operating point of a cilia-based amplifier
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.0700356104
link: http://www.ncbi.nlm.nih.gov/pubmed/17640919
Abstract:

The remarkable sensitivity and frequency selectivity of the mammalian cochlea is attributed to a unique amplification process that resides in outer hair cells {(OHCs).} Although the mammalian-specific somatic motility is considered a substrate of cochlear amplification, it has also been proposed that somatic motility in mammals simply acts as an operating-point adjustment for the ubiquitous stereocilia-based amplifier. To address this issue, we created a mouse model in which a mutation {(C1)} was introduced into the {OHC} motor protein prestin, based on previous results in transfected cells. In {C1/C1} knockin mice, localization of C1-prestin, as well as the length and number of {OHCs,} were all normal. In {OHCs} isolated from {C1/C1} mice, nonlinear capacitance and somatic motility were both shifted toward hyperpolarization, so that, compared with {WT} controls, the amplitude of cycle-by-cycle (alternating, or {AC)} somatic motility remained the same, but the unidirectional {(DC)} component reversed polarity near the {OHC's} presumed in vivo resting membrane potential. No physiological defects in cochlear sensitivity or frequency selectivity were detected in {C1/C1} or C1/+ mice. Hence, our results do not support the idea that {OHC} somatic motility adjusts the operating point of a stereocilia-based amplifier. However, they are consistent with the notion that the {AC} component of {OHC} somatic motility plays a dominant role in mammalian cochlear amplification.

M. C. Holley, F. Kalinec, B. Kachar (1992): Structure of the cortical cytoskeleton in mammalian outer hair cells
Type: article by Journal of Cell Science.
link: http://www.ncbi.nlm.nih.gov/pubmed/1506434
Abstract:

The cortical cytoskeletal lattice in outer hair cells is a two-dimensional actin-based structure, which can be labelled with rhodamine/phalloidin and disrupted by the enzyme deoxyribonuclease I. Structural information from thin sectioned, freeze-etched and negatively stained preparations shows that it is based upon two types of filament that form a cross-linked lattice of circumferential filaments. The cross-links are 70-80 nm long. Measurements of the spacing between circumferential filaments suggest that the lattice is stiffer circumferentially than it is longitudinally. Analysis of the orientation of circumferential filaments shows that it is composed of discrete domains of up to 10 microns 2. Relative movements between domains could allow substantial changes of cell shape without disrupting the unit structure of the lattice, thus allowing the cell cortex to retain its elastic responses to high-frequency deformations.

P. G. Gillespie, R. G. Walker (2001): Molecular basis of mechanosensory transduction
Type: article by Nature.
doi: 10.1038/35093011
link: http://dx.doi.org/10.1038/35093011
Abstract:

Mechanotransduction — a cell's conversion of a mechanical stimulus into an electrical signal — reveals vital features of an organism's environment. From hair cells and skin mechanoreceptors in vertebrates, to bristle receptors in flies and touch receptors in worms, mechanically sensitive cells are essential in the life of an organism. The scarcity of these cells and the uniqueness of their transduction mechanisms have conspired to slow molecular characterization of the ensembles that carry out mechanotransduction. But recent progress in both invertebrates and vertebrates is beginning to reveal the identities of proteins essential for transduction.

J. Howard, A. J. Hudspeth (1987): Mechanical relaxation of the hair bundle mediates adaptation in mechanoelectrical transduction by the bullfrog's saccular hair cell
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/3495007
Abstract:

Mechanoelectrical transduction by hair cells of the frog's internal ear displays adaptation: the electrical response to a maintained deflection of the hair bundle declines over a period of tens of milliseconds. We investigated the role of mechanics in adaptation by measuring changes in hair-bundle stiffness following the application of force stimuli. Following step stimulation with a glass fiber, the hair bundle of a saccular hair cell initially had a stiffness of approximately equal to 1 {mN} X m-1. The stiffness then declined to a steady-state level near 0.6 {mN} X m-1 with a time course comparable to that of adaptation in the receptor current. The hair bundle may be modeled as the parallel combination of a spring, which represents the rotational stiffness of the stereocilia, and a series spring and dashpot, which respectively, represent the elastic element responsible for channel gating and the apparatus for adaptation.

E. Neher, A. Marty (1982): Discrete changes of cell membrane capacitance observed under conditions of enhanced secretion in bovine adrenal chromaffin cells
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/6959149
Abstract:

The capacitance of the surface membrane of small adrenal chromaffin cells was measured with patch-clamp pipettes. Continuous and discrete changes of capacitance were observed. They were interpreted as changes of surface area connected to exocytotic or endocytotic processes. Most of the measurements were performed in the "whole-cell" recording configuration {[Hamill,} O. P., Marty, A., Neher, E., Sakmann, B. & Sigworth, F. J. (1981) Pflügers Arch. 391, 85-100], which allows the intracellular Ca2+ concentration to be controlled. With an internal solution highly buffered to low values of Ca2+ concentration (10 {nM),} the surface capacitance usually decreased and could not be markedly changed by electrical stimulation. At low buffering capacity and medium Ca2+ concentrations (0.1-1 {microM),} the capacitance measurement showed large fluctuations and discrete steps, reflecting both capacitance decrease and increase. A large transient increase of capacitance could be induced by electrical stimulation under these conditions. It was linked to Ca2+ currents through the membrane. Relatively large (2-6 x 10(-14) F) steps of capacitance decrease were common after extensive stimulation. The size distribution of step-like capacitance changes is well compatible with the idea that steps of capacitance increase reflect individual events of exocytosis of chromaffin granules, whereas steps of the opposite polarity reflect the formation of vesicles or vacuoles by endocytosis.

D. Oliver, D. Z. He, N. Klöcker, J. Ludwig, U. Schulte, S. Waldegger, J. P. Ruppersberg, P. Dallos, B. Fakler (2001): Intracellular anions as the voltage sensor of prestin, the outer hair cell motor protein
Type: article by Science {(New} York, {N.Y.)}.
doi: 10.1126/science.1060939
link: http://www.ncbi.nlm.nih.gov/pubmed/11423665
Abstract:

Outer hair cells {(OHCs)} of the mammalian cochlea actively change their cell length in response to changes in membrane potential. This electromotility, thought to be the basis of cochlear amplification, is mediated by a voltage-sensitive motor molecule recently identified as the membrane protein prestin. Here, we show that voltage sensitivity is conferred to prestin by the intracellular anions chloride and bicarbonate. Removal of these anions abolished fast voltage-dependent motility, as well as the characteristic nonlinear charge movement ("gating currents") driving the underlying structural rearrangements of the protein. The results support a model in which anions act as extrinsic voltage sensors, which bind to the prestin molecule and thus trigger the conformational changes required for motility of {OHCs.}

P. Martin, A. D. Mehta, A. J. Hudspeth (2000): Negative hair-bundle stiffness betrays a mechanism for mechanical amplification by the hair cell
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.210389497
link: http://www.ncbi.nlm.nih.gov/pubmed/11027302
Abstract:

Hearing and balance rely on the ability of hair cells in the inner ear to sense miniscule mechanical stimuli. In each cell, sound or acceleration deflects the mechanosensitive hair bundle, a tuft of rigid stereocilia protruding from the cell's apical surface. By altering the tension in gating springs linked to mechanically sensitive transduction channels, this deflection changes the channels' open probability and elicits an electrical response. To detect weak stimuli despite energy losses caused by viscous dissipation, a hair cell can use active hair-bundle movement to amplify its mechanical inputs. This amplificatory process also yields spontaneous bundle oscillations. Using a displacement-clamp system to measure the mechanical properties of individual hair bundles from the bullfrog's ear, we found that an oscillatory bundle displays negative slope stiffness at the heart of its region of mechanosensitivity. Offsetting the hair bundle's position activates an adaptation process that shifts the region of negative stiffness along the displacement axis. Modeling indicates that the interplay between negative bundle stiffness and the motor responsible for mechanical adaptation produces bundle oscillation similar to that observed. Just as the negative resistance of electrically excitable cells and of tunnel diodes can be embedded in a biasing circuit to amplify electrical signals, negative stiffness can be harnessed to amplify mechanical stimuli in the ear.

J. D. Axelrod (2008): Basal bodies, kinocilia and planar cell polarity
Type: article by Nat Genet.
doi: 10.1038/ng0108-10
link: http://dx.doi.org/10.1038/ng0108-10

P. Dallos, B. Fakler (2002): Prestin, a new type of motor protein
Type: article by Nature Reviews. Molecular Cell Biology.
doi: 10.1038/nrm730
link: http://www.ncbi.nlm.nih.gov/pubmed/11836512
Abstract:

Prestin, a transmembrane protein found in the outer hair cells of the cochlea, represents a new type of molecular motor, which is likely to be of great interest to molecular cell biologists. In contrast to enzymatic-activity-based motors, prestin is a direct voltage-to-force converter, which uses cytoplasmic anions as extrinsic voltage sensors and can operate at microsecond rates. As prestin mediates changes in outer hair cell length in response to membrane potential variations, it might be responsible for sound amplification in the mammalian hearing organ.

P. Martin, A. J. Hudspeth (1999): Active hair-bundle movements can amplify a hair cell's response to oscillatory mechanical stimuli
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/10588701
Abstract:

To enhance their mechanical sensitivity and frequency selectivity, hair cells amplify the mechanical stimuli to which they respond. Although cell-body contractions of outer hair cells are thought to mediate the active process in the mammalian cochlea, vertebrates without outer hair cells display highly sensitive, sharply tuned hearing and spontaneous otoacoustic emissions. In these animals the amplifier must reside elsewhere. We report physiological evidence that amplification can stem from active movement of the hair bundle, the hair cell's mechanosensitive organelle. We performed experiments on hair cells from the sacculus of the bullfrog. Using a two-compartment recording chamber that permits exposure of the hair cell's apical and basolateral surfaces to different solutions, we examined active hair-bundle motion in circumstances similar to those in vivo. When the apical surface was bathed in artificial endolymph, many hair bundles exhibited spontaneous oscillations of amplitudes as great as 50 nm and frequencies in the range 5 to 40 Hz. We stimulated hair bundles with a flexible glass probe and recorded their mechanical responses with a photometric system. When the stimulus frequency lay within a band enclosing a hair cell's frequency of spontaneous oscillation, mechanical stimuli as small as +/-5 nm entrained the hair-bundle oscillations. For small stimuli, the bundle movement was larger than the stimulus. Because the energy dissipated by viscous drag exceeded the work provided by the stimulus probe, the hair bundles powered their motion and therefore amplified it.

J. R. Holt, D. P. Corey (2000): Two mechanisms for transducer adaptation in vertebrate hair cells
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.97.22.11730
link: http://www.ncbi.nlm.nih.gov/pubmed/11050202
Abstract:

Deflection of the hair bundle atop a sensory hair cell modulates the open probability of mechanosensitive ion channels. In response to sustained deflections, hair cells adapt. Two fundamentally distinct models have been proposed to explain transducer adaptation. Both models support the notion that channel open probability is modulated by calcium that enters via the transduction channels. Both also suggest that the primary effect of adaptation is to shift the deflection-response {[I(X)]} relationship in the direction of the applied stimulus, thus maintaining hair bundle sensitivity. The models differ in several respects. They operate on different time scales: the faster on the order of a few milliseconds or less and the slower on the order of 10 ms or more. The model proposed to explain fast adaptation suggests that calcium enters and binds at or near the transduction channels to stabilize a closed conformation. The model proposed to explain the slower adaptation suggests that adaptation is mediated by an active, force-generating process that regulates the effective stimulus applied to the transduction channels. Here we discuss the evidence in support of each model and consider the possibility that both may function to varying degrees in hair cells of different species and sensory organs.

F. Mammano, J. F. Ashmore (1993): Reverse transduction measured in the isolated cochlea by laser Michelson interferometry
Type: article by Nature.
doi: 10.1038/365838a0
link: http://www.ncbi.nlm.nih.gov/pubmed/8413667
Abstract:

It is thought that the sensitivity of mammalian hearing depends on amplification of the incoming sound within the cochlea by a select population of sensory cells, the outer hair cells. It has been suggested that these cells sense displacements and feedback forces which enhance the basilar membrane motion by reducing the inherent damping of the cochlear partition. In support of this hypothesis, outer hair cells show membrane-potential-induced length changes at acoustic rates. This process has been termed 'reverse transduction'. For amplification, the forces should be large enough to move the basilar membrane. Using a displacement-sensitive interferometer, we tested this hypothesis in an isolated cochlea while stimulating the outer hair cells with current passed across the partition. We show here that the cochlear partition distorts under the action of electrically driven hair cell length changes and produces place-specific vibration of the basilar membrane of a magnitude comparable to that observed near auditory threshold (about 1 nm). Such measurements supply direct evidence that cochlear amplification arises from the properties of the outer hair cell population.

F. Jülicher, D. Andor, T. Duke (2001): Physical basis of two-tone interference in hearing
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: 10.1073/pnas.151257898
link: http://www.ncbi.nlm.nih.gov/pubmed/11481473
Abstract:

The cochlea uses active amplification to capture faint sounds. It has been proposed that the amplifier comprises a set of self-tuned critical oscillators: each hair cell contains a force-generating dynamical system that is maintained at the threshold of an oscillatory instability, or Hopf bifurcation. While the active response to a pure tone provides frequency selectivity, exquisite sensitivity, and wide dynamic range, its intrinsic nonlinearity causes tones of different frequency to interfere with one another in the cochlea. Here we determine the response to two tones, which provides a framework for understanding how the ear processes the more complex sounds of speech and music. Our calculations of two-tone suppression and the spectrum of distortion products generated by a critical oscillator accord with experimental observations of basilar membrane motion and the nervous response. We discuss how the response of a set of self-tuned oscillators, covering a range of characteristic frequencies, represents the structure of a complex sound. The frequency components of the stimulus can be inferred from the timing of neural spikes elicited by the vibrating hair cells. Passive prefiltering by the basilar membrane improves pitch discrimination by reducing interference between tones. Our analysis provides a general framework for examining the relation between the physical nature of the peripheral detection apparatus and psychophysical phenomena such as the sensation of dissonance and auditory illusions.

A. K. Rzadzinska, M. E. Schneider, C. Davies, G. P. Riordan, B. Kachar (2004): An actin molecular treadmill and myosins maintain stereocilia functional architecture and self-renewal
Type: article by The Journal of Cell Biology.
doi: 10.1083/jcb.200310055
link: http://www.ncbi.nlm.nih.gov/pubmed/15024034
Abstract:

We have previously shown that the seemingly static paracrystalline actin core of hair cell stereocilia undergoes continuous turnover. Here, we used the same approach of transfecting hair cells with actin-green fluorescent protein {(GFP)} and {espin-GFP} to characterize the turnover process. Actin and espin are incorporated at the paracrystal tip and flow rearwards at the same rate. The flux rates (approximately 0.002-0.04 actin subunits s(-1)) were proportional to the stereocilia length so that the entire staircase stereocilia bundle was turned over synchronously. Cytochalasin D caused stereocilia to shorten at rates matching paracrystal turnover. Myosins {VI} and {VIIa} were localized alongside the actin paracrystal, whereas myosin {XVa} was observed at the tips at levels proportional to stereocilia lengths. Electron microscopy analysis of the abnormally short stereocilia in the shaker 2 mice did not show the characteristic tip density. We argue that actin renewal in the paracrystal follows a treadmill mechanism, which, together with the myosins, dynamically shapes the functional architecture of the stereocilia bundle.

G. Frank, W. Hemmert, A. W. Gummer (1999): Limiting dynamics of high-frequency electromechanical transduction of outer hair cells
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/10200277
Abstract:

High-frequency resolution is one of the salient features of peripheral sound processing in the mammalian cochlea. The sensitivity originates in the active amplification of the travelling wave on the basilar membrane by the outer hair cells {(OHCs),} where electrically induced mechanical action of the {OHC} on a cycle-by-cycle basis is believed to be the crucial component. However, it is still unclear if this electromechanical action is sufficiently fast and can produce enough force to enhance mechanical tuning up to the highest frequencies perceived by mammals. Here we show that isolated {OHCs} in the microchamber configuration are able to overcome fluid forces with almost constant displacement amplitude and phase up to frequencies well above their place-frequency on the basilar membrane. The high-frequency limit of the electromotility, defined as the frequency at which the amplitude drops by 3 {dB} from its asymptotic low-frequency value, is inversely dependent on cell length. The frequency limit is at least 79 {kHz.} For frequencies up to 100 {kHz,} the electromotile response was specified by an overdamped {(Q} = 0.42) second-order resonant system. This finding suggests that the limiting factor for frequencies up to 100 {kHz} is not the speed of the motor but damping and inertia. The isometric force produced by the {OHC} was constant at least up to 50 {kHz,} with amplitudes as high as 53 {pN/mV} being observed. We conclude that the electromechanical transduction process of {OHCs} possesses the necessary high-frequency properties to enable amplification of the travelling wave over the entire hearing range.

Kapitel 35

J. Lidmar, L. Mirny, D. R. Nelson (2003): Virus shapes and buckling transitions in spherical shells
Type: article by Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics.
link: http://www.ncbi.nlm.nih.gov/pubmed/14682823
Abstract:

We show that the icosahedral packings of protein capsomeres proposed by Caspar and Klug for spherical viruses become unstable to faceting for sufficiently large virus size, in analogy with the buckling instability of disclinations in two-dimensional crystals. Our model, based on the nonlinear physics of thin elastic shells, produces excellent one-parameter fits in real space to the full three-dimensional shape of large spherical viruses. The faceted shape depends only on the dimensionless Foppl-von Kármán number {gamma=YR(2)/kappa,} where Y is the two-dimensional Young's modulus of the protein shell, kappa is its bending rigidity, and R is the mean virus radius. The shape can be parametrized more quantitatively in terms of a spherical harmonic expansion. We also investigate elastic shell theory for extremely large gamma, 10(3){textless}gamma{textless}10(8), and find results applicable to icosahedral shapes of large vesicles studied with freeze fracture and electron microscopy.

X. Agirrezabala, J. Martín-Benito, J. R. Castón, R. Miranda, J. M. Valpuesta, J. L. Carrascosa (2005): Maturation of phage T7 involves structural modification of both shell and inner core components
Type: article by The {EMBO} Journal.
doi: 10.1038/sj.emboj.7600840
link: http://www.ncbi.nlm.nih.gov/pubmed/16211007
Abstract:

The double-stranded {DNA} bacteriophages are good model systems to understand basic biological processes such as the macromolecular interactions that take place during the virus assembly and maturation, or the behavior of molecular motors that function during the {DNA} packaging process. Using cryoelectron microscopy and single-particle methodology, we have determined the structures of two phage T7 assemblies produced during its morphogenetic process, the {DNA-free} prohead and the mature virion. The first structure reveals a complex assembly in the interior of the capsid, which involves the scaffolding, and the core complex, which plays an important role in {DNA} packaging and is located in one of the phage vertices. The reconstruction of the mature virion reveals important changes in the shell, now much larger and thinner, the disappearance of the scaffolding structure, and important rearrangements of the core complex, which now protrudes the shell and interacts with the tail. Some of these changes must originate by the pressure exerted by the {DNA} in the interior of the head.

J. F. Conway, W. R. Wikoff, N. Cheng, R. L. Duda, R. W. Hendrix, J. E. Johnson, A. C. Steven (2001): Virus maturation involving large subunit rotations and local refolding
Type: article by Science {(New} York, {N.Y.)}.
doi: 10.1126/science.1058069
link: http://www.ncbi.nlm.nih.gov/pubmed/11326105
Abstract:

Large-scale conformational changes transform viral precursors into infectious virions. The structure of bacteriophage {HK97} capsid, {Head-II,} was recently solved by crystallography, revealing a catenated cross-linked topology. We have visualized its precursor, {Prohead-II,} by cryoelectron microscopy and modeled the conformational change by appropriately adapting {Head-II.} Rigid-body rotations ( approximately 40 degrees) cause switching to an entirely different set of interactions; in addition, two motifs undergo refolding. These changes stabilize the capsid by increasing the surface area buried at interfaces and bringing the cross-link-forming residues, initially approximately 40 angstroms apart, close together. The inner surface of {Prohead-II} is negatively charged, suggesting that the transition is triggered electrostatically by {DNA} packaging.

T. T. Nguyen, R. F. Bruinsma, W. M. Gelbart (2005): Elasticity theory and shape transitions of viral shells
Type: article by Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics.
link: http://www.ncbi.nlm.nih.gov/pubmed/16383661
Abstract:

Recently, continuum elasticity theory has been applied to explain the shape transition of icosahedral viral capsids--single-protein-thick crystalline shells--from spherical to "buckled" or faceted as their radius increases through a critical value determined by the competition between stretching and bending energies of a closed two-dimensional {(2D)} elastic network. In the present work we generalize this approach to capsids with nonicosahedral symmetries, e.g., spherocylindrical and conical shells. One key additional physical ingredient is the role played by nonzero spontaneous curvature. Another is associated with the special way in which the energy of the 12 topologically required fivefold sites depends on the "background" local curvature of the shell in which they are embedded. Systematic evaluation of these contributions leads to a shape "phase" diagram in which transitions are observed from icosahedral to spherocylindrical capsids as a function of the ratio of stretching to bending energies and of the spontaneous curvature of the {2D} protein network. We find that the transition from icosahedral to spherocylindrical symmetry is continuous or weakly first order near the onset of buckling, leading to extensive shape degeneracy. These results are discussed in the context of experimentally observed variations in the shapes of a variety of viral capsids.

N. Kol, Y. Shi, M. Tsvitov, D. Barlam, R. Z. Shneck, M. S. Kay, I. Rousso (2007): A stiffness switch in human immunodeficiency virus
Type: article by Biophysical Journal.
doi: 10.1529/biophysj.106.093914
link: http://www.ncbi.nlm.nih.gov/pubmed/17158573
Abstract:

After budding from the cell, human immunodeficiency virus {(HIV)} and other retrovirus particles undergo a maturation process that is required for their infectivity. During maturation, {HIV} particles undergo a significant internal morphological reorganization, changing from a roughly spherically symmetric immature particle with a thick protein shell to a mature particle with a thin protein shell and conical core. However, the physical principles underlying viral particle production, maturation, and entry into cells remain poorly understood. Here, using nanoindentation experiments conducted by an atomic force microscope {(AFM),} we report the mechanical measurements of {HIV} particles. We find that immature particles are more than 14-fold stiffer than mature particles and that this large difference is primarily mediated by the {HIV} envelope cytoplasmic tail domain. Finite element simulation shows that for immature virions the average Young's modulus drops more than eightfold when the cytoplasmic tail domain is deleted (930 vs. 115 {MPa).} We also find a striking correlation between the softening of viruses during maturation and their ability to enter cells, providing the first evidence, to our knowledge, for a prominent role for virus mechanical properties in the infection process. These results show that {HIV} regulates its mechanical properties at different stages of its life cycle (i.e., stiff during viral budding versus soft during entry) and that this regulation may be important for efficient infectivity. Our report of this maturation-induced "stiffness switch" in {HIV} establishes the groundwork for mechanistic studies of how retroviral particles can regulate their mechanical properties to affect biological function.

D. L. Caspar, A. Klug (1962): Physical principles in the construction of regular viruses
Type: article by Cold Spring Harbor Symposia on Quantitative Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/14019094

P. A. Thuman-Commike, B. Greene, J. Jakana, B. V. Prasad, J. King, P. E. Prevelige, W. Chiu (1996): Three-dimensional structure of scaffolding-containing phage p22 procapsids by electron cryo-microscopy
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/8676394
Abstract:

The procapsids of bacterial viruses are the products of the polymerization of coat and scaffolding subunits, as well as the precursors in {DNA} packaging. Electron cryo-microscopy has been used to study the three-dimensional structures of bacteriophage P22 procapsids containing wild-type and mutant scaffolding proteins. The scaffolding mutant structure has been resolved to 19 A resolution and agrees with the 22 A resolution wild-type procapsid reconstruction. Both procapsid reconstructions contain an outer icosahedral coat protein shell and an inner scaffolding protein core. The outer core protein forms a T = 7 icosahedral lattice with distinctive channels present at the centers of the pentons and hexons. In addition, the hexons display a prominent skew. Computational isolation of the skewed hexon shows the presence of a local 2-fold axis that reduces the number of unique conformations in the asymmetric unit to four at this resolution. We have classified the four unique subunits into three distinct classes, based upon the shape of the upper domain and the presence of a channel leading to the inner coat protein surface. In addition, at the inner surface of the coat protein, finger-like regions that extend towards the scaffolding protein core are present in two of the subunits. The finger-like regions suggest the presence of an ordered interaction between the inner coat protein and the scaffolding protein. However, an icosahedral scaffolding protein shell is not formed, and the innermost scaffolding protein core does not pack with icosahedral symmetry.

P. Ceres, A. Zlotnick (2002): Weak protein-protein interactions are sufficient to drive assembly of hepatitis B virus capsids
Type: article by Biochemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/12269796
Abstract:

Hepatitis B virus {(HBV)} is an enveloped {DNA} virus with a spherical capsid (or core). The capsid is constructed from 120 copies of the homodimeric capsid protein arranged with T = 4 icosahedral symmetry. We examined in vitro assembly of purified E. coli expressed {HBV} capsid protein. After equilibration, concentrations of capsid and dimer were evaluated by size exclusion chromatography. The extent of assembly increased as temperature and ionic strength increased. The concentration dependence of capsid assembly conformed to the equilibrium expression: K(capsid) = [capsid]/[dimer](120). Given the known geometry for {HBV} capsids and dimers, the per capsid assembly energy was partitioned into energy per subunit-subunit contact. We were able to make three major conclusions. (i) Weak interactions (from -2.9 kcal/mol at 21 degrees C in low salt to -4.4 kcal/mol at 37 degrees C in high salt) at each intersubunit contact result in a globally stable capsid; weak intersubunit interactions may be the basis for the phenomenon of capsid breathing. (ii) {HBV} assembly is characterized by positive enthalpy and entropy. The reaction is entropy-driven, consistent with the largely hydrophobic contacts found in the crystal structure. (iii) Increasing {NaCl} concentration increases the magnitude of free energy, enthalpy, and entropy, as if ionic strength were increasing the amount of hydrophobic surface buried by assembly. This last point leads us to suggest that salt acts by inducing a conformational change in the dimer from an assembly-inactive form to an assembly-active form. This model of conformational change linked to assembly is consistent with immunological differences between dimer and capsid.

T. S. Baker, N. H. Olson, S. D. Fuller (1999): Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs
Type: article by Microbiology and Molecular Biology Reviews.

H. S. Seung, D. R. Nelson (1988): Defects in flexible membranes with crystalline order
Type: article by Physical Review. A.
link: http://www.ncbi.nlm.nih.gov/pubmed/9900464

P. G. Leiman, P. R. Chipman, V. A. Kostyuchenko, V. V. Mesyanzhinov, M. G. Rossmann (2004): {Three-Dimensional} Rearrangement of Proteins in the Tail of Bacteriophage T4 on Infection of Its Host
Type: article by Cell.
doi: 10.1016/j.cell.2004.07.022

A. R. Bausch, M. J. Bowick, A. Cacciuto, A. D. Dinsmore, M. F. Hsu, D. R. Nelson, M. G. Nikolaides, A. Travesset, D. A. Weitz (2003): Grain Boundary Scars and Spherical Crystallography
Type: article by Science.
doi: 10.1126/science.1081160
link: http://www.sciencemag.org/cgi/content/abstract/299/5613/1716

Kapitel 36

S. Tzlil, J. T. Kindt, W. M. Gelbart, A. Ben-Shaul (2003): Forces and pressures in {DNA} packaging and release from viral capsids
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(03)74971-6
link: http://www.ncbi.nlm.nih.gov/pubmed/12609865
Abstract:

In a previous communication {(Kindt} et al., 2001) we reported preliminary results of Brownian dynamics simulation and analytical theory which address the packaging and ejection forces involving {DNA} in bacteriophage capsids. In the present work we provide a systematic formulation of the underlying theory, featuring the energetic and structural aspects of the strongly confined {DNA.} The free energy of the {DNA} chain is expressed as a sum of contributions from its encapsidated and released portions, each expressed as a sum of bending and interstrand energies but subjected to different boundary conditions. The equilibrium structure and energy of the capsid-confined and free chain portions are determined, for each ejected length, by variational minimization of the free energy with respect to their shape profiles and interaxial spacings. Numerical results are derived for a model system mimicking the lambda-phage. We find that the fully encapsidated genome is highly compressed and strongly bent, forming a spool-like condensate, storing enormous elastic energy. The elastic stress is rapidly released during the first stage of {DNA} injection, indicating the large force (tens of pico Newtons) needed to complete the (inverse) loading process. The second injection stage sets in when approximately 1/3 of the genome has been released, and the interaxial distance has nearly reached its equilibrium value (corresponding to that of a relaxed torus in solution); concomitantly the encapsidated genome begins a gradual morphological transformation from a spool to a torus. We also calculate the loading force, the average pressure on the capsid's walls, and the anisotropic pressure profile within the capsid. The results are interpreted in terms of the (competing) bending and interaction components of the packing energy, and are shown to be in good agreement with available experimental data.

M. E. Cerritelli, N. Cheng, A. H. Rosenberg, C. E. McPherson, F. P. Booy, A. C. Steven (1997): Encapsidated conformation of bacteriophage T7 {DNA}
Type: article by Cell.
link: http://www.ncbi.nlm.nih.gov/pubmed/9346244
Abstract:

The structural organization of encapsidated T7 {DNA} was investigated by cryo-electron microscopy and image processing. A tail-deletion mutant was found to present two preferred views of phage heads: views along the axis through the capsid vertex where the connector protein resides and via which {DNA} is packaged; and side views perpendicular to this axis. The resulting images reveal striking patterns of concentric rings in axial views, and punctate arrays in side views. As corroborated by computer modeling, these data establish that the T7 chromosome is spooled around this axis in approximately six coaxial shells in a quasi-crystalline packing, possibly guided by the core complex on the inner surface of the connector.

B. Alberts, A. Johnson, P. Walter, J. Lewis, M. Raff, K. Roberts (2008): Molecular Biology of the Cell
Type: book by Taylor & Francis.

J. Adamcík, V. Víglaský, F. Valle, M. Antalík, D. Podhradský, G. Dietler (2002): Effect of bacteria growth temperature on the distribution of supercoiled {DNA} and its thermal stability
Type: article by Electrophoresis.
doi: 10.1002/1522-2683(200210)23:19<3300::AID-ELPS3300>3.0.CO;2-Q
link: http://www.ncbi.nlm.nih.gov/pubmed/12373757
Abstract:

Changes in {DNA} supercoiling might be essential to generate the response of cellular machinery to temperature stress. The heat-induced structural transition for a topoisomer depends on the value of its specific linking difference. We detect only less negatively supercoiled {DNA} and an abundance of alternative irregular {DNA} forms at culture temperatures close to the growth limit of Escherichia coli. We show that the irregular forms are derived from regular plasmid {DNAs} and their population in the cells is temperature-dependent. Here, we show that it is possible to isolate and characterize individual {DNA} topoisomers directly from cells without a topoisomerase treatment. Temperature gradient gel electrophoresis {(TGGE)} and atomic force microscopy {(AFM)} were used to study the effect of bacteria growth temperature on the distribution of supercoiled {DNA} and its thermal stability.

R. Podgornik, D. C. Rau, V. A. Parsegian (1994): Parametrization of direct and soft steric-undulatory forces between {DNA} double helical polyelectrolytes in solutions of several different anions and cations
Type: article by Biophysical Journal.
doi: 10.1016/S0006-3495(94)80877-X
link: http://www.ncbi.nlm.nih.gov/pubmed/8038400
Abstract:

Directly measured forces between {DNA} helices in ordered arrays have been reduced to simple force coefficients and mathematical expressions for the interactions between pairs of molecules. The tabulated force parameters and mathematical expressions can be applied to parallel molecules or, by transformation, to skewed molecules of variable separation and mutual angle. This "toolbox" of intermolecular forces is intended for use in modelling molecular interactions, assembly, and conformation. The coefficients characterizing both the exponential hydration and the electrostatic interactions depend strongly on the univalent counterion species in solution, but are only weakly sensitive to anion type and temperature (from 5 to 50 degrees C). Interaction coefficients for the exponentially varying hydration force seen at spacings less than 10 to 15 A between surfaces are extracted directly from pressure versus interaxial distance curves. Electrostatic interactions are only observed at larger spacings and are always coupled with configurational fluctuation forces that result in observed exponential decay lengths that are twice the expected {Debye-Huckel} length. The extraction of electrostatic force parameters relies on a theoretical expression describing steric forces of molecules "colliding" through soft exponentially varying direct interactions.

K. J. Polach, J. Widom (1995): Mechanism of protein access to specific {DNA} sequences in chromatin: a dynamic equilibrium model for gene regulation
Type: article by Journal of Molecular Biology.
doi: 10.1006/jmbi.1995.0606
link: http://www.ncbi.nlm.nih.gov/pubmed/7490738
Abstract:

We present evidence for a mechanism by which regulatory proteins may gain access to their target {DNA} sequences in chromatin. In this model, nucleosomes are dynamic structures, transiently exposing stretches of their {DNA.} Regulatory proteins gain access to {DNA} target sites in the exposed state, and bind with an apparent dissociation constant equal to their dissociation constant for naked {DNA} divided by a position-dependent equilibrium constant for site exposure within the nucleosome. A sensitive assay, based on the kinetics of restriction digestion of sites within nucleosomes, reveals this dynamic behaviour and quantifies the equilibrium constants for site exposure. Our results have implications for many aspects of chromatin function. They offer new mechanisms for cooperativity (synergy) in regulatory protein binding and for active invasion of nucleosomes.

T. D. Yager, C. T. McMurray, K. E. van Holde (1989): Salt-induced release of {DNA} from nucleosome core particles
Type: article by Biochemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/2719953
Abstract:

At elevated salt concentrations, the structure of chromatin is destabilized. This paper is concerned with the processes by which {DNA} is released from nucleosome core particles in free, uncomplexed form. Our experiments indicate that the {DNA} release reaction has distinctly different characteristics below and above approximately 0.75 M {NaCl.} Below this concentration of salt, release of the histones from the {DNA} is highly cooperative, so that no dissociation intermediates are even seen. Above this salt concentration, histone release is not so cooperative; {H2A} and {H2B} are released from the {DNA} more readily than are H3 and H4. This results in an apparently heterogeneous population of {(H2A,} {H2B)-depleted} intermediate species sedimenting at rates between that of free {DNA} and that of intact core particles. Dissociation of core particles at {NaCl} concentrations below 0.75 M is readily reversible. Reassociation of {DNA} and histones from higher salt concentrations is nearly quantitative if carried out by gradual decrease of salt concentration, but rapid dilution to low salt results in the formation of a fraction of metastable nucleosome multimers. To help organize our description of the {DNA} release process, we introduce a stability diagram for the core particle, defined with respect to the independent variables of salt concentration and particle concentration. We draw upon our own experimental work and also upon the work of several other laboratories. We distinguish five major regions in this diagram.

R. Bruinsma (2002): Physics of Biomolecules and Cells
Type: incollection

B. Essevaz-Roulet, U. Bockelmann, F. Heslot (1997): Mechanical separation of the complementary strands of {DNA}
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/9342340
Abstract:

We describe the mechanical separation of the two complementary strands of a single molecule of bacteriophage lambda {DNA.} The 3' and 5' extremities on one end of the molecule are pulled progressively apart, and this leads to the opening of the double helix. The typical forces along the opening are in the range of 10-15 {pN.} The separation force signal is shown to be related to the local {GC} vs. {AT} content along the molecule. Variations of this content on a typical scale of 100-500 bases are presently detected.

K. K. Kunze, R. R. Netz (2000): Salt-induced {DNA-histone} complexation
Type: article by Physical Review Letters.
link: http://www.ncbi.nlm.nih.gov/pubmed/11060645
Abstract:

We study numerically the binding of one semiflexible charged polymer onto an oppositely charged sphere. Using parameters appropriate for {DNA-histone} complexes, we find complete wrapping for intermediate salt concentrations only, in agreement with experiments. For high salt concentrations, a strongly discontinuous dewrapping occurs. For low salt concentrations, we find multiple conformational transitions, leading to an extended {DNA} configuration. The wrapped states are characterized by spontaneously broken rotational and mirror symmetries, giving rise to four distinct structures.

K. J. Breslauer, R. Frank, H. Blöcker, L. A. Marky (1986): Predicting {DNA} duplex stability from the base sequence
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/3459152
Abstract:

We report the complete thermodynamic library of all 10 {Watson-Crick} {DNA} nearest-neighbor interactions. We obtained the relevant thermodynamic data from calorimetric studies on 19 {DNA} oligomers and 9 {DNA} polymers. We show how these thermodynamic data can be used to calculate the stability and predict the temperature-dependent behavior of any {DNA} duplex structure from knowledge of its base sequence. We illustrate our method of calculation by using the nearest-neighbor data to predict transition enthalpies and free energies for a series of {DNA} oligomers. These predicted values are in excellent agreement with the corresponding values determined experimentally. This agreement demonstrates that a {DNA} duplex structure thermodynamically can be considered to be the sum of its nearest-neighbor interactions. Armed with this knowledge and the nearest-neighbor thermodynamic data reported here, scientists now will be able to predict the stability (delta G degree) and the melting behavior (delta H degree) of any {DNA} duplex structure from inspection of its primary sequence. This capability should prove valuable in numerous applications, such as predicting the stability of a probe-gene complex; selecting optimal conditions for a hybridization experiment; deciding on the minimum length of a probe; predicting the influence of a specific transversion or transition on the stability of an affected {DNA} region; and predicting the relative stabilities of local domains within a {DNA} duplex.

D. Pörschke, M. Eigen (1971): Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic {pH}
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/5138337

K. Luger, A. W. Mäder, R. K. Richmond, D. F. Sargent, T. J. Richmond (1997): Crystal structure of the nucleosome core particle at 2.8 A resolution
Type: article by Nature.
doi: 10.1038/38444
link: http://www.ncbi.nlm.nih.gov/pubmed/9305837
Abstract:

The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of {DNA} are organized into a superhelix around it. Both histone/histone and {histone/DNA} interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. Histone amino-terminal tails pass over and between the gyres of the {DNA} superhelix to contact neighbouring particles. The lack of uniformity between multiple {histone/DNA-binding} sites causes the {DNA} to deviate from ideal superhelix geometry.

W. M. Gelbart, R. F. Bruinsma, P. A. Pincus, V. A. Parsegian (2000): {DNA-inspired} electrostatics
Type: article by Physics Today.

J. F. Marko, E. D. Siggia (1995): Stretching {DNA}
Type: article by Macromolecules.
doi: 10.1021/ma00130a008
link: http://dx.doi.org/10.1021/ma00130a008

J. C. Wang (1980): Superhelical {DNA}
Type: article by Trends in Biochemical Sciences.
doi: 10.1016/S0968-0004(80)80012-0
Abstract:

Since the finding of the late J. Vinograd and his co-workers 15 years ago that the {DNA} of the animal virus polyoma is superhelical, {DNAs} of this class have emerged as the most abundant form of genetic material. Some unique properties of such {DNAs} and the discovery of enzymes that can relax or supercoil {DNA} are summarized in this review.

C. Calladine, H. Drew, C. R. Calladine (1997): Understanding {DNA:} The Molecule and How It Works
Type: book by Academic Press Inc.

F. Jacob, J. Monod (1961): Genetic regulatory mechanisms in the synthesis of proteins
Type: article by Journal of Molecular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/13718526

R. D. Kornberg (2006): The molecular basis of eukaryotic cells
Type: misc

J. Gore, Z. Bryant, M. D. Stone, M. Nöllmann, N. R. Cozzarelli, C. Bustamante (2006): Mechanochemical analysis of {DNA} gyrase using rotor bead tracking
Type: article by Nature.
doi: 10.1038/nature04319
link: http://www.ncbi.nlm.nih.gov/pubmed/16397501
Abstract:

{DNA} gyrase is a molecular machine that uses the energy of {ATP} hydrolysis to introduce essential negative supercoils into {DNA.} The directionality of supercoiling is ensured by chiral wrapping of the {DNA} around a specialized domain of the enzyme before strand passage. Here we observe the activity of gyrase in real time by tracking the rotation of a submicrometre bead attached to the side of a stretched {DNA} molecule. In the presence of gyrase and {ATP,} we observe bursts of rotation corresponding to the processive, stepwise introduction of negative supercoils in strict multiples of two. Changes in {DNA} tension have no detectable effect on supercoiling velocity, but the enzyme becomes markedly less processive as tension is increased over a range of only a few tenths of piconewtons. This behaviour is quantitatively explained by a simple mechanochemical model in which processivity depends on a kinetic competition between dissociation and rapid, tension-sensitive {DNA} wrapping. In a high-resolution variant of our assay, we directly detect rotational pauses corresponding to two kinetic substeps: an {ATP-independent} step at the end of the reaction cycle, and an {ATP-binding} step in the middle of the cycle, subsequent to {DNA} wrapping.

D. E. Smith, S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, C. Bustamante (2001): The bacteriophage straight phi29 portal motor can package {DNA} against a large internal force
Type: article by Nature.
doi: 10.1038/35099581
link: http://www.ncbi.nlm.nih.gov/pubmed/11607035
Abstract:

As part of the viral infection cycle, viruses must package their newly replicated genomes for delivery to other host cells. Bacteriophage straight phi29 packages its 6.6-microm long, double-stranded {DNA} into a 42 x 54 nm capsid by means of a portal complex that hydrolyses {ATP.} This process is remarkable because entropic, electrostatic and bending energies of the {DNA} must be overcome to package the {DNA} to near-crystalline density. Here we use optical tweezers to pull on single {DNA} molecules as they are packaged, thus demonstrating that the portal complex is a force-generating motor. This motor can work against loads of up to 57 {pN} on average, making it one of the strongest molecular motors reported to date. Movements of over 5 microm are observed, indicating high processivity. Pauses and slips also occur, particularly at higher forces. We establish the force-velocity relationship of the motor and find that the rate-limiting step of the motor's cycle is force dependent even at low loads. Notably, the packaging rate decreases as the prohead is filled, indicating that an internal force builds up to approximately 50 {pN} owing to {DNA} confinement. Our data suggest that this force may be available for initiating the ejection of the {DNA} from the capsid during infection.

L. Finzi, J. Gelles (1995): Measurement of lactose repressor-mediated loop formation and breakdown in single {DNA} molecules
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/7824935
Abstract:

In gene regulatory systems in which proteins bind to multiple sites on a {DNA} molecule, the characterization of chemical mechanisms and single-step reaction rates is difficult because many chemical species may exist simultaneously in a molecular ensemble. This problem was circumvented by detecting {DNA} looping by the lactose repressor protein of Escherichia coli in single {DNA} molecules. The looping was detected by monitoring the nanometer-scale Brownian motion of microscopic particles linked to the ends of individual {DNA} molecules. This allowed the determination of the rates of formation and breakdown of a protein-mediated {DNA} loop in vitro. The measurements reveal that mechanical strain stored in the loop does not substantially accelerate loop breakdown, and the measurements also show that subunit dissociation of tetrameric repressor is not the predominant loop breakdown pathway.

R. B. Winter, O. G. Berg, P. H. von Hippel (1981): Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions
Type: article by Biochemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/7032584
Abstract:

The association and dissociation kinetics of the Escherichia coli lac repressor--operator {(RO)} complex have been examined as a function of monovalent ion concentration and operator-containing {DNA} fragment length in order to investigate the mechanisms used by repressor in locating (and dissociating from) the operator site. Association rate constants (ka) measured with an 80- or a 203-base-pair lac operator containing {DNA} fragment are 3--5-fold smaller than those determined with a 6700-base-pair operator fragment or with intact lambda plac5 {DNA} (50000 base pairs) at all salt concentrations tested. At salt concentrations less than approximately 0.1 M {KCl,} association rate constants to all operator-containing {DNA} fragments (except lambda plac5 {DNA)} are insensitive to variations in salt concentration, but the limiting low salt value of ka appears to depend upon operator-containing {DNA} length. The value of ka for lambda plac5 {DNA} decreases significantly from the approximately 0.1 M {KCl} maximum at low salt. Above approximately 0.1 M {KCl,} repressor--operator association rate constants for all operator-containing {DNA} substrates tested show a similar decrease with increasing salt concentration, which does not appear to depend upon the length of the {DNA} molecule (except for the very small {DNA} fragments). In contrast to the association reaction, kd, the dissociation rate constant, decreases linearly (on a log kd vs. log {[KCl]} plot) with decreasing salt concentration over virtually the entire salt concentration range studied (0.05--0.2 M {KCl).} These results are consistent with the explanation of the unusually fast association kinetics for this system in terms of a two-step model in which repressor initially diffuses to a nonoperator {DNA} binding site (forming an {RD} complex) and then rapidly "scans" (in a locally correlated fashion) adjacent sites until the operator is located or the repressor dissociates from the chain. Dissociation of the {RO} complex follows the same two-step process in reverse. Quantitative comparisons are made between these results and the theoretical predictions of the two facilitating translocation mechanisms (one-dimensional "sliding" along the {DNA} double helix and direct transfer between {DNA} segments) developed in the first paper of this series {[Berg,} O. G., Winter, R. B., & von Hippel, P. H. (1981) Biochemistry (first paper of three in this issue)]. We conclude that the experimental data for the "faster-than-diffusion-controlled" interaction of repressor and operator can be quantitatively modeled by a two-step process in which sliding is the dominant transfer mechanism. Molecular models of the initial nonspecific binding event (including "hopping") as well as sliding and interchain transfer are discussed, and the possible roles of facilitated translocation mechanisms of the diffusion-driven type in this and other in vitro and in vivo protein--nucleic acid interaction processes are considered.

W. K. Olson, A. A. Gorin, X. J. Lu, L. M. Hock, V. B. Zhurkin (1998): {DNA} sequence-dependent deformability deduced from {protein-DNA} crystal complexes
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/9736707
Abstract:

The deformability of double helical {DNA} is critical for its packaging in the cell, recognition by other molecules, and transient opening during biochemically important processes. Here, a complete set of sequence-dependent empirical energy functions suitable for describing such behavior is extracted from the fluctuations and correlations of structural parameters in {DNA-protein} crystal complexes. These elastic functions provide useful stereochemical measures of the local base step movements operative in sequence-specific recognition and protein-induced deformations. In particular, the pyrimidine-purine dimers stand out as the most variable steps in the {DNA-protein} complexes, apparently acting as flexible "hinges" fitting the duplex to the protein surface. In addition to the angular parameters widely used to describe {DNA} deformations (i.e., the bend and twist angles), the translational parameters describing the displacements of base pairs along and across the helical axis are analyzed. The observed correlations of base pair bending and shearing motions are important for nonplanar folding of {DNA} in nucleosomes and other nucleoprotein complexes. The knowledge-based energies also offer realistic three-dimensional models for the study of long {DNA} polymers at the global level, incorporating structural features beyond the scope of conventional elastic rod treatments and adding a new dimension to literal analyses of genomic sequences.

O. G. Berg, R. B. Winter, P. H. von Hippel (1981): Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
Type: article by Biochemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/7317363
Abstract:

Genome regulatory proteins (e.g., repressors or polymerases) that function by binding to specific chromosomal target base pair sequences (e.g., operators or promoters) can appear to arrive at their targets at faster than diffusion-controlled rates. These proteins also exhibit appreciable affinity for nonspecific {DNA,} and thus this apparently facilitated binding rate must be interpreted in terms of a two-step binding mechanism. The first step involves free diffusion to any nonspecific binding site on the {DNA,} and the second step comprises a series of protein translocation events that are also driven by thermal fluctuations. Because of nonspecific binding, the search process in the second step is of reduced dimensionality (or volume); this results in an accelerated apparent rate of target location. In this paper we define four types of processes that may be involved in these protein translocation events between {DNA} sites. These are (i) "macroscopic" dissociation--reassociation processes within the domain of the {DNA} molecule, (ii) "microscopic" dissociation--reassociation events between closely spaced sites in the {DNA} molecule, (iii) "intersegment transfer" (via "ring-closure") processes between different segments of the {DNA} molecule, and (iv) "sliding" along the {DNA} molecule. We present mathematical and physical descriptions of each of these processes, and the consequences of each for the overall rate of target location are worked out as a function of both the nonspecific binding affinity between protein and {DNA} and the length of the {DNA} molecule containing the target sequence. The theory is developed in terms of the Escherichia coli lac repressor--operator interaction since data for testing these approaches are available for this system {[Barkley,} M. (1981) Biochemistry 20, 3833; Winter, R. B., & von Hippel, P. H. (1981) Biochemistry (second paper of three in this issue); Winter, R. B., Berg, O. G., & von Hippel, P. H. (1981) Biochemistry (third paper of three in this issue)]. However, we emphasize that this approach is general for the analysis of mechanisms of biological target location involving facilitated transfer processes via nonspecific binding to the general system of which the target forms a small part.

H. Yin, M. D. Wang, K. Svoboda, R. Landick, S. M. Block, J. Gelles (1995): Transcription against an applied force
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/7502073
Abstract:

The force produced by a single molecule of Escherichia coli {RNA} polymerase during transcription was measured optically. Polymerase immobilized on a surface was used to transcribe a {DNA} template attached to a polystyrene bead 0.5 micrometer in diameter. The bead position was measured by interferometry while a force opposing translocation of the polymerase along the {DNA} was applied with an optical trap. At saturating nucleoside triphosphate concentrations, polymerase molecules stalled reversibly at a mean applied force estimated to be 14 piconewtons. This force is substantially larger than those measured for the cytoskeletal motors kinesin and myosin and exceeds mechanical loads that are estimated to oppose transcriptional elongation in vivo. The data are consistent with efficient conversion of the free energy liberated by {RNA} synthesis into mechanical work.

B. Maier, D. Bensimon, V. Croquette (2000): Replication by a single {DNA} polymerase of a stretched single-stranded {DNA}
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 97
link: http://www.pnas.org/content/97/22/12002.abstract
Abstract:

A new approach to the study of {DNA/protein} interactions has been

opened through the recent advances in the manipulation of single {DNA} molecules. These allow the behavior of individual molecular motors to be studied under load and compared with bulk measurements. One example of such a motor is the {DNA} polymerase, which replicates {DNA.} We measured the replication rate by a single enzyme of a stretched single strand of {DNA.} The marked difference between the elasticity of single- and double-stranded {DNA} allows for the monitoring of replication in real time. We have found that the rate of replication depends strongly on the stretching force applied to the template. In particular, by varying the load we determined that the biochemical steps limiting replication are coupled to movement. The replication rate increases at low forces, decreases at forces greater than 4 {pN,} and ceases when the single-stranded {DNA} substrate is under a load greater than ≈20 {pN.} The decay of the replication rate follows an Arrhenius law and indicates that multiple bases on the template strand are involved in the rate-limiting step of each cycle. This observation is consistent with the induced-fit mechanism for error detection during replication.

O. Lambert, L. Letellier, W. M. Gelbart, J.-L. Rigaud (2000): {DNA} delivery by phage as a strategy for encapsulating toroidal condensates of arbitrary size into liposomes
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 97
link: http://www.pnas.org/content/97/13/7248.abstract
Abstract:

We report a strategy for encapsulating and condensing {DNA.} When T5 phage binds to its membrane protein receptor, {FhuA,} its double stranded {DNA} (120,000 bp) is progressively released base pair after base pair in the surrounding medium. Using cryoelectron microscopy, we have visualized the structures formed after T5 phage {DNA} is released into neutral unilamellar proteoliposomes reconstituted with the receptor {FhuA.} In the presence of spermine, toroidal condensates of circumferentially wrapped {DNA} were formed. Most significantly, the sizes of these toroids were shown to vary, from 90 to 200 nm in their outer diameters, depending on the number of {DNA} stands transferred. We have also analyzed T5 {DNA} release in bulk solution containing the detergent-solubilized {FhuA} receptor. After {DNA} release in a spermine containing solution, huge {DNA} condensates with a diameter of about 300 nm were formed containing the {DNAs} from as many as 10–20 capsids. At alkaline {pH,} the condensates appeared as large hollow cylinders with a diameter of 200 nm and a height of 100–200 nm. Overall, the striking feature of our experiments is that, because of the progressive release of {DNA} from the phage capsid, the mechanism of toroid formation is fundamentally different from that in the classical studies in which highly dilute, “naked” {DNA} is condensed by direct addition of polyvalent cations; as a consequence, our method leads to toroids of arbitrary size.

J. O. Radler, I. Koltover, T. Salditt, C. R. Safinya (1997): Structure of {DNA-Cationic} Liposome Complexes: {DNA} Intercalation in Multilamellar Membranes in Distinct Interhelical Packing Regimes
Type: article by Science.
doi: 10.1126/science.275.5301.810
link: http://www.sciencemag.org/cgi/content/abstract/275/5301/810

M. Tsuboi, K. Matsuo, M. Nakanishi (1968): Helix-with-loops structure of polynucleotide. {II.} {Poly(I} + {CU)}
Type: article by Biopolymers.
doi: 10.1002/bip.1968.360060111
link: http://dx.doi.org/10.1002/bip.1968.360060111
Abstract:

Copolymers of ribocytidylic acid {(C)} and ribouridylic acid {(U)} with C contents of 66.5 and 43 mole-% have been prepared. Ultraviolet, absorption measurements were made of aqueous solutions of the mixtures of these copolymers (poly {CU)} and polyriboinosinic acid (poly I). In every set of examinations, a maximum hypochromicity (at 230, 248, or 260 mmu) was observed when the solution contained equal moles of C residue in the copolymer and I residue in the homopolymer. This fact was interpreted as indicating that a helix-with-loops structure, similar to that proposed by Fresco and Alberts7, is formed. It was shown that this structure is formed more rapidly and melts more sharply than that observed by Fresco and Alberts. An infrared examination was also made of this ldquohelix-with-loopsrdquo structure. It was found that a few absorption bands are assignable to the helix part and a few other bands to the loop part of the structure.

R. D. Kornberg (2007): The molecular basis of eukaryotic transcription
Type: article by Proceedings of the National Academy of Sciences.
doi: 10.1073/pnas.0704138104
link: http://www.pnas.org/content/104/32/12955.short

Kapitel 37

T. Baumgart, S. T. Hess, W. W. Webb (2003): Imaging coexisting fluid domains in biomembrane models coupling curvature and line tension
Type: article by Nature.
doi: 10.1038/nature02013
link: http://dx.doi.org/10.1038/nature02013
Abstract:

Lipid bilayer membranes—ubiquitous in biological systems and closely associated with cell function—exhibit rich shape-transition behaviour, including bud formation1 and vesicle fission2. Membranes formed from multiple lipid components can laterally separate into coexisting liquid phases, or domains, with distinct compositions. This process, which may resemble raft formation in cell membranes, has been directly observed in giant unilamellar vesicles3, 4. Detailed theoretical frameworks5, 6, 7, 8, 9, 10, 11 link the elasticity of domains and their boundary properties to the shape adopted by membranes and the formation of particular domain patterns, but it has been difficult to experimentally probe and validate these theories. Here we show that high-resolution fluorescence imaging using two dyes preferentially labelling different fluid phases directly provides a correlation between domain composition and local membrane curvature. Using freely suspended membranes of giant unilamellar vesicles, we are able to optically resolve curvature and line tension interactions of circular, stripe and ring domains. We observe long-range domain ordering in the form of locally parallel stripes and hexagonal arrays of circular domains, curvature-dependent domain sorting, and membrane fission into separate vesicles at domain boundaries. By analysing our observations using available membrane theory, we are able to provide experimental estimates of boundary tension between fluid bilayer domains.

O. Medalia, I. Weber, A. S. Frangakis, D. Nicastro, G. Gerisch, W. Baumeister (2002): Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography
Type: article by Science {(New} York, {N.Y.)}.
doi: 10.1126/science.1076184
link: http://www.ncbi.nlm.nih.gov/pubmed/12424373
Abstract:

Electron tomography of vitrified cells is a noninvasive three-dimensional imaging technique that opens up new vistas for exploring the supramolecular organization of the cytoplasm. We applied this technique to Dictyostelium cells, focusing on the actin cytoskeleton. In actin networks reconstructed without prior removal of membranes or extraction of soluble proteins, the cross-linking of individual microfilaments, their branching angles, and membrane attachment sites can be analyzed. At a resolution of 5 to 6 nanometers, single macromolecules with distinct shapes, such as the {26S} proteasome, can be identified in an unperturbed cellular environment.

P. Hensley (1996): Defining the structure and stability of macromolecular assemblies in solution: the re-emergence of analytical ultracentrifugation as a practical tool
Type: article by Structure {(London,} England: 1993).
link: http://www.ncbi.nlm.nih.gov/pubmed/8740359

W. F. Stafford, K. Mabuchi, K. Takahashi, T. Tao (1995): Physical characterization of calponin. A circular dichroism, analytical ultracentrifuge, and electron microscopy study
Type: article by The Journal of Biological Chemistry.
link: http://www.ncbi.nlm.nih.gov/pubmed/7737994
Abstract:

Calponin is a thin filament-associated smooth muscle protein that has been suggested to play a role in the regulation of smooth muscle contraction. We have used circular dichroism spectroscopy, electron microscopy, and analytical ultracentrifugation to study the physical properties of recombinant chicken gizzard alpha-calponin. The alpha-helix content of alpha-calponin was estimated from its circular dichroism spectrum to be approximately 13%, {alpha-Calponin} melts with a single sharp transition at approximately 57 degrees C. Rotary shadowing electron micrographs of alpha-calponin reveal diverse shapes ranging from elongated rods to collapsed coils. The lengths of the rod-shaped structures are approximately 18 nm. Analytical ultracentrifugation studies found alpha-calponin to be homogeneous with a monomer molecular mass of 31.4 {kDa,} and a s20,w value of 2.34 S. These data could be used to model alpha-calponin as a prolate ellipsoid of revolution with an axial ratio of 6.16, a length of 16.2 nm, and a diameter of 2.6 nm. Taken together, our results indicate that calponin is a flexible, elongated molecule whose contour length is sufficient to span three actin subunits along the long pitch helix of an F-actin filament.

J. Lebowitz, M. S. Lewis, P. Schuck (2002): Modern analytical ultracentrifugation in protein science: a tutorial review
Type: article by Protein Science: A Publication of the Protein Society.
doi: 10.1110/ps.0207702
link: http://www.ncbi.nlm.nih.gov/pubmed/12192063
Abstract:

Analytical ultracentrifugation {(AU)} is reemerging as a versatile tool for the study of proteins. Monitoring the sedimentation of macromolecules in the centrifugal field allows their hydrodynamic and thermodynamic characterization in solution, without interaction with any matrix or surface. The combination of new instrumentation and powerful computational software for data analysis has led to major advances in the characterization of proteins and protein complexes. The pace of new advancements makes it difficult for protein scientists to gain sufficient expertise to apply modern {AU} to their research problems. To address this problem, this review builds from the basic concepts to advanced approaches for the characterization of protein systems, and key computational and internet resources are provided. We will first explore the characterization of proteins by sedimentation velocity {(SV).} Determination of sedimentation coefficients allows for the modeling of the hydrodynamic shape of proteins and protein complexes. The computational treatment of {SV} data to resolve sedimenting components has been achieved. Hence, {SV} can be very useful in the identification of the oligomeric state and the stoichiometry of heterogeneous interactions. The second major part of the review covers sedimentation equilibrium {(SE)} of proteins, including membrane proteins and glycoproteins. This is the method of choice for molar mass determinations and the study of self-association and heterogeneous interactions, such as protein-protein, protein-nucleic acid, and protein-small molecule binding.

S. Vogel (1996): Life in Moving Fluids: The Physical Biology of Flow
Type: book by Princeton Univ Pr.

D. B. Murphy, W. B. Murphy (2009): Fundamentals of Light Microscopy and Electronic Imaging
Type: book by {Wiley-Blackwell}.

G. Sluder, D. E. Wolf (2007): Digital Microscopy: Methods in Cell Biology: 81 {(Methods} in Cell Biology): Methods in Cell Biology: 81
Type: book by Academic Pr Inc.

G. Schmahl, D. Rudolph, B. Niemann, P. Guttmann, J. Thieme, G. Schneider (1996): Röntgenmikroskopie
Type: article by Naturwissenschaften.
link: http://adsabs.harvard.edu/abs/1996NW.....83...61S

J. Pawley (2006): Handbook of Biological Confocal Microscopy
Type: book by Springer, Berlin.

M. Pluta (1988): Advanced Light Microscopy: Principles and Basic Properties: 001
Type: book by Elsevier Science Ltd.

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.6, Hydrodynamik: {BD} 6
Type: book by Deutsch {(Harri)}.

G. Wiegand, K. R. Neumaier, E. Sackmann (1998): Microinterferometry: {Three-Dimensional} Reconstruction of Surface Microtopography for {Thin-Film} and Wetting Studies by Reflection Interference Contrast Microscopy {(RICM)}
Type: article by Applied Optics.
link: http://www.ncbi.nlm.nih.gov/pubmed/18301506
Abstract:

We present an improved theory of image formation by reflection interference contrast microscopy {(RICM)} for structural studies of stratified films on planar substrates and propose a new theoretical approach to analyzing the surface profile of nonplanar films. We demonstrate the validity of the new approach by analyzing the fringe patterns of {RICM} images from wedge-shaped liquid films and spherical probes. By simulation of various scenarios, we study the effect of finite-aperture illumination and the shape of the nonplanar interface on the interference fringe pattern of {RICM} images. We show how the reconstruction of the microscopic topography of the sample from the fringe spacing is corrected by angular and curvature correction terms. We discuss the variation of the mean intensity of the fringe patterns and the decay in the fringe amplitude with increasing fringe order that is caused by nonplanar interfaces of different slope.

C. Tse, T. Sera, A. P. Wolffe, J. C. Hansen (1998): Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by {RNA} polymerase {III}
Type: article by Molecular and Cellular Biology.
link: http://www.ncbi.nlm.nih.gov/pubmed/9671473
Abstract:

We have examined the effects of core histone acetylation on the transcriptional activity and higher-order folding of defined 12-mer nucleosomal arrays. Purified {HeLa} core histone octamers containing an average of 2, 6, or 12 acetates per octamer (8, 23, or 46% maximal site occupancy, respectively) were assembled onto a {DNA} template consisting of 12 tandem repeats of a 208-bp Lytechinus {5S} {rRNA} gene fragment. Reconstituted nucleosomal arrays were transcribed in a Xenopus oocyte nuclear extract and analyzed by analytical hydrodynamic and electrophoretic approaches to determine the extent of array compaction. Results indicated that in buffer containing 5 {mM} free Mg2+ and 50 {mM} {KCl,} high levels of acetylation (12 acetates/octamer) completely inhibited higher-order folding and concurrently led to a 15-fold enhancement of transcription by {RNA} polymerase {III.} The molecular mechanisms underlying the acetylation effects on chromatin condensation were investigated by analyzing the ability of differentially acetylated nucleosomal arrays to fold and oligomerize. In {MgCl2-containing} buffer the folding of 12-mer nucleosomal arrays containing an average of two or six acetates per histone octamer was indistinguishable, while a level of 12 acetates per octamer completely disrupted the ability of nucleosomal arrays to form higher-order folded structures at all ionic conditions tested. In contrast, there was a linear relationship between the extent of histone octamer acetylation and the extent of disruption of Mg2+-dependent oligomerization. These results have yielded new insight into the molecular basis of acetylation effects on both transcription and higher-order compaction of nucleosomal arrays.

R. Y. Tsien (1998): The green fluorescent protein
Type: article by Annual Review of Biochemistry.
doi: 10.1146/annurev.biochem.67.1.509
link: http://www.ncbi.nlm.nih.gov/pubmed/9759496
Abstract:

In just three years, the green fluorescent protein {(GFP)} from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology. Its amazing ability to generate a highly visible, efficiently emitting internal fluorophore is both intrinsically fascinating and tremendously valuable. High-resolution crystal structures of {GFP} offer unprecedented opportunities to understand and manipulate the relation between protein structure and spectroscopic function. {GFP} has become well established as a marker of gene expression and protein targeting in intact cells and organisms. Mutagenesis and engineering of {GFP} into chimeric proteins are opening new vistas in physiological indicators, biosensors, and photochemical memories.

J. O. Rädler, T. J. Feder, H. H. Strey, E. Sackmann (1995): Fluctuation analysis of tension-controlled undulation forces between giant vesicles and solid substrates
Type: article by Physical Review E.
doi: 10.1103/PhysRevE.51.4526
link: http://link.aps.org/abstract/PRE/v51/p4526
Abstract:

Using reflection interference contrast microscopy, we studied the thermal fluctuations of giant vesicles that weakly adhere to flat solid substrates. The absolute membrane-substrate separation distance was imaged and the average contact contour, including the contact area, the contact rounding, and the asymptotic contact angle, was determined. The static fluctuations in the flat, adhering part of the vesicle were analyzed. The spectrum of mean square amplitudes yielded the lateral membrane tension and the second derivative of the interaction potential. The vertical roughness and lateral correlation length were measured from the spatial autocorrelation of the undulations. The roughness was shown to obey the behavior predicted by functional renormalization in the observed tension regime of 10-6 to 10-4 J/m2. Moreover, the measured separation distances can be explained within the framework of undulation and van der Waals forces and confirmed the model of tension-induced adhesion. However, the adhesion energies as well as the measured separation distances exhibit a weaker dependence on the membrane tension than predicted.

M. Meselson, F. W. Stahl (1958): The replication of {DNA} in Escherichia Coli
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/16590258

Übungsaufgaben

H. C. Berg (2003): The rotary motor of bacterial flagella
Type: article by Annual Review of Biochemistry.
doi: 10.1146/annurev.biochem.72.121801.161737
link: http://www.ncbi.nlm.nih.gov/pubmed/12500982
Abstract:

Flagellated bacteria, such as Escherichia coli, swim by rotating thin helical filaments, each driven at its base by a reversible rotary motor, powered by an ion flux. A motor is about 45 nm in diameter and is assembled from about 20 different kinds of parts. It develops maximum torque at stall but can spin several hundred Hz. Its direction of rotation is controlled by a sensory system that enables cells to accumulate in regions deemed more favorable. We know a great deal about motor structure, genetics, assembly, and function, but we do not really understand how it works. We need more crystal structures. All of this is reviewed, but the emphasis is on function.

E. Karatekin, O. Sandre, H. Guitouni, N. Borghi, P.-H. Puech, F. Brochard-Wyart (2003): Cascades of Transient Pores in Giant Vesicles: Line Tension and Transport
Type: article by Biophysical Journal.
link: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302742
Abstract:

Under ordinary circumstances, the membrane tension of a giant unilamellar vesicle is essentially nil. Using visible light, we stretch the vesicles, increasing the membrane tension until the membrane responds by the sudden opening of a large pore (several micrometers in size). Only a single pore is observed at a time in a given vesicle. However, a cascade of transient pores appear, up to 30–40 in succession, in the same vesicle. These pores are transient: they reseal within a few seconds as the inner liquid leaks out. The membrane tension, which is the driving force for pore opening, is relaxed with the opening of a pore and the leakage of the inner liquid; the line tension of the pore's edge is then able to drive the closure of a pore. We use fluorescent membrane probes and real-time videomicroscopy to study the dynamics of the pores. These can be visualized only if the vesicles are prepared in a viscous solution to slow down the leakout of the internal liquid. From measurements of the closure velocity of the pores, we are able to infer the line tension, T. We have studied the effect of the shape of inclusion molecules on T. Cholesterol, which can be modeled as an inverted cone-shaped molecule, increases the line tension when incorporated into the bilayers. Conversely, addition of cone-shaped detergents reduces T. The effect of some detergents can be dramatic, reducing Tby two orders of magnitude, and increasing pore lifetimes up to several minutes. We give some examples of transport through transient pores and present a rough measurement of the leakout velocity of the inner liquid through a pore. We discuss how our results can be extended to less viscous aqueous solutions which are more relevant for biological systems and biotechnological applications.

M. Doi, S. F. Edwards (1988): The Theory of Polymer Dynamics
Type: book by Oxford University Press.

B. Alberts, A. Johnson, P. Walter, J. Lewis, M. Raff, K. Roberts (2008): Molecular Biology of the Cell
Type: book by Taylor & Francis.

Y. C. Fung (1993): Biomechanics. Mechanical Properties of Living Tissues
Type: book by {Springer-Verlag} {GmbH}.

P. C. Hiemenz, R. Rajagopalan (1997): Principles of Colloid and Surface Chemistry
Type: book by Marcel Dekker Inc.

R. Lipowsky, E. Sackmann (1996): Architecture and Function. Handbook of Biological Physics Vol I
Type: book by Elsevier.
Abstract:

The first volume of the Handbook deals with the amazing world of biomembranes and lipid bilayers. Part A describes all aspects related to the morphology of these membranes, beginning with the complex architecture of biomembranes, continues with a description of the bizarre morphology of lipid bilayers and concludes with technological applications of these membranes. The first two chapters deal with biomembranes, providing an introduction to the membranes of eucaryotes and a description of the evolution of membranes. The following chapters are concerned with different aspects of lipids including the physical properties of model membranes composed of lipid-protein mixtures, lateral phase separation of lipids and proteins and measurement of lipid-protein bilayer diffusion. Other chapters deal with the flexibility of fluid bilayers, the closure of bilayers into vesicles which attain a large variety of different shapes, and applications of lipid vesicles and liposomes.

Part B covers membrane adhesion, membrane fusion and the interaction of biomembranes with polymer networks such as the cytoskeleton. The first two chapters of this part discuss the generic interactions of membranes from the conceptual point of view. The following two chapters summarize the experimental work on two different bilayer systems. The next chapter deals with the process of contact formation, focal bounding and macroscopic contacts between cells. The cytoskeleton within eucaryotic cells consists of a network of relatively stiff filaments of which three different types of filaments have been identified. As explained in the next chapter much has been recently learned about the interaction of these filaments with the cell membrane. The final two chapters deal with membrane fusion.

Y. Rondelez, G. Tresset, T. Nakashima, Y. Kato-Yamada, H. Fujita, S. Takeuchi, H. Noji (2005): Highly coupled {ATP} synthesis by {F1-ATPase} single molecules
Type: article by Nature.
doi: 10.1038/nature03277
link: http://www.ncbi.nlm.nih.gov/pubmed/15716957
Abstract:

{F1-ATPase} is the smallest known rotary motor, and it rotates in an anticlockwise direction as it hydrolyses {ATP.} Single-molecule experiments point towards three catalytic events per turn, in agreement with the molecular structure of the complex. The physiological function of F1 is {ATP} synthesis. In the ubiquitous {F0F1} complex, this energetically uphill reaction is driven by F0, the partner motor of F1, which forces the backward (clockwise) rotation of F1, leading to {ATP} synthesis. Here, we have devised an experiment combining single-molecule manipulation and microfabrication techniques to measure the yield of this mechanochemical transformation. Single F1 molecules were enclosed in femtolitre-sized hermetic chambers and rotated in a clockwise direction using magnetic tweezers. When the magnetic field was switched off, the F1 molecule underwent anticlockwise rotation at a speed proportional to the amount of synthesized {ATP.} At 10 Hz, the mechanochemical coupling efficiency was low for the alpha3beta3gamma subcomplex {(F1-epsilon)),} but reached up to 77% after reconstitution with the epsilon-subunit {(F1+epsilon)).} We provide here direct evidence that F1 is designed to tightly couple its catalytic reactions with the mechanical rotation. Our results suggest that the epsilon-subunit has an essential function during {ATP} synthesis.

J. N. Israelachvili (1991): Intermolecular and Surface Forces: With Applications to Colloidal and Biological Systems
Type: book by Academic Pr Inc.

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.7, Elastizitätstheorie: {BD} 7
Type: book by Deutsch {(Harri)}.

J. Nicholls (2001): From Neuron to Brain: A Cellular and Molecular Approach to the Function of the Nervous System
Type: book by Palgrave Macmillan.

O. Albrecht, H. Gruler, E. Sackmann (1978): Polymorphism of phospholipid monolayers
Type: article by Journal de Physique.
doi: 10.1051/jphys:01978003903030100

P. Schwille, E. Haustein (2001): Fluorescence Correlation Spectroscopy
Type: book
Abstract:

The recent development of single molecule detection techniques has opened new horizons for the study of individual macromolecules under physiological conditions. Conformational subpopulations, internal dynamics and activity of single biomolecules, parameters that have so far been hidden in large ensemble averages, are now being unveiled. Herein, we review a particular attractive solution-based single molecule technique, fluorescence correlation spectroscopy {(FCS).} This time-averaging fluctuation analysis which is usually performed in Confocal setups combines maximum sensitivity with high statistical confidence. {FCS} has proven to be a very versatile and powerful tool for detection and temporal investigation of biomolecules at ultralow concentrations on surfaces, in solution, and in living cells. The introduction of dual-color cross-correlation and two-photon excitation in {FCS} experiments is currently increasing the number of promising applications of {FCS} to biological research.

M. A. Dichtl, E. Sackmann (1999): Colloidal probe study of short time local and long time reptational motion of semiflexible macromolecules in entangled networks
Type: article by New Journal of Physics.
link: http://adsabs.harvard.edu/abs/1999NJPh....1...18D

E. Evans, W. Rawicz (1990): Entropy-driven tension and bending elasticity in condensed-fluid membranes
Type: article by Physical Review Letters.
doi: 10.1103/PhysRevLett.64.2094
link: http://link.aps.org/abstract/PRL/v64/p2094
Abstract:

Sensitive micropipet methods have been used to measure the relation between tension and the projected surface area in fluid membranes of vesicles over a 4-order-of-magnitude range in tension (10-3–10 dyn/cm). In the low-tension regime ({textless}0.5 dyn/cm), the data confirm the prediction of equilibrium theory that the projected area should increase logarithmically with tension as shape fluctuations become progressively restricted. The slope of log(tension) versus area dilation yields and the elastic bending modulus of the membrane. In the high-tension regime, the projected area crosses over to vary linearly with tension due to direct expansion of area per molecule.

T. D. Pollard, W. C. Earnshaw, J. Lippincott-Schwartz (2007): Cell Biology
Type: book by Saunders.

E. Neher, A. Marty (1982): Discrete changes of cell membrane capacitance observed under conditions of enhanced secretion in bovine adrenal chromaffin cells
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/6959149
Abstract:

The capacitance of the surface membrane of small adrenal chromaffin cells was measured with patch-clamp pipettes. Continuous and discrete changes of capacitance were observed. They were interpreted as changes of surface area connected to exocytotic or endocytotic processes. Most of the measurements were performed in the "whole-cell" recording configuration {[Hamill,} O. P., Marty, A., Neher, E., Sakmann, B. & Sigworth, F. J. (1981) Pflügers Arch. 391, 85-100], which allows the intracellular Ca2+ concentration to be controlled. With an internal solution highly buffered to low values of Ca2+ concentration (10 {nM),} the surface capacitance usually decreased and could not be markedly changed by electrical stimulation. At low buffering capacity and medium Ca2+ concentrations (0.1-1 {microM),} the capacitance measurement showed large fluctuations and discrete steps, reflecting both capacitance decrease and increase. A large transient increase of capacitance could be induced by electrical stimulation under these conditions. It was linked to Ca2+ currents through the membrane. Relatively large (2-6 x 10(-14) F) steps of capacitance decrease were common after extensive stimulation. The size distribution of step-like capacitance changes is well compatible with the idea that steps of capacitance increase reflect individual events of exocytosis of chromaffin granules, whereas steps of the opposite polarity reflect the formation of vesicles or vacuoles by endocytosis.

M. Rief, R. S. Rock, A. D. Mehta, M. S. Mooseker, R. E. Cheney, J. A. Spudich (2000): {Myosin-V} stepping kinetics: A molecular model for processivity
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 97
link: http://www.pnas.org/content/97/17/9482.abstract
Abstract:

{Myosin-V} is a molecular motor that moves processively along its actin track. We have used a feedback-enhanced optical trap to examine the stepping kinetics of this movement. By analyzing the distribution of time periods separating discrete ≈36-nm mechanical steps, we characterize the number and duration of rate-limiting biochemical transitions preceding each such step. These data show that {myosin-V} is a tightly coupled motor whose cycle time is limited by {ADP} release. On the basis of these results, we propose a model for {myosin-V} processivity.

W. S. Rhode (1971): Observations of the vibration of the basilar membrane in squirrel monkeys using the Mössbauer technique
Type: article by The Journal of the Acoustical Society of America.
link: http://www.ncbi.nlm.nih.gov/pubmed/4994693

L. D. Landau, E. M. Lifschitz (1991): Lehrbuch der theoretischen Physik, 10 Bde., Bd.6, Hydrodynamik: {BD} 6
Type: book by Deutsch {(Harri)}.

G. Wald (1968): Molecular basis of visual excitation
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/4877437

L. Finzi, J. Gelles (1995): Measurement of lactose repressor-mediated loop formation and breakdown in single {DNA} molecules
Type: article by Science {(New} York, {N.Y.)}.
link: http://www.ncbi.nlm.nih.gov/pubmed/7824935
Abstract:

In gene regulatory systems in which proteins bind to multiple sites on a {DNA} molecule, the characterization of chemical mechanisms and single-step reaction rates is difficult because many chemical species may exist simultaneously in a molecular ensemble. This problem was circumvented by detecting {DNA} looping by the lactose repressor protein of Escherichia coli in single {DNA} molecules. The looping was detected by monitoring the nanometer-scale Brownian motion of microscopic particles linked to the ends of individual {DNA} molecules. This allowed the determination of the rates of formation and breakdown of a protein-mediated {DNA} loop in vitro. The measurements reveal that mechanical strain stored in the loop does not substantially accelerate loop breakdown, and the measurements also show that subunit dissociation of tetrameric repressor is not the predominant loop breakdown pathway.

L. D. Landau, E. M. Lifschitz (1987): Lehrbuch der theoretischen Physik, 10 Bde., Bd.5, Statistische Physik: {BD} 5
Type: book by Deutsch {(Harri)}.

S. Chu (1992): Laser Trapping of neutral Particles
Type: article by Scientific American.
Abstract:

Lasers can be used to trap and manipulate electrically neutral particles. These techniques have allowed scientists to cool vapors to near absolute zero, develop new atomic clocks, and stretch single molecules of {DNA}

J. N. Murrell (1967): Elektronenspektren Organischer Moleküle.
Type: book by Bibliographisches Institut.

J. M. Berg, L. Stryer, J. L. Tymoczko (2007): Biochemie
Type: book by Spektrum Akademischer Verlag.

R. F. Schmidt, G. Thews, F. Lang (2000): Physiologie des Menschen
Type: book by Springer Berlin.

A. K. Rzadzinska, M. E. Schneider, C. Davies, G. P. Riordan, B. Kachar (2004): An actin molecular treadmill and myosins maintain stereocilia functional architecture and self-renewal
Type: article by The Journal of Cell Biology.
doi: 10.1083/jcb.200310055
link: http://www.ncbi.nlm.nih.gov/pubmed/15024034
Abstract:

We have previously shown that the seemingly static paracrystalline actin core of hair cell stereocilia undergoes continuous turnover. Here, we used the same approach of transfecting hair cells with actin-green fluorescent protein {(GFP)} and {espin-GFP} to characterize the turnover process. Actin and espin are incorporated at the paracrystal tip and flow rearwards at the same rate. The flux rates (approximately 0.002-0.04 actin subunits s(-1)) were proportional to the stereocilia length so that the entire staircase stereocilia bundle was turned over synchronously. Cytochalasin D caused stereocilia to shorten at rates matching paracrystal turnover. Myosins {VI} and {VIIa} were localized alongside the actin paracrystal, whereas myosin {XVa} was observed at the tips at levels proportional to stereocilia lengths. Electron microscopy analysis of the abnormally short stereocilia in the shaker 2 mice did not show the characteristic tip density. We argue that actin renewal in the paracrystal follows a treadmill mechanism, which, together with the myosins, dynamically shapes the functional architecture of the stereocilia bundle.

N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, E. Teller, others (1953): Equation of state calculations by fast computing machines
Type: article by The journal of chemical physics.

H. Dietz, M. Rief (2006): Protein structure by mechanical triangulation
Type: article by Proceedings of the National Academy of Sciences of the United States of America.

H. Dietz, T. Bornschlögl, R. Heym, F. König, M. Rief (2007): Programming protein self assembly with coiled coils
Type: article by New Journal of Physics.

T. Bornschlögl, M. Rief (2008): {Single-Molecule} Dynamics of Mechanical {Coiled-Coil} Unzipping†
Type: article by Langmuir.

R. A Fontanilla, R. Nuccitelli (1998): Characterization of the sperm-induced calcium wave in Xenopus eggs using confocal microscopy
Type: article by Biophysical journal.

E. Neher, G. J. Augustine (1992): Calcium gradients and buffers in bovine chromaffin cells.
Type: article by The Journal of Physiology.
doi: VL - 450
link: http://jp.physoc.org/content/450/1/273.abstract
Abstract:

1. Digital imaging and photometry were used in conjunction with the fluorescent Ca2+ indicator, Fura-2, to examine intracellular Ca2+ signals produced by depolarization of single adrenal chromaffin cells. 2. Depolarization with a patch pipette produced radial gradients of Ca2+ within the cell, with Ca2+ concentration highest in the vicinity of the plasma membrane. These gradients dissipated within a few hundred milliseconds when the voltage-gated Ca2+ channels were closed. 3. Dialysis of Fura-2 into the chromaffin cell caused concentration-dependent changes in the depolarization-induced Ca2+ signal, decreasing its magnitude and slowing its recovery time course. These changes were used to estimate the properties of the endogenous cytoplasmic Ca2+ buffer with which Fura-2 competes for Ca2+. 4. The spatially averaged Fura-2 signal was well described by a model assuming fast competition between Fura-2 and an endogenous buffer on a millisecond time scale. Retrieval of calcium by pumps and slow buffers occurs on a seconds-long time scale. No temporal changes indicative of buffers with intermediate kinetics could be detected. 5. Two independent estimates of the capacity of the fast endogenous Ca2+ buffer suggest that 98-99% of the Ca2+ entering the cell normally is taken up by this buffer. This buffer appears to be immobile, because it does not wash out of the cell during dialysis. It has a low affinity for Ca2+ ions, because it does not saturate with 1 {microM-Ca2+} inside the cell. 6. The low capacity, affinity and mobility of the endogenous Ca2+ buffer makes it possible for relatively small amounts of exogenous Ca2+ buffers, such as Fura-2, to exert a significant influence on the characteristics of the Ca2+ concentration signal as measured by fluorescence ratios. On the other hand, even at moderate Fura-2 concentrations (0.4 {mM)} Fura-2 will dominate over the endogenous buffers. Under these conditions radiometric Ca2+ concentration signals are largely attenuated, but absolute fluorescence changes (at 390 nm) accurately reflect calcium fluxes.

Y. X. Li, J. Rinzel, J. Keizer, S. S. Stojilković (1994): Calcium oscillations in pituitary gonadotrophs: comparison of experiment and theory
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 91
link: http://www.pnas.org/content/91/1/58.abstract
Abstract:

We have developed a mathematical model that describes several aspects of agonist-induced Ca2+ signaling in single pituitary gonadotrophs. Our model is based on fast activation of the inositol 1,4,5-trisphosphate {(InsP3)} receptor Ca2+ channels at low free cytosolic Ca2+ concentration {([Ca2+]i)} and slow inactivation at high {[Ca2+]i.} Previous work has shown that these gating properties, when combined with a {Ca(2+)-ATPase,} are sufficient to generate simulated Ca2+ oscillations. The {Hodgkin-Huxley-like} description we formulate here incorporates these different gating properties explicitly and renders their effects transparent and easy to modulate. We introduce regulatory mechanisms of channel opening which enable the model, both in the absence and in the presence of Ca2+ entry, to give responses to a wide range of agonist doses that are in good agreement with experimental findings, including subthreshold responses, superthreshold oscillations with frequency determined by {[InsP3],} and nonoscillatory "biphasic" responses followed occasionally by small-amplitude oscillations. A particular added feature of our model, enhanced channel opening by reduced concentration of Ca2+ in the lumen of the endoplasmic reticulum, allows oscillations to continue during pool depletion. The model predicts that ionomycin and thapsigargin can induce oscillations with basal {[InsP3]} and zero Ca2+ entry, while Ca2+ injection cannot. Responses to specific pairings of sub- or superthreshold stimuli of agonist, ionomycin, and thapsigargin are also correctly predicted. Since this model encompasses a wide range of observed dynamic behaviors within a single framework, based on well-established mechanisms, its relevance should not be restricted to gonadotrophs.

H. Heerklotz (2004): The microcalorimetry of lipid membranes
Type: article by Journal of Physics Condensed Matter.

P. L. Privalov, A. I. Dragan (2007): Microcalorimetry of biological macromolecules
Type: article by Biophysical Chemistry.

L. Rusu, A. Gambhir, S. McLaughlin, J. Rädler (2004): Fluorescence correlation spectroscopy studies of peptide and protein binding to phospholipid vesicles
Type: article by Biophysical journal.

I. N. Bronstein, K. A. Semendjajew (1991): Taschenbuch der Mathematik, 25
Type: article by Aufl., Stuttgart ua.

S. T. Milner, S. A. Safran (1987): Dynamical fluctuations of droplet microemulsions and vesicles
Type: article by Physical Review A.

D. R. Gaskell (1996): In: Cahn {RW,} Hassen P, editors. Physical Metallurgy
Type: book by Elsevier Science {BV}.

J. Rädler, H. Strey, E. Sackmann (1995): Phenomenology and kinetics of lipid bilayer spreading on hydrophilic surfaces
Type: article by Langmuir.

L. D. Harmon, E. R. Lewis (1966): Neural modeling
Type: article by Physiological Reviews.

R. S. Zucker Calcium and transmitter release
Type: article by Journal of {Physiology-Paris}.
doi: 10.1016/0928-4257(93)90021-K

A. B. Moy, J. Van Engelenhoven, J. Bodmer, J. Kamath, C. Keese, I. Giaever, S. Shasby, D. M. Shasby (1996): Histamine and thrombin modulate endothelial focal adhesion through centripetal and centrifugal forces.
Type: article by Journal of Clinical Investigation.

S. Gritsch, P. Nollert, F. Jahnig, E. Sackmann (1998): Impedance Spectroscopy of Porin and Gramicidin Pores Reconstituted into Supported Lipid Bilayers on {Indium−Tin-Oxide} Electrodes†
Type: article by Langmuir.
doi: 10.1021/la9710381
link: http://dx.doi.org/10.1021/la9710381
Abstract:

We prepared electrolytemembraneelectrolytesemiconductor {(EMES)} interfaces by fusion and high-temperature annealing of positively charged lipid vesicles (containing 49 mol % cholesterol and 42 mol % lecithin besides 9 mol % positively charged lipid) on optical transparent indiumtin-oxide {(ITO)} semiconductor electrodes. Membrane resistances of up to 109 {kOmega} cm2 were reached. By conductivity measurements in the presence of the redox couple {K3Fe(CN)6/K4Fe(CN)6} the area fraction of defects exhibited in the supported membranes was determined to be less than 0.0001. We show that by measurement of the impedance over a large frequency range (10-1105 Hz) it is possible to discriminate between changes (1) of the capacitance of the {ITO} electrodes, (2) the membrane capacitance, and (3) the membrane conductivity of the sensor device. The membrane pore gramicidin and the outer membrane proteins {OmpF} and {OmpA} (from E. coli) where reconstituted into the supported membranes by transfer from vesicles. The functionality and selectivity of gramicidin and {OmpF} in supported membranes are demonstrated by measuring the membrane resistance in the presence of pores for various electrolyte compositions.

R. Wehner, M. V. Srinivasan (1981): Searching behaviour of desert ants, {genusCataglyphis} {(Formicidae,} Hymenoptera)
Type: article by Journal of Comparative Physiology A: Neuroethology, Sensory, Neural, and Behavioral Physiology.

G. Tsiavaliaris, D. J. Manstein (2003): {TIRF-Mikroskopie} und ihre Anwendung in der Biologie
Type: article by Biospektrum.

A. Yildiz, J. N. Forkey, S. A. McKinney, T. Ha, Y. E. Goldman, P. R. Selvin (2003): Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization
Type: article by Science.

R. E. Thompson, D. R. Larson, W. W. Webb (2002): Precise nanometer localization analysis for individual fluorescent probes
Type: article by Biophysical journal.

J. Schilling, K. Sengupta, S. Goennenwein, A. R. Bausch, E. Sackmann (2004): Absolute interfacial distance measurements by dual-wavelength reflection interference contrast microscopy
Type: article by Physical Review E.
doi: 10.1103/PhysRevE.69.021901
link: http://link.aps.org/abstract/PRE/v69/e021901
Abstract:

Dual-wavelength reflection interference contrast microscopy {(DW-RICM)} is established as a microinterferometric technique to measure absolute optical distances between transparent planar substrates and hard or soft surfaces such as colloidal beads or artificial and biological membranes, which hover over the substrate. In combination with a fast image processing algorithm the technique was applied to analyze the trajectories of colloidal beads sedimenting under gravity. As the beads approach the surface of the substrate, they slow down because of hydrodynamic coupling of the bead motion to the substrate. The effective surface friction coefficients were measured as a function of the absolute distance of the beads from the surface. The height dependence of the friction coefficient was found to be in quantitative agreement with previous theoretical predictions. Furthermore, we demonstrate that the {DW-RICM} technique allows the determination of the height of membranes above substrates and the amplitude and direction of height fluctuations. Without any further need to label the membrane the unambiguous reconstruction of the surface profile of soft surfaces is possible.

L. Turner, S. R. Caplan, H. C. Berg (1996): Temperature-induced switching of the bacterial flagellar motor
Type: article by Biophysical journal.

W. Nachtigall (1997): Vorbild Natur: {Bionik-Design} für funktionelles Gestalten
Type: book by Springer.

R. Zenobi, V. Deckert (2000): Optische Nahfeldmikroskopie und-spektroskopie als Werkzeug in der chemischen Analytik
Type: article by Angewandte Chemie.

K. M. Hartmann, W. Hoppe, W. Lohmann, H. Markl, H. Ziegler (1982): {Biophysik-Ein} Lehrbuch
Type: book

P. M. Sellick, R. Patuzzi, B. M. Johnstone (1983): Comparison between the tuning properties of inner hair cells and basilar membrane motion
Type: article by Hearing Research.

N. P. Cooper, W. S. Rhode (1992): Basilar membrane mechanics in the hook region of cat and guinea-pig cochleae: sharp tuning and nonlinearity in the absence of baseline position shifts
Type: article by Hearing research.

E. Murugasu, I. J. Russell (1996): The effect of efferent stimulation on basilar membrane displacement in the basal turn of the guinea pig cochlea
Type: article by Journal of Neuroscience.

I. J. Russell, K. E. Nilsen (1997): The location of the cochlear amplifier: Spatial representation of a single tone on the guinea pig basilar membrane
Type: article by Proceedings of the National Academy of Sciences of the United States of America.
doi: VL - 94
link: http://www.pnas.org/content/94/6/2660.abstract
Abstract:

Acoustic stimulation vibrates the cochlear basilar membrane, initiating a wave of displacement that travels toward the apex and reaches a peak over a restricted region according to the stimulus frequency. In this characteristic frequency region, a tone at the characteristic frequency maximally excites the sensory hair cells of the organ of Corti, which transduce it into electrical signals to produce maximum activity in the auditory nerve. Saturating, nonlinear, feedback from the motile outer hair cells is thought to provide electromechanical amplification of the travelling wave. However, neither the location nor the extent of the source of amplification, in relation to the characteristic frequency, are known. We have used a laser–diode interferometer to measure the distribution along the basilar membrane of nonlinear, saturating vibrations to 15 {kHz} tones. We estimate that the site of amplification for the 15 {kHz} region is restricted to a 1.25 mm length of basilar membrane centered on the 15 {kHz} place.

R. V. Mustacich, B. R. Ware (1974): Observation of protoplasmic streaming by laser-light scattering
Type: article by Physical Review Letters.

D. A. Kuzmanovic, I. Elashvili, C. Wick, C. O'Connell, S. Krueger (2006): The {MS2} Coat Protein Shell is Likely Assembled Under Tension: A Novel Role for the {MS2} Bacteriophage A Protein as Revealed by Small-angle Neutron Scattering
Type: article by Journal of Molecular Biology.
doi: 10.1016/j.jmb.2005.11.040

T. S. Baker, N. H. Olson, S. D. Fuller (1999): Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs
Type: article by Microbiology and Molecular Biology Reviews.

G. Witz, K. Rechendorff, J. Adamcik, G. Dietler (2008): Conformation of Circular {DNA} in Two Dimensions
Type: article by Physical Review Letters.
doi: 10.1103/PhysRevLett.101.148103
link: http://link.aps.org/abstract/PRL/v101/e148103

F. Kuhner, M. Erdmann, H. E. Gaub (2006): Scaling Exponent and Kuhn Length of Pinned Polymers by Single Molecule Force Spectroscopy
Type: article by Physical Review Letters.
doi: 10.1103/PhysRevLett.97.218301
link: http://link.aps.org/abstract/PRL/v97/e218301

M. Diez, B. Zimmermann, M. Börsch, M. König, E. Schweinberger, S. Steigmiller, R. Reuter, S. Felekyan, V. Kudryavtsev, C. A.M Seidel, others (2004): Proton-powered subunit rotation in single membrane-bound F 0 F {1-ATP} synthase
Type: article by Nature structural & molecular biology.

F. Pouthas, C. Gentil, D. Cote, G. Zeck, B. Straub, U. Bockelmann (2004): Spatially resolved electronic detection of biopolymers
Type: article by Physical Review E.

F. Ziemann, J. Rädler, E. Sackmann (1994): Local measurements of viscoelastic moduli of entangled actin networks using an oscillating magnetic bead micro-rheometer
Type: article by Biophysical Journal.

P. Mangeol, D. Côte, T. Bizebard, O. Legrand, U. Bockelmann (2006): Probing {DNA} and {RNA} single molecules with a double optical tweezer
Type: article by The European Physical Journal E.
doi: 10.1140/epje/i2005-10060-4

H. Hillebrandt, A. Abdelghani, C. Abdelghani-Jacquin, M. Aepfelbacher, E. Sackmann (2001): Electrical and optical characterization of thrombin-induced permeability of cultured endothelial cell monolayers on semiconductor electrode arrays
Type: article by Applied Physics A: Materials Science & Processing.
doi: 10.1007/s003390100879
link: http://dx.doi.org/10.1007/s003390100879
Abstract:

Abstract. Impedance spectroscopy and phase-contrast microscopy are combined to monitor the electrical and morphological properties of

human umbilical vein endothelial cell monolayers. The cells were cultured on optically transparent indium-tin-oxide {(ITO)} semiconductor electrode arrays coated with collagen {IV,} and the effect of the inflammatory mediator thrombin on monolayer permeability was monitored in real time. {ITO} electrodes provide several advantages for these kinds of experiments, because they are optically transparent, polarizable and highly sensitive due to the absence of insulating oxide layers. A qualitative correlation between the thrombin-induced gap formation and the electrical parameters of the cell layer is established.

J. del Castillo, B. Katz (1954): Quantal components of the end-plate potential
Type: article by The Journal of Physiology.

R. Schittenhelm, A. Oppelt (1990): Biomagnetische Diagnostik
Type: article by Physik in unserer Zeit.
doi: 10.1002/piuz.19900210404
link: http://dx.doi.org/10.1002/piuz.19900210404
Abstract:

Durch Messung der Magnetfeldverteilung mit einem Vielkanalsystem höchster Nachweisempfindlichkeit können im menschlichen Körper ablaufende elektrische Prozesse lokalisiert und zeitlich verfolgt werden. Der Diagnostik eröffnen sich damit neue Wege zur Untersuchung der elektrischen Funktion insbesondere von Herz und Gehirn.

J. N. Murrell (1963): The theory of the electronic spectra of organic molecules
Type: book by Methuen.

S. W. Schneider, S. Nuschele, A. Wixforth, C. Gorzelanny, A. Alexander-Katz, R. R. Netz, M. F. Schneider (2007): Shear-induced unfolding triggers adhesion of von Willebrand factor fibers
Type: article by Proceedings of the National Academy of Sciences.
doi: 10.1073/pnas.0608422104
link: http://www.pnas.org/content/104/19/7899.abstract
Abstract:

von Willebrand factor {(VWF),} a protein present in our circulatory system, is necessary to stop bleeding under high shear-stress conditions as found in small blood vessels. The results presented here help unravel how an increase in hydrodynamic shear stress activates {VWF's} adhesion potential, leading to the counterintuitive phenomena of enhanced adsorption rate under strong shear conditions. Using a microfluidic device, we were able to mimic a wide range of bloodflow conditions and directly visualize the conformational dynamics of this protein under shear flow. In particular, we find that {VWF} displays a reversible globule-stretch transition at a critical shear rate γ̇ in the absence of any adsorbing surface. Computer simulations reproduce this sharp transition and identify the large size of {VWF's} repeating units as one of the keys for this unique hydrodynamic activation. In the presence of an adsorbing collagen substrate, we find a large increase in the protein adsorption at the same critical shear rate, suggesting that the globule unfolding in bulk triggers the surface adsorption in the case of a collagen substrate, which provides a sufficient density of binding sites. Monitoring the adsorption process of multiple {VWF} fibers, we were able to follow the formation of an immobilized network that constitutes a “sticky” grid necessary for blood platelet adhesion under high shear flow. Because areas of high shear stress coincide with a higher chance for vessel wall damage by mechanical forces, we identified the shear-induced increase in the binding probability of {VWF} as an effective self-regulating repair mechanism of our microvascular system.