Dynamical Networks in Physics and Biology: At the Frontier of Physics and Biology Les Houches Workshop, March 17–21, 1997

310 Pages·1998·8.749 MB·English

by  G. Forgacs (auth.), D. A. Beysens, G. Forgacs (eds.)

DYNAMICAL NETWORKS
IN PHYSICS AND BIOLOGY
At the Frontier of Physics and Biology
Les Houches Workshop, March 17-21, 1997
Editors
D.BEYSENS
G. FORGACS
EDP Sciences
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Springer-Verlag France S.A.R.L
Centre de Physique des Bouches
Books already published in this series
1 Porous Silicon Science and Technology 7 Scale Invariance and Beyond
J.-c. VIAL and J. DERRIEN, Eds. 1995 B. DUBRULLE, F. GRANER
2 Nonlinear Excitations in Biomolecules and D. SORNETTE, Eds. 1997
M. PEYRARD, Ed. 1995 8 New Non-Perturbative Methods and
3 Beyond Quasicrystals Quantization on the Light Cone
F. AXEL and D. GRATIAS, Eds. 1995 P. GRANGE, A. NEVEU, H.c. PAULI,
4 Quantum Mechanical Simulation Methods S. PINSKY and E. WERNER, Eds 1998
for Studying Biological Systems 9 Starbursts Triggers, Nature, and Evolution
D. BICOUT and M. FIELD, Eds. 1996 B. GUIDERDONI and A. KEMBHA VI,
5 New Tools in Turbulence Modelling Eds 1998
O. METAlS and J. FERZIGER, Eds. 1997
6 Catalysis by Metals
A. J. RENOUPREZ
and H. JOBIC, Eds. 1997
Book series coordinated by Michele LEDUC
Editors of "Dynamical Networks in Physics and Biology" (N° 10)
D. Beysens (CEA, Grenoble, France)
G. Forgacs (Clarkson University, Potsdam, USA)
ISBN 978-3-540-65349-3 ISBN 978-3-662-03524-5 (eBook)
DOI 10.1007/978-3-662-03524-5
This work is subject to copyright. All rights are reserved, whether the whole or part of the material is
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casting, reproduction on microfilms or in other ways, and storage in data banks. Duplication of this
publication or parts thereof is only permitted under the provisions of the French and German Copyright
laws of March 11,1957 and September 9,1965, respectively. Violations fall underthe prosecution act of
the French and German Copyright Laws.
© Springer-Verlag France 1998
Originally published by EDP Sciences, Les Viis; Springer-Verlag, Berlin, Heidelberg New York in
1998.
PREFACE
The 1997 Les Houches workshop on "Dynamical Network in Physics and
Biology" was the third in a series of meetings "At the Frontier between
Physics and Biology". Our objective with these workshops is to create a
truly interdisciplinary forum for researchers working on outstanding
problems in biology, but using different approaches (physical, chemical or
biological). Generally speaking, the biologists are trained in the particular
and motivated by the specifics, while, in contrast, the physicists deal with
generic and "universal" models. All agree about the necessity of developing
"robust" models.
The specific aim of the workshop was to bridge the gap between
physics and biology in the particular field of interconnected dynamical
networks. The proper functioning of a living organism of any complexity
requires the coordinated activity of a great number of "units". Units, or, in
physical terms, degrees of freedom that couple to one another, typically form
networks. The physical or biological properties of interconnected networks
may drastically differ from those of the individual units: the whole is not
simply an assembly of its parts, as can be demonstrated by the following
examples. Above a certain (critical) concentration the metallic islands,
randomly distributed in an insulating matrix, form an interconnected
network. At this point the macroscopic conductivity of the system becomes
finite and the amorphous metal is capable of carrying current. The value of
the macroscopic conductivity typically is very different from the
conductivity of the individual metallic islands. At the critical concentration,
branching polymers in a solution form a macroscopic coupled mesh. The
viscosity of the liquid then grows indefinitely, and the system becomes an
elastic gel. The macroscopic elastic constants again have very little to do
with the elastic properties of the individual polymers. The above networks,
extensively studied in the physical and mathematical sciences, are examples
of percolation assemblies, lacking an obvious, ordered repetition of the units.
An example of an ordered network is a solid crystalline body, being a
collection of individual atoms or molecules. As the crystal grows, its
physical properties change. Macroscopic attributes not even defined for
individual atoms (i.e. resistivity, thermal expansion, elasticity) appear.
Interconnected dynamical networks show up at various scales and
developmental stages in an organism. The nuclear matrix is a scaffolding
made mainly of 9- and 13-nm core filaments. On a slightly larger scale, the
cytoskeleton may be viewed as an interconnected network of actin and
IV
intermediate filaments, as well as microtubules. On a still larger scale, the
extracellular matrix fills the space between various tissues and organs and
contains an intricate mesh of interacting macromolecules (i.e. collagen,
elastin, fibronectin, laminin). At the extreme scale a living system could be
viewed as a network of organs coupled through the circulatory or muscular
system. Specific components of an organism are often studied in terms of
interconnected assemblies. Intensive studies have been carried out in the
fields of genetic networks, intracellular protein or enzyme networks,
neuronal nets, immunological networks and metabolic networks. The major
reason for such an approach is again the realization that the proper
understanding of the biological functions performed by these complexes is
possible only through the study of the intricate dynamical coupling between
a vast number of individual units. It is precisely the dynamical nature of
microfilament networks that is employed during cell locomotion: actin
subunits are organized into linear polymers, which are crosslinked at the
lamella's leading edge. The crosslinked filaments are then disassembled
away from the edge, and the resulting subunits are again used for assembly.
A fundamental question in developmental biology is the formation of such
intra- and extracellular patterns.
Many outstanding questions in both the physical and biological
sciences are currently being investigated using networks. Physicists and
mathematicians have worked out a number of general methods to study the
complex properties of both ordered and random interacting assemblies.
Biologists dealing with the networks mentioned above typically build then
into in their studies on specificity.
The meeting was attended by 63 scientists. Physicists were brought
together with molecular and cell biologists, immunologists and geneticists to
discuss the importance of cooperactivity embodied in dynamical networks.
Special emphasis was given to the following topics: genetic networks,
metabolic networks, cytoskeletal networks, neuronal networks, immune
networks, extracellular matrix networks, structure formation in tissues and
other complex fluids, percolation and its application in physics, biology and
chemistry.
The workshop began, as in the past, with overviews on the general
theme from the perspective of a physicist (G. Forgacs, Clarkson University)
and a biologist (P. Janmey, Harvard Medical School). 38 talks were given,
and each of the above mentioned topics was introduced by an internationally
known expert.
The resolution of outstanding problems facing biology today requires
more and more accurate measurements and quantitative analysis of the data
obtained. At the same time, the changing needs of our societies force
physicists to broaden their horizon and venture into territories traditionally
v
not in the realm of physics. The success of the present workshop, which can
be measured by the number of collaborations initiated during the meeting,
underscores the conviction of the organizers that the Les Houches
workshops "At the Frontier of Physics and Biology" fulfill an important role
in helping physicists and biologists to better understand each other's
scientific approaches and methods and develop fruitful interactions.
Acknowledgments
We wish to kindly acknowledge the generous support of the following
agencies, without which this workshop could have not been organized:
the Commissariat it I' Energie Atomique,
the Centre National de la Recherche Scientifique,
the Direction des Recherches, Etudes et Techniques du Ministere
de la Defense,
the Ministere des Affaires Etrangeres.
We also would like to thank 1. Glenat for her help in the administrative
organization of the meeting, and the whole team at the Centre de Physique
des Houches for making everyday life during the workshop as comfortable
as possible.
D. Beysens and G. Forgacs
CONTENTS
INTRODUCTION
LECTURE 1
Cooperative Phenomena in Physical Networks
by G. F orgacs
1. Introduction............................................................................................. 3
2. Ordered and disordered networks ........................................................... 4
3. Percolation phenomena........................................................................... 6
4. An analytically treatable example: the bethe lattice.. .............................. 10
5. Summary ................................................................................................. 11
NETWORKS OF BIOPOLYMERS
LECTURE 2
Complex Networks in Cell Biology
by P.A. Janmey, J.Y. Shah and J.x. Tang
1. Introduction and examples of biological protein networks ..................... 17
1.1 Stable network-forming proteins.................................................... 17
1.2 Dynamic biopolymer networks and the cytoskeleton ..................... 18
2. Rheology of cytoskeletal polymer networks........................................... 19
3. Molecular basis of biopolymer viscoelasticity ........................................ 21
4. Filament diffusion within networks ......... ...... ......................................... 22
5. The polyelectrolyte nature of biopolymers ............................................. 22
6. Conclusions.. ............. .... .... .... ........ .......................................................... 24
LECTURE 3
The Keratocyte Cytoskeleton:
A Dynamic Structural Network
by K.I. Anderson
1. Introduction.. ............. ...... ...... .... ............................................ .................. 27
2. Protrusion and retraction: the two steps of crawling .......... .... ................. 29
VIII
3. Actin polymerization in the lamellipodium............................................. 30
4. Cell body transport.................................................................................. 33
5. Coordination of protrusion and retraction............................................... 35
LECTURE 4
Adhesion Mediated Signaling: The Role of Junctional
Plaque Proteins in the Regulation of Tumorigenesis
by A. Ben-Ze' ev
1. Introduction................. ............................................................................ 41
2. Results and discussion............................................................................. 42
2.1 Induction of vinculin and a-actinin expression in growth-
activated cells in vitro and in vivo .................................................. 42
2.2 The effects of vinculin and a-actinin overexpression..................... 44
2.3 The effects of suppressing vinculin and a-actinin levels
and targeted inactivation of the vinculin gene ................................ 44
2.4 Vinculin and a-actinin levels and the transformed phenotype ....... 45
2.5 Suppression of tumorigenicity by transfection with vinculin
and a-actinin................................................................................... 45
2.6 Plakoglobin and p-catenin: cell-cell junctional molecules
involved in signaling and regulation of tumorigenesis ................... 46
3. Conclusions............................................................................................. 48
LECTURES
Of Proteins, Redox States and Living Things
by L. Moldovan and P.J. Goldschmidt-Clermont
1. Introduction ............................................................................................. 51
2. Redox state and protein structure ............................................................ 52
3. The actin network as an integrator of cellular functions ......................... 53
4. Complex control of the actin cytoskeleton organization and dynamics.. 55
5. Regulation of actin by small GTP-binding proteins................................ 56
6. Rac as an activator of phagocytic cell NADPH oxidase ......................... 58
7. Could ROS be mediators of actin reorganization? .................................. 59
8. Mechanisms and conclusions .................................................................. 62
IX
LECTURE 6
Tensegrity and the Emergence of a Cellular Biophysics
by D.E. Ingber
1. Introduction.. ................................. ............... .......... .............. ................... 67
2. Conventional view of the cell ........................................ ......................... 68
2.1 Molecular polymers of the cytoskeleton......................................... 69
3. An alternative model: cellular tensegrity ................................................ 71
3.1 Tensegrity architecture ................................................................... 71
3.2 Tensegrity in the living cytoskeleton.............................................. 73
3.3 How robust is the model? ............................................................... 75
3.4 Tensegrity versus percolation theory.............................................. 76
4. Implications for cellular biophysics ........................................................ 77
5. Conclusion .............................................................................................. 78
LECTURE 7
The Leukocyte Actin Cytoskeleton
by F. Richelme, A.-M. Benoliel and P. Bongrand
1. Introduction............................................................................................. 81
2. A conventional study of the role of calcium in the shape control
of human neutrophils.................... ...... ............... .................... .................. 83
3. Use of the micropipette aspiration technique to study the influence
of calcium on cytoskeletal regulation................ ............................ .......... 84
4. Conclusion. ....................................... ............ ......................... ................. 90
LECTURES
Branched Polymers and Gels
byM. Daoud
1. Introduction........ ............. ........................................................... ............. 93
2. Percolation and sol-gel transition............................................................ 94
3. Effects of dilution.................................................................................... 97
3.1 The single polymer ......................................................................... 97
3.2 The semi-dilute regime ................................................................... 98
4. Rheology ................................................................................................. 99
5. Conclusion .............................................................................................. 101
x
LECTURE 9
Statistical Mechanisms of Semiflexible Polymers:
Theory and Experiment
by E. Frey, K. Kroy, J. Wilhelm and E. Sackmann
1. Introduction and overview...................................................................... 103
2. Single-chain properties............................................................................ 107
2.1 The wormlike chain model.. .......... .......................... ....................... 107
2.2 Linear force-extension relation...................................... ................. 107
2.3 Nonlinear response and radial distribution function ....................... 108
2.4 Dynamic structure factor ................................................................ 110
3. Many-chain properties ............................................................................ 112
3.1 Entanglement transition.................................................................. 112
3.2 Plateau modulus.............................................................................. 113
3.3 Terminal relaxation......................................................................... 115
3.4 Stochastic network models ............................................................. 116
LECTURE 10
Scale Effects, Anisotropy and Non-Linearity of Tensegrity
Structures: Applications to Cell Mechanical Behavior
by S. Wendling, E. Planus, D. Isabey and C. Oddou
1. Introduction............................................................................................. 121
2. Mechanical models of the cytoskeleton .................................................. 121
3. Results and discussion............................................................................. 124
4. Conclusion .............................................................................................. 126
CELLULAR AND EXTRACELLULAR NETWORKS
LECTURE 11
Networks of Extracellular Matrix and Adhesion Proteins
by J. Engel
1. Introduction............................................................................................. 131
2. The five stranded coiled-coil domain of cartilage oligomeric
matrix protein CaMP.............................................................................. 132
3. Is the coiled-coil domain of CaMP a prototype ion channel? ................ 134
4. Artificial pentamerization of the adhesion protein E-cadherin ............... 135
5. Outlook ................................................................................................... 137