Physics of Bio-Molecules and Cells

585 Pages·2002·11.044 MB·English

by  Henrik Flyvbjerg, Frank Jülicher, Pal Ormos, Francois David

CONTENTS
Lecturers xi
Participants xiii
Pr´eface xvii
Preface xxi
Contents xxv
Course 1. Physics of Protein-DNA Interaction
by R.F. Bruinsma 1
1 Introduction 3
1.1 The central dogma and bacterial gene expression . . . . . . . . . . 3
1.1.1 Two families . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.1.2 Prokaryote gene expression . . . . . . . . . . . . . . . . . . 5
1.2 Molecular structure . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.2.1 Chemical structure of DNA . . . . . . . . . . . . . . . . . . 8
1.2.2 Physical structureof DNA. . . . . . . . . . . . . . . . . . . 10
1.2.3 Chemical structure of proteins . . . . . . . . . . . . . . . . 12
1.2.4 Physical structureof proteins . . . . . . . . . . . . . . . . . 14
2 Thermodynamics and kinetics of repressor-DNA interaction 16
2.1 Thermodynamics and thelac repressor . . . . . . . . . . . . . . . . 16
2.1.1 The law of mass action . . . . . . . . . . . . . . . . . . . . 16
2.1.2 Statistical mechanics and operator occupancy . . . . . . . . 19
2.1.3 Entropy,enthalpy,and direct read-out . . . . . . . . . . . . 20
2.1.4 The lac repressor complex: A molecular machine . . . . . . 23
2.2 Kinetics of repressor-DNA interaction . . . . . . . . . . . . . . . . 26
2.2.1 Reaction kinetics . . . . . . . . . . . . . . . . . . . . . . . . 26
2.2.2 Debye–Smoluchowski theory. . . . . . . . . . . . . . . . . . 28
2.2.3 BWH theory . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2.2.4 Indirect read-out and induced fit . . . . . . . . . . . . . . . 32
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3 DNA deformability and protein-DNA interaction 34
3.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
3.1.1 Eukaryotic gene expression and Chromatin condensation . . 34
3.1.2 A mathematical experiment and White’s theorem. . . . . . 37
3.2 The worm-like chain . . . . . . . . . . . . . . . . . . . . . . . . . . 40
3.2.1 Circular DNA and thepersistence length . . . . . . . . . . 42
3.2.2 Nucleosomes and theMarky–Manning transition . . . . . . 42
3.2.3 Protein-DNA interaction undertension . . . . . . . . . . . 45
3.2.4 Force-Extension Curves . . . . . . . . . . . . . . . . . . . . 47
3.3 The RSTmodel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
3.3.1 Structural sequencesensitivity . . . . . . . . . . . . . . . . 50
3.3.2 Thermal fluctuations . . . . . . . . . . . . . . . . . . . . . . 52
4 Electrostatics in water and protein-DNA interaction 53
4.1 Macro-ions and aqueous electrostatics . . . . . . . . . . . . . . . . 54
4.2 The primitivemodel . . . . . . . . . . . . . . . . . . . . . . . . . . 56
4.2.1 The primitive model: Ion-free . . . . . . . . . . . . . . . . . 57
4.2.2 The primitive model: DH regime . . . . . . . . . . . . . . . 57
4.3 Manning condensation . . . . . . . . . . . . . . . . . . . . . . . . . 58
4.3.1 Charge renormalization . . . . . . . . . . . . . . . . . . . . 58
4.3.2 Primitive model: Oosawa theory . . . . . . . . . . . . . . . 59
4.3.3 Primitive model: Free energy . . . . . . . . . . . . . . . . . 61
4.4 Counter-ion release and non-specificprotein-DNAinteraction . . . 63
4.4.1 Counter-ion release . . . . . . . . . . . . . . . . . . . . . . . 63
4.4.2 Nucleosome formation and theisoelectric instability . . . . 64
Course 2. Mechanics of Motor Proteins
by J. Howard 69
1 Introduction 71
2 Cell motility and motor proteins 72
3 Motility assays 73
4 Single-molecules assays 75
5 Atomic structures 77
6 Proteins as machines 78
7 Chemical forces 80
8 Effect of force on chemical equilibria 81
9 Effect of force on the rates of chemical reactions 82
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10 Absolute rate theories 85
11 Role of thermal fluctuations in motor reactions 87
12 A mechanochemical model for kinesin 89
13 Conclusions and outlook 92
Course 3. Modelling Motor Protein Systems
by T. Duke 95
1 Making a move: Principles of energy transduction 98
1.1 Motor proteins and Carnot engines . . . . . . . . . . . . . . . . . . 98
1.2 Simple Brownian ratchet . . . . . . . . . . . . . . . . . . . . . . . . 99
1.3 Polymerization ratchet . . . . . . . . . . . . . . . . . . . . . . . . . 100
1.4 Isothermal ratchets . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
1.5 Motor proteins as isothermal ratchets . . . . . . . . . . . . . . . . 104
1.6 Design principles for effective motors . . . . . . . . . . . . . . . . . 105
2 Pulling together: Mechano-chemical model of actomyosin 108
2.1 Swinging lever-arm model . . . . . . . . . . . . . . . . . . . . . . . 108
2.2 Mechano-chemical coupling . . . . . . . . . . . . . . . . . . . . . . 110
2.3 Equivalent isothermal ratchet . . . . . . . . . . . . . . . . . . . . . 111
2.4 Many motors working together . . . . . . . . . . . . . . . . . . . . 112
2.5 Designed to work . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
2.6 Force-velocity relation . . . . . . . . . . . . . . . . . . . . . . . . . 116
2.7 Dynamical instability and biochemical synchronization . . . . . . . 118
2.8 Transient response of muscle . . . . . . . . . . . . . . . . . . . . . 119
3 Motors at work: Collective properties of motor proteins 119
3.1 Dynamical instabilities . . . . . . . . . . . . . . . . . . . . . . . . . 119
3.2 Bidirectional movement . . . . . . . . . . . . . . . . . . . . . . . . 120
3.3 Critical behaviour . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
3.4 Oscillations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
3.5 Dynamic bucklinginstability . . . . . . . . . . . . . . . . . . . . . 125
3.6 Undulation of flagella . . . . . . . . . . . . . . . . . . . . . . . . . 127
4 Sense and sensitivity: Mechano-sensation in hearing 129
4.1 System performance . . . . . . . . . . . . . . . . . . . . . . . . . . 129
4.2 Mechano-sensors: Hair bundles . . . . . . . . . . . . . . . . . . . . 130
4.3 Activeamplification . . . . . . . . . . . . . . . . . . . . . . . . . . 131
4.4 Self-tuned criticality . . . . . . . . . . . . . . . . . . . . . . . . . . 133
4.5 Motor-driven oscillations . . . . . . . . . . . . . . . . . . . . . . . . 134
4.6 Channel compliance and relaxation oscillations . . . . . . . . . . . 136
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4.7 Channel-driven oscillations . . . . . . . . . . . . . . . . . . . . . . 138
4.8 Hearing at thenoise limit . . . . . . . . . . . . . . . . . . . . . . . 139
Course 4. Dynamic Force Spectroscopy
by E. Evans and P. Williams 145
Part 1: E. Evans and P. Williams 147
1 Dynamic force spectroscopy. I. Single bonds 147
1.1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
1.1.1 Intrinsic dependenceof bond strength on time frame
for breakage . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
1.1.2 Biomolecular complexity and role for dynamic force
spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . 148
1.1.3 Biochemical and mechanical perspectives of bond strength . 150
1.1.4 Relevant scales for length, force, energy, and time. . . . . . 153
1.2 Brownian kineticsin condensed liquids: Old-timephysics . . . . . 154
1.2.1 Two-state transitions in a liquid . . . . . . . . . . . . . . . 155
1.2.2 Kinetics of first-orderreactions in solution . . . . . . . . . . 156
1.3 Link between force – time – and bond chemistry . . . . . . . . . . 158
1.3.1 Dissociation of a simple bond underforce . . . . . . . . . . 158
1.3.2 Dissociation of a complex bond underforce:
Stationary rate approximation . . . . . . . . . . . . . . . . 159
1.3.3 Evolution of states in complex bonds . . . . . . . . . . . . . 163
1.4 Testing bond strength and themethod of dynamic force
spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
1.4.1 Probe mechanics and bond loading dynamics . . . . . . . . 165
1.4.2 Stochastic process of bond failure underrising force . . . . 168
1.4.3 Distributions of bond lifetime and ruptureforce. . . . . . . 169
1.4.4 Crossover from near equilibrium to far from equilibrium
unbonding. . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
1.4.5 Effect of soft-polymer linkages on dynamic strengths
of bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
1.4.6 Failure of a complex bond and unexpected transitions
in strength . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
1.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Part 2: P. Williams and E. Evans 186
2 Dynamic force spectroscopy. II. Multiple bonds 187
2.1 Hiddenmechanics in detachment of multiplebonds . . . . . . . . . 187
2.2 Impact of cooperativity . . . . . . . . . . . . . . . . . . . . . . . . 188
2.3 Uncorrelated failure of bonds loaded in series . . . . . . . . . . . . 191
2.3.1 Markov sequenceof random failures . . . . . . . . . . . . . 191
2.3.2 Multiple-complex bonds . . . . . . . . . . . . . . . . . . . . 193
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2.3.3 Multiple-ideal bonds . . . . . . . . . . . . . . . . . . . . . . 194
2.3.4 Equivalent single-bond approximation . . . . . . . . . . . . 195
2.4 Uncorrelated failure of bondsloaded in parallel . . . . . . . . . . . 198
2.4.1 Markov sequenceof random failures . . . . . . . . . . . . . 198
2.4.2 Equivalent single-bond approximation . . . . . . . . . . . . 198
2.5 Poisson statistics and bond formation . . . . . . . . . . . . . . . . 199
2.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Seminar 1. Polymerization Forces
by M. Dogterom 205
Course 5. The Physics of Listeria Propulsion
by J. Prost 215
1 Introduction 217
2 A genuine gel 218
2.1 A little chemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
2.2 Elastic behaviour . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
3 Hydrodynamics and mechanics 220
3.1 Motion in thelaboratory frame . . . . . . . . . . . . . . . . . . . . 220
3.2 Propulsion and steady velocity regimes . . . . . . . . . . . . . . . . 221
3.3 Gel/bacterium friction and saltatory behaviour . . . . . . . . . . . 223
4 Biomimetic approach 225
4.1 A spherical Listeria. . . . . . . . . . . . . . . . . . . . . . . . . . . 225
4.2 Spherical symmetry . . . . . . . . . . . . . . . . . . . . . . . . . . 226
4.3 Steady state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
4.4 Growth with spherical symmetry . . . . . . . . . . . . . . . . . . . 229
4.5 Symmetry breaking. . . . . . . . . . . . . . . . . . . . . . . . . . . 229
4.6 Limitations of theapproach and possible improvements . . . . . . 231
5 Conclusion 234
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Course 6. Physics of Composite Cell Membrane
and Actin Based Cytoskeleton
by E. Sackmann, A.R. Bausch and L. Vonna 237
1 Architecture of composite cell membranes 239
1.1 The lipid/protein bilayer is a multicomponent smectic phase
with mosaic like architecture . . . . . . . . . . . . . . . . . . . . . 239
1.2 The spectrin/actin cytoskeleton as hyperelastic cell stabilizer . . . 242
1.3 The actin cortex: Architectureand function . . . . . . . . . . . . . 245
2 Physics of the actin based cytoskeleton 249
2.1 Actin is a living semiflexible polymer . . . . . . . . . . . . . . . . . 249
2.2 Actin network as viscoelastic body . . . . . . . . . . . . . . . . . . 253
2.3 Correlation between macroscopic viscoelasticity and molecular
motional processes . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
3 Heterogeneous actin gels in cells and biological function 260
3.1 Manipulation of actin gels . . . . . . . . . . . . . . . . . . . . . . . 260
3.2 Control of organization and function of actin cortex
bycell signalling . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
4 Micromechanics and microrheometry of cells 267
5 Activation of endothelial cells: On the possibility
of formation of stress fibers as phase transition of actin-network
triggered by cell signalling pathways 271
6 On cells as adaptive viscoplastic bodies 274
7 Controll of cellular protrusions controlled by actin/myosin
cortex 278
Course 7. Cell Adhesion as Wetting Transition?
by E. Sackmann and R. Bruinsma 285
1 Introduction 287
2 Mimicking cell adhesion 292
3 Microinterferometry: A versatile tool to evaluate adhesion
strength and forces 294
4 Soft shell adhesion is controlled by a double well interfacial
potential 294
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5 How is adhesion controlled by membrane elasticity? 297
6 Measurement of adhesion strength by interferometric contour
analysis 299
7 Switching on specific forces: Adhesion as localized dewetting
process 300
8 Measurement of unbinding forces, receptor-ligand leverage
and a new role for stress fibers 300
9 An application: Modification of cellular adhesion strength
by cytoskeletal mutations 303
10 Conclusions 303
A Appendix: Generic interfacial forces 304
Course 8. Biological Physics in Silico
by R.H. Austin 311
1 Why micro/nanofabrication? 315
Lecture 1a: Hydrodynamic Transport 319
1 Introduction: The need to control flows in 2 1/2 D 319
2 Somewhat simple hydrodynamics in 2 1/2 D 321
3 The N-port injector idea 328
4 Conclusion 333
Lecture 1b: Dielectrophoresis and Microfabrication 335
1 Introduction 335
2 Methods 337
2.1 Fabrication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
2.2 Viscosity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338
2.3 Electronics and imaging . . . . . . . . . . . . . . . . . . . . . . . . 338
2.4 DNA samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338
3 Results 339
3.1 Basic results and dielectrophoretic force extraction . . . . . . . . . 339
4 Data and analysis 343
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5 Origin of the low frequency dielectrophoretic force in DNA 347
6 Conclusion 353
Lecture 2a: Hex Arrays 356
1 Introduction 356
2 Experimental approach 360
3 Conclusions 364
Lecture 2b: The DNA Prism 366
1 Introduction 366
2 Design 366
3 Results 367
4 Conclusions 372
Lecture 2c: Bigger is Better in Rachets 374
1 The problems with insulators in rachets 374
2 An experimental test 375
3 Conclusions 381
Lecture 3: Going After Epigenetics 382
1 Introduction 382
2 The nearfield scanner 383
3 The chip 384
4 Experiments with molecules 387
5 Conclusions 391
Lecture 4: Fractionating Cells 392
1 Introduction 392
2 Blood specifics 392
3 Magnetic separation 397
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4 Microfabrication 398
5 Magnetic field gradients 399
6 Device interface 401
7 A preliminary blood cell run 406
8 Conclusions 409
Lecture 5: Protein Folding on a Chip 411
1 Introduction 411
2 Technology 412
3 Experiments 415
4 Conclusions 418
Course 9. Some Physical Problems in Bioinformatics
by E.D. Siggia 421
1 Introduction 423
2 New technologies 425
3 Sequence comparison 427
4 Clustering 430
5 Gene regulation 432
Course 10. Three Lectures on Biological Networks
by M.O. Magnasco 435
1 Enzymatic networks. Proofreading knots:
How DNA topoisomerases disentangle DNA 438
1.1 Length scales and energy scales . . . . . . . . . . . . . . . . . . . . 439
1.2 DNA topology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 440
1.3 Topoisomerases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441
1.4 Knots and supercoils . . . . . . . . . . . . . . . . . . . . . . . . . . 444
1.5 Topological equilibrium . . . . . . . . . . . . . . . . . . . . . . . . 446
1.6 Can topoisomerases recognize topology? . . . . . . . . . . . . . . . 447
1.7 Proposal: Kinetic proofreading . . . . . . . . . . . . . . . . . . . . 448
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1.8 How todo it twice . . . . . . . . . . . . . . . . . . . . . . . . . . . 449
1.9 The care and proofreading of knots . . . . . . . . . . . . . . . . . . 451
1.10 Suppression of supercoils. . . . . . . . . . . . . . . . . . . . . . . . 453
1.11 Problems and outlook . . . . . . . . . . . . . . . . . . . . . . . . . 455
1.12 Disquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457
2 Gene expression networks. Methods for analysis
of DNA chip experiments 457
2.1 The regulation of gene expression . . . . . . . . . . . . . . . . . . 457
2.2 Gene expression arrays . . . . . . . . . . . . . . . . . . . . . . . . . 460
2.3 Analysis of array data . . . . . . . . . . . . . . . . . . . . . . . . . 463
2.4 Some simplifying assumptions . . . . . . . . . . . . . . . . . . . . . 464
2.5 Probeset analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466
2.6 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 470
3 Neural and gene expression networks: Song-induced gene
expression in the canary brain 471
3.1 The studyof songbirds . . . . . . . . . . . . . . . . . . . . . . . . . 472
3.2 Canary song. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473
3.3 ZENK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 474
3.4 The blush . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476
3.5 Histological analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 476
3.6 Natural vs. artificial . . . . . . . . . . . . . . . . . . . . . . . . . . 479
3.7 The Blush II:gAP . . . . . . . . . . . . . . . . . . . . . . . . . . . 480
3.8 Meditation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481
Course 11. Thinking About the Brain
by W. Bialek 485
1 Introduction 487
2 Photon counting 491
3 Optimal performance at more complex tasks 501
4 Toward a general principle? 518
5 Learning and complexity 538
6 A little bit about molecules 552
7 Speculative thoughts about the hard problems 564
Seminars by participants 579