INTRODUCTION T O

MOLECULARBIOPHYSICS

Jack A. TuszynskiMichal Kurzynski

1 Origins and Evolution of Life

11 .1 Initiation 11 .2 Machinery of prokaryotic cells 31 .3 The photosynthetic revolution 1 01 .4 Origins of diploidal eukaryotic cells 1 51 .5 Summary: further stages of evolution 1 9

References 2 1

2 Structures of Biomolecules

232 .1 Elementary building blocks 2 32 .2 Generalized ester bonds 2 62 .3 Directionality of chemical bonds 302 .4 Weaker intratomic interactions 3 9

2 .4 .1 Ionic interactions 402.4.2 Covalent bonds 422 .4 .3 Free radicals 462 .4 .4 Van der Waals bonds 46

2 .5 Hydrogen bonds and hydrophobic interactions 522 .5 .1 Polysaccharides 59

2 .6 Amphiphilic molecules in water environments 602 .7 Structures of proteins 62

2 .7 .1 Polypeptide chains 672 .7 .2 Proteins 6 82 .7 .3 Protein folding 772 .7 .4 Electrophoresis of proteins 792 .7 .5 Protein interactions with environment 802 .7 .6 Electron transfers in proteins 8 1

2 .8 Structures of nucleic acids 822 .8 .1 Electrostatic potential of DNA 862 .8 .2 DNA: information and damage 8 82 .8 .3 Fluorescence in biomolecules 89References 93

3 Dynamics of Biomolecules

953 .1 Diffusion 95

3 .1 .1 Diffusional flow across membranes 993 .1 .2 Cells without sources 1003 .1 .3 Cells with sources 103

3 .2 Vibrations versus conformational transitions 1093 .3 Stochastic theory of reaction rates 1143 .4 Conformational transitions of proteins 12 2

3 .4 .1 Protein-glass model 124

3 .4 .2 Protein-machine model 1243 .5 Models of random walks on fractal lattices 1273 .6 Introduction to polymer biophysics 13 2

3 .6 .1 Elastic properties of polymers 1363 .7 Cellular automata 137

3 .7 .1 Conway's game of life 1373 .8 Bioenergetics : The Davydov model 13 93 .9 Biological coherence: The Froehlich model 14 23 .10 Ionic currents through electrolytes 14 53 .11 Electron conduction and tunneling 1473 .12 Proton transport 15 1

3 .13 Interactions with electromagnetic radiation 15 2References 15 6

4 Structure of a Biological Cell

15 94 .1 General characteristics of a cell 15 94 .2 Membrane and membrane proteins 16 1

4 .2 .1 Elastic pressure of membrane 16 54 .2 .2 Mass diffusion across membranes 16 54 .2 .3 Membrane proteins 16 64 .2 .4 Electrical potentials of cellular membranes 16 7

4.3 Ion channels and ion pumps 17 14.4 Cytoplasm 17 2

4 .4 .1 Osmotic pressures of cells 17 34 .4 .2 Osmotic work 17 5

4.5 Cytoskeleton : the proteins participatingin cytoskeletal organization 17 64 .5 .1 Cytoskeleton 17 64 .5 .2 Biopolymers of cytoskeleton 17 64 .5 .3 Tubulin 17 84 .5 .4 Microtubules 18 04 .5 .5 Microtubule-associated proteins 18 74 .5 .6 Microfilaments 18 74 .5.7 Actin 18 94 .5 .8 Actin filaments 18 94 .5 .9 Actin-binding proteins 19 04 .5 .10 Intermediate filaments 19 1

4 .6 Networks, stress fibers and tensegrity 19 34.7 Motor proteins and their roles in cellular processes 19 5

4 .7 .1 Myosin family 19 74 .7 .2 Kinesin family 19 84 .7 .3 NCD dimer structure 201

4.7 .4 An overview of KN motion models 20 1

4 .7 .5 Dyneins 20 2

4.8 Centrioles, basal bodies, cilia, and flagella 20 34 .8 .1 Cilia and flagella 20 3

4.9 Cell energetics : chloroplasts and mitochondria 20 64 .9 .1 Cell as a thermodynamic machine 20 94 .9 .2 Active transport 21 1

4 .10 Other organelles 21 14 .11 Nucleus : nuclear chromatin, chromosomes ,

and nuclear lamina 21 24 .11 .1 Chromatin and chromosomes 21 34 .11 .2 Nucleolus 21 34 .11 .3 Nuclear envelope 21 4

4 .11 .4 Nuclear pores 21 44 .12 Cell division 214

4.12 .1 Centrioles, centrosomes, and aster formation 21 64 .12 .2 Chromosome segregation 21 7

4 .12.3 Cytokinesis 21 8

4 .12 .4 Spindle and chromosome motility 2204 .13 Cell intelligence 22 14 .14 Biological signaling 222

References 225

S Nonequilibrium Thermodynamics and Biochemical Reactions

2295 .1 Second law of thermodynamics 2295 .2 Nonequilibrium thermodynamics 23 3

5 .3 Rates of nonequilibrium thermodynamic processes 24 1

5 .4 Single unimolecular chemical reaction 2445.5 Bimolecular reactions : protolysis 2495.6 Redox reactions 25 3

5 .7 The steady state approximation: the theoryof reaction rates 25 7

5 .8 Chemical mechanisms of enzymatic catalysis 2605 .9 Michaelis-Menten kinetics 264

5 .10 Control of enzymatic reactions 269References 27 5

6 Molecular Biological Machines

2776 .1 Biological motion 277

6 .2 Free energy transduction 27 86 .3 Chemochemical machines 2826 .4 Biological machines as biased Maxwell's demons 2866 .5 Pumps and motors as chemochemical machines 28 7

6 .6 Flux-force dependence 29 16 .7 Overview of motor protein biophysics 2966 .8 Biochemical energy currency: ATP molecules 299

6 .8 .1 Structure of ATP 30 06 .8 .2 Functions of ATP 30 16 .8 .3 Double energy packet 30 26 .8 .4 Methods of producing ATP 30 36 .8 .5 Chloroplasts 30 4

6 .9 Assembly of microtubules 30 46 .10 Assembly of actin filaments 30 86 .11 Muscle contraction : biophysical mechanism s

and contractile proteins 31 3References 31 6

7 Nerve Cells

31 97 .1 Anatomy of a nerve cell 31 97 .2 Conducting properties of neurons 32 17 .3 Action potential generation : Hodgkin-Huxley

equations 32 57 .4 Structure and function of synapse 33 17 .5 Neural network models 33 5

7 .5 .1 Memory 33 8References 33 9

8 Tissue and Organ Biophysics

34 18 .1 Introduction 34 1

8 .1 .1 Pressure in human organs 34 18 .2 Anatomy and physiology of human circulatory system 34 2

8 .2 .1 Circulation of blood 34 28 .2 .2 Cardiovascular system 34 38 .2 .3 Regulation of fluid between cells (interstitial fluid) 34 98 .2 .4 Gas exchange with circulatory system 35 0

8 .3 Heart dynamics 35 28 .4 Energy management in the human body 35 38 .5 Respiration biophysics 35 58 .6 Kidney physiology and dialysis 36 08 .7 Muscle biophysics 36 18 .8 Bone stiffness and strength 36 78 .9 Vision biophysics 36 8

8 .9 .1 Wavelength responses 37 08 .9 .2 Optical properties 37 18 .9 .3 Light absorption and black-and-white vision 37 28 .9 .4 Color vision 37 38 .9 .5 Resolution of the human eye 37 58 .9 .6 Quantum response of the eye 37 6

8 .10 Sound perception biophysics 37 88 .11 Gross features of the nervous system 38 08 .12 Bioelectricity and biomagnetism 384

8 .12 .1 Biological piezoelectricity 38 88 .12 .2 Biomagnetism 38 8

8 .13 Immune system and its models 38 9References 39 2

9 Biological Self-Regulation and Self-Organization

3959 .1 Introduction 39 59 .2 Self-organization 39 59 .3 Homeostasis 39 79 .4 First law of thermodynamics and living organisms 3989.5 Physics of animal thermoregulation 3999.6 Allometric laws in physiology 403

9 .6 .1 Introductory scaling concepts 40 39 .6 .2 Overview of allometric laws of physiology 4049.6 .3 Fractals and living systems 407

9.7 Entropy and information 4089 .8 Entropy reduction in living systems 4099 .9 Biological information 4149 .10 Evolutionary theories 416

9 .10 .1 Punctuated equilibria 4169 .10 .2 Mathematical modeling of evolution 41 79 .10 .3 Mathematical models of population genetics 41 89 .10 .4 Artificial life 419References 420

10 Epilogue: Toward New Physics and New Biology

42510 .1 Toward new physics 42510 .2 Toward new biology 426

10 .2.1 Biocomputing 42710 .2.2 Biophysics : the physics of animate matter

or an experimental biological tool? 430References 43 1

Appendix ARandom Walks and Diffusion

433Introduction 43 3Gaussian probability distributions 43 8Diffusion equation 440Probability of displacement for a three-dimensionalrandom walk 44 1Diffusion equation 443Example 445Diffusion equation (differential form) 448Example 450Particle conservation 45 3

Appendix B Models of Phase Transitions and Criticality

45 5Introduction 45 5Ctystals 455

Structural phase trastions 456Perroelectrictiy 45 7Magnetic orderings 45 7Ordering transitions in binary alloys 45 7Subpeconductivity 457Superfluidity 458Liquid crystals 458References 478

Appendix C Foundations of Nonlinear Physics

48 1Multistability and bifurcation 48 1Stochastic analogue of a bifurcation 484Harmonic versus anharmonic motion 48 6External driving and dissipation 48 7Relaxation dynamics and asymptotic stability 49 1Coupled systems and limit cycles 49 3Nonlinear waves and solitons 49 6Pattern formation 50 3

Pattern formation in fluid dynamics 503Pattern formation in liquid crystals 503Pattern formation in polymers 504Crystal growth and structural transitions 504Chemical instabilities 505

Chaos and turbulence 505Landau scenario 506Ruelle-Takens-Newhouse scenario 507Feigenbaum picture 507Pomeau-Manneville scenario 509

Fractals 509Self-organized criticality 510References 51 3

Appendix D Master Equations

517References 51 9

Index

521