9780471628019
Proteins: A Theoretical Perspective Of Dynamics, Structure, And Thermodynamics - Charles L. Brooks, Martin Karplus, B. Montgomery Pettitt
Wiley-Interscience (1988)
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Science

Presenting a wide-ranging view of current developments in protein research, the papers in this collection, each written by highly regarded experts in the field, examine various aspects of protein structure, functions, dynamics, and experimentation. Topics include dynamical simulation methods, the biological role of atom fluctuations, protein folding, influences on protein dynamics, and a variety of analytical techniques, such as X-ray diffraction, vibrational spectroscopy, photodissociation and rebinding kinetics. This is part of a series devoted to providing general information on a wide variety of topics in chemical physics in order to stimulate new research and to serve as a text for beginners in a particular area of chemical physics.



CONTENTS

I. INTRODUCTION 1

II. PROTEIN STRUCTURE AND DYNAMICS-AN OVERVIEW 7
A. The Structure of Proteins 7
B. Overview of Protein Motions 14

III. POTENTIAL FUNCTIONS 23
A. Theoretical Basis 23
B. Form of Potential Functions 25
C. Parameter Determination 30

IV. DYNAMICAL SIMULATION METHODS 33
A. General Features of Molecular Dynamics Methods 33
B. Molecular Dynamics with Conventional Periodic Boundary Conditions 36
C. Molecular Dynamics with Stochastic Boundary Conditions 38
D. Stochastic Dynamics with a Potential of Mean Force 44
E. Activated Dynamics 46
F. Harmonic and Quasi-Harmonic Dynamics 49
G. Algorithms for Molecular and Stochastic Dynamics 51
H. Minimization Algorithms 54

V. THERMODYNAMIC METHODS 59
A. Vacuum Calculations 59
B. Free Energies in the Condensed Phase 62
C. Thermodynamic Perturbation Theory 66

VI. ATOM AND SIDECHAIN MOTIONS 75
A. Atom Motions 75
1. Amplitudes and Distributions 76
2. Time Dependence: Local and Collective Effects 84
3. Harmonic Dynamics 87
4. Biological Role of Atom Fluctuations 94
B. Sidechain Motions 95
1. Aromatic Sidechains 95
2. Ligand-Protein Interaction in Myoglobin and Hemoglobin 111

VII. RIGID-BODY MOTIONS 117
A. Helix Motions 117
B. Domain Motions 119
C. Subunit Motions 125

VIII. LARGER-SCALE MOTIONS 127
A. Helix-Coil Transition 128
B. Protein Folding 129
C. Disorder-to-Order Transitions 132
1. Trypsinogen-Trypsin Transition 133
2. Triosephosphate Isomerase 135

IX. SOLVENT INFLUENCE ON PROTEIN DYNAMICS 137
A. Global Influences on the Structure and Motional Amplitudes 137
B. Influence on Dynamics 142
1. Alanine Dipeptide Results 143
2. Protein Results 146
3. Stochastic Dynamics Simulations of Barrier Crossing
in Solution 153
C. Solvent Dynamics and Structure 154
D. Role of Water in Enzyme Active Sites 161
E. Solvent Role in Ligand-Binding Reactions 169

X. THERMODYNAMIC ASPECTS 175
A. Conformational Equilibria of Peptides 175
B. Configurational Entropy of Proteins 180
C. Ligand Binding, Mutagenesis, and Drug Design 183

XI. EXPERIMENTAL COMPARISONS AND ANALYSIS 191
A. X-Ray Diffraction 191
B. Nuclear Magnetic Resonance 199
C. Fluorescence Depolarization 211
D. Vibrational Spectroscopy 216
E. Electron Spin Relaxation 218
F. Hydrogen Exchange 219
G. Mossbauer Spectroscopy 221
H. Photodissociation and Rebinding Kinetics 223

XII. CONCLUDING DISCUSSION 225

REFERENCES 233

INDEX 251

Product Details
LoC Classification QD453.A27 .vol. 71
Dewey 547.7/5
Format Hardcover
Cover Price 290,00 €
No. of Pages 259
Height x Width 240 mm