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McCammon A.J., Harvey S. — Dynamics Of Proteins And Nucleic Acids
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Название: Dynamics Of Proteins And Nucleic AcidsАвторы: McCammon A.J., Harvey S. Аннотация: This book is a self-contained introduction to the theory of atomic motion in proteins and nucleic acids. An understanding of such motion is essential because it plays a crucially important role in biological activity. The authors, both of whom are well known for their work in this field, describe in detail the major theoretical methods that are likely to be useful in the computer-aided design of drugs, enzymes and other molecules. A variety of theoretical and experimental studies is described and these are critically analyzed to provide a comprehensive picture of dynamic aspects of biomolecular structure and function. The book will be of interest to graduate students and research workers in structural biochemistry (X-ray diffraction and NMR), theoretical chemistry (liquids and polymers), biophysics, enzymology, molecular biology, pharmaceutical chemistry, genetic engineering and biotechnology.
Язык: Рубрика: Медицина и здравоохранение /Статус предметного указателя: Готов указатель с номерами страниц ed2k: ed2k stats Год издания: 1987Количество страниц: 234Добавлена в каталог: 20.11.2006Операции: Положить на полку |
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Предметный указатель
Motions, intramolecular, hinge bending, lac repressor 169—170 Motions, intramolecular, hinge bending, ligand binding 155 Motions, intramolecular, hinge bending, lysozyme 90 140—144 Motions, intramolecular, hinge bending, ribonuclease 90 Motions, intramolecular, hinge bending, tRNA 147—149 Motions, intramolecular, hydrogen bonds 103—104 110—111 Motions, intramolecular, ligand binding 154—155 165—166 Motions, intramolecular, local unfolding 31 142—145 Motions, intramolecular, methyl groups 100—102 Motions, intramolecular, nucleic acids 31—33 Motions, intramolecular, packing rearrangements 30 Motions, intramolecular, proteins 28—31 Motions, intramolecular, rapid 28 31 79—116 Motions, intramolecular, rapid, nucleic acids 105—115 Motions, intramolecular, rapid, proteins 80—105 Motions, intramolecular, secondary structure, effects 32 Motions, intramolecular, sugar repuckering 32 126—129 Motions, intramolecular, table 29 Motions, intramolecular, time scale 115 Motions, intramolecular, time scale, table 29 Motions, intramolecular, torsions 111—112 117 Motions, intramolecular, tyrosine rotation 28 31 54 118—123 172 Motions, intramolecular, tyrosine rotation, experiments 124 Moving pictures 108 113 Multiple minima, effects on dynamics 83 Multiple minimum problem 164 Muscle contraction 137 Myoglobin, collective motions 89 Myoglobin, ligand binding 57 68 118 123 135 154 165—166 Myoglobin, local motion 98—99 Myoglobin, methyl group motions 101 Myoglobin, Mossbauer spectroscopy 102 Myoglobin, structure refinement 162 Myosin, hinge bending 145 Neutron scattering 104 Newton — Raphson method 48—49 Nonbonded exclusions 184 Nonbonded interactions, cutoff distance 40 184 Nonbonded interactions, hydration effects 42—43 Nonbonded interactions, potential function 40 Nonbonded pair list 184 Normal mode analysis 36 57—60 99 138 Normal mode analysis, anharmonic effects 36 59 67 83—84 91 105 Normal mode analysis, damping effects 105 Normal mode analysis, DNA 107 113—115 146 Normal mode analysis, hinge bending 140 Normal mode analysis, low frequency motions 89—90 Normal mode analysis, Monte Carlo methods 161 Normal mode analysis, moving pictures 60 Normal mode analysis, solvent effects 37 Normal mode analysis, thermodynamic parameters 67 Normal mode analysis, torsion space 89—90 Nuclear magnetic resonance, dynamic information 100—105 123—124 Nuclear magnetic resonance, structure refinement 163—164 Nuclear Overhauser effect 100 163—164 Nucleic acids, dynamics 4 31—33 Nucleic acids, function 1—2 Nucleic acids, structure 3 16—22 Nucleic acids, structure, primary 16—17 Nucleic acids, structure, reviews 22 Nucleic acids, structure, secondary 18—21 Nucleic acids, structure, tertiary 19—21 Nucleosome 137 146 Order parameter 100—102 Parameter file 45 184 Partial charges 185 Partial charges, scaling 42 105 Path integrals 39 43 Penicillopepsin 155 Periodic boundary conditions 45 63 Periodic boundary conditions, fluctuating 160 191—193 Periodic boundary conditions, longitudinal 105 Perturbation theory 69—72 Perturbation theory, hydration 71 Perturbation theory, polar hydrogen 182 Polyelectrolyte 34 105 potential energy 187 Potential energy function 39—45 58 Potential energy function, approximations 170—171 Potential energy function, hydration effects 42 Potential energy function, polarization effects 170 Potential of mean force 39—40 42 55 59 67 83 92—93 120 131 138—139 142 150 160 165 171 Potential of mean force, umbrella sampling 69 Potential of mean torque 92 Proteins, dynamics 4 28—31 Proteins, function 1—2 Proteins, structure 3 11—16 Proteins, structure, prediction 164 Proteins, structure, reviews 16 Proteins, structure, rrimary 11—12 Proteins, structure, secondary 15 Proteins, structure, tertiary 16 Pseudodihedral 53 Pseudorotation pathway 126 129 Quantum effects 38—39 60 66 96 Quantum effects, simulation 167 Quasiharmonic approximation 36 67—68 138 160 Quasiharmonic approximation, effects of multiple minima 36 Raman spectroscopy 57 Rate constant 135 Reaction coordinate 46 54—55 66—67 73 Reaction coordinate, choice of 74 172 Reaction coordinate, transition state 131 Reaction coordinate, tyrosine ring flip 119 Ribonuclease, hinge bending 90 Ribonuclease, hydrogen exchange 103 SHAKE 174—180 Site-directed mutagenesis 167 Smoluchowski theory 151—152 Solutions, aqueous, nonpolar solutes 8—9 Solutions, aqueous, polar solutes 10 Steepest descent 47—53 Steepest descent, efficiency 51 Steepest descent, step size 50 Stokes law 26 Stokes law, internal molecular motion 141 Structure, dependence on time scale 6 Structure, refinement by computer simulation 65 161—164 Sugar pucker 21 129 Sugar pucker, DNA helix twist 125 Sugar pucker, fluctuations 111 127—130 Sugar pucker, purines vs pyrimidines 125—127 Sugar pucker, repuckering 126—130 Supercomputers 158—160 Superoxide dismutase 152—154 165 Surface area, solvent-accessible 43 Surface area, solvent-accessible, correlated to motions 108 Temperature factor 91 97 162 Temperature factor, antigenicity, relationship 169 Temperature factor, contributions to 97 Temperature factor, correlations 162 Temperature factor, hydrogen exchange, relationship 104 Temperature factor, simulation 162 Temperature factor, tRNA 107 Theoretical methods 35—78 Theoretical methods, reviews 4 Thermodynamic cycle perturbation method 71—73 Thermodynamic cycle perturbation method, enzyme activity 167—168 Thermodynamic cycle perturbation method, ligand binding 72 166 Thermodynamic cycle perturbation method, umbrella sampling, comparison 71 Topology file 45 183 186 Torsions, backbone: nucleic acids 17 Torsions, backbone: proteins 11 Torsions, improper 183 Torsions, potential function 40 Torsions, sugar 129 Trajectory 46 Transition state theory 131—136 Transition state theory, nonequilibrium effects 135 Transitions, local 117—136 Transitions, local, biological relevance 134 Transitions, local, damping 133 Transitions, local, nucleic acids 124—131 Transitions, local, proteins 118—124 Transitions, local, time scale 117 Transmission coefficient 73 131—132 Transmission coefficient, calculation 75 Transmission coefficient, tyrosine ring flip 121 Triosephosphate isomerase 155 tRNA, anticodon-codon interaction 2 tRNA, crystal structures 20 tRNA, hinge bending 147—149 tRNA, hydrogen bond motions 110—111 tRNA, local motions 106—111 tRNA, molecular dynamics 106 185—187 tRNA, molecular weight 3 tRNA, structure 19—21 Tropomyosin 32 Trypsin 85 145 155 Trypsin inhibitor 80 Trypsin inhibitor, collective motions 89 91 Trypsin inhibitor, global motions 139 Trypsin inhibitor, hydration 84—85 94 100 Trypsin inhibitor, local motions 80—81 83 Trypsin inhibitor, methyl group motions 100—102 Trypsin inhibitor, neutron scattering 104 Trypsin inhibitor, normal mode analysis 60 83 89—90 104 Trypsin inhibitor, structure refinement 162 164 Trypsin, enzyme activity 167 Trypsin, ligand binding 166 Trypsin, molecular dynamics 159 Trypsinogen 145 Tyrosine librations 31 91—95 104 Tyrosine ring flip 54 118—124 Umbrella sampling 68—69 74 Umbrella sampling, large scale deformations 139 Umbrella sampling, thermodynamic cycle perturbation method, comparison 71 Umbrella sampling, tyrosine ring flip 120 Variable metric method 53—54 163 Verlet method 173—174 Verlet method, constrained 176—180 Vibrational motions, normal mode analysis 58 Virtual bonds 53 Virus coat proteins 137 viscosity 26 Viscosity and ligand binding 123 136 Water, dielectric constant 10 Water, diffusion 86 Water, dynamics 25—28 Water, hydrogen bonding 7 Water, molecular dynamics 62 Water, molecule 7 Water, structure 7—8 Water, structure, reviews 11 Water, structure, solute effects 8—11 25—26 X-ray crystallography, dynamic information 96—100 X-ray crystallography, structure refinement by computer simulation 65 161—163 Young's modulus, DNA helix twisting 114 Young's modulus, protein hinge bending 140
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