McCammon A.J., Harvey S. — Dynamics Of Proteins And Nucleic Acids :: Электронная библиотека попечительского совета мехмата МГУ

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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 Acids

Авторы: 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.

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Рубрика: Медицина и здравоохранение/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 1987

Количество страниц: 234

Добавлена в каталог: 20.11.2006

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Предметный указатель

Activated process      54 116 131
Activated process, reaction coordinate      131 172
Activated process, simulation by activated molecular dynamics      73—75
Activation volume      135
Adiabatic mapping      35—37 46 54—57 117—118
Adiabatic mapping, convergence      55—57
Adiabatic mapping, DNA helix bending      145—147
Adiabatic mapping, DNA helix twist      125 145—146
Adiabatic mapping, DNA melting      125
Adiabatic mapping, global motions      138
Adiabatic mapping, hinge bending: lysozyme      140;
Adiabatic mapping, hinge bending: tRNA      147—149
Adiabatic mapping, large scale deformations      54 57 139
Adiabatic mapping, myoglobin      118
Adiabatic mapping, thermodynamic considerations      47 55
Adiabatic mapping, tyrosine ring flip      54 119—120
Adopted basis set Newton — Raphson method      49
Allosteric transitions      172
Alpha helix      15
AMBER      181
Anharmonicity      36 59 72 82—84 99 107 109—110 116 162
Anharmonicity, quasiharmonic approximation      67—68
Anisotropy      81 84 107—109
Antibodies      137
Antibodies, hinge bending      149
Antibody-antigen interactions flexibility      169
Arabinose-binding protein, hinge bending      141 144 169
Arabinose-binding protein, ligand binding      172
Arabinose-binding protein, solvation      150 172
Argon, liquid      62 65
Array processors      159
Atom type      183 185
Base pairing      18—19
Base stacking      19
Beeman method      174—175
Beta sheet      15
Bond angle, potential function      40
Born — Oppenheimer treatment      39 42 66
Brownian dynamics      37—38 75—78 161 171
Brownian dynamics, diffusional encounter      152—154 165 170
Brownian dynamics, DNA helix bending      146
Brownian dynamics, hydrodynamic interactions      77
Brownian dynamics, Langevin equation, relationship      139
Brownian dynamics, large scale motions      139
Brownian dynamics, local motions      145
Brownian dynamics, protein denaturation      142
Brownian dynamics, rate constant calculations      77—78
Catabolite activator protein      170
Cedar      181
CHARMM      181
Collagen      32
Collision frequency      93--5 190
Computer programs, description      181—187
Computing methods, advances in hardware      158—160
Computing methods, advances in methodology      160—161
Conjugate gradient      47—48 51—53
Conjugate gradient, convergence on quadratic surface      51
Conjugate gradient, efficiency      52
Constraints, during molecular dynamics      176—180
Constraints, forces      46
Coordinate file      45 183
Correlation function, time, definition      84
Correlation function, time, Langevin oscillator      95
Correlation function, time, range of validity      94
Counterion condensation      19
Covalent bond, potential function      40
Crankshaft motions      112
Cutoff distance      40 184
Cytochrome c      14 80 98
Cytochrome c, collective motions      82 87—89 91
Debye — Hueckel model      153
Debye — Waller factor      97
Denaturation      31 33
Denaturation, Brownian dynamics      142
Denaturation, local      138 142
Denaturation, molecular dynamics      97
Descent techniques, iterative      50
Dielectric coefficient      42
Dielectric coefficient, distance-dependent      42
Dielectric coefficient, effective      43—44
Dielectric coefficient, scaling      105
dielectric constant      153
Dielectric constant, liquid hydrocarbons      10
Dielectric constant, water      10
Dielectric screening      40 42—43 97 105 150 171
Diffusion      26
Diffusion coefficient      26
Diffusion coefficient, hydrodynamic models      77
Diffusion coefficient, relative      33 76
Diffusion coefficient, water at protein surface      86
Diffusion in solids      132
Diffusion, Brownjan dynamics simulations      37 75—78 152—154 165 170
Diffusion, denaturation      138 142
Diffusion, Einstein relationship      26 93
Diffusion, flexible solutes      27
Diffusion, gated      34 155
Diffusion, hydrodynamic interactions, effects of      33 76—77
Diffusion, internal motions in macromolecules      93
Diffusion, intramolecular flexibility      145
Diffusion, intramolecular flexibility: tRNA      147
Diffusion, ligand binding      34 154 165
Diffusion, molecular associations      151—152 170:
Diffusion, oxygen in protein      104
Diffusion, rotational      93 100
Diffusion, superoxide dismutase      152—154
Diffusional encounter      33 151—154
Dispersion forces      16 19
Distribution function moments      82 107
DNA, A-DNA      19
DNA, atomic displacements      107
DNA, B-DNA      19
DNA, B-Z transition      33 130
DNA, double helix      19
DNA, function      1
DNA, helix bending      145—147
DNA, helix twist      125 145—146
DNA, hydration      19
DNA, left-handed      3 19
DNA, molecular weight      3
DNA, secondary structure      3 18—19
DNA, secondary structure: melting      125
DNA, structure: reviews      19;
DNA, structure: sequence-dependence      3 112—113
DNA, sugar pucker      125
DNA, torsional stiffness      114
DNA, Z-DNA      19 107 111—114 127
DNA, Z-DNA, structure refinement      162
Electron transfer      39 171
Electrostatic interactions, diffusional encounter      153—154
Electrostatic interactions, polarization effects      39 42 132—133 135;
Electrostatic interactions, polarization effects, modeling      171
Electrostatic interactions, potential function      40
Electrostatic interactions, solvent screening      11 19 44 153—154
Energy minimization      36 47—54
Energy minimization, Crystallographic refinement      46
Energy minimization, molecular dynamics: relationship      44—47
Energy minimization, thermodynamic considerations      47
Enthalpy, activation      135
Enthalpy, configurational      66
Enthalpy, entropy      36 47 121
Enthalpy, hydration      9
Enthalpy, ligand binding      118
Enthalpy, molecular association      22—23 169
Enthalpy, normal mode analysis      67
Enthalpy, quasiharmonic approximation      67
Enthalpy, thermodynamic cycle perturbation method      166
Enthalpy, umbrella sampling      69
Enthalpy, vibrational      130
Enzyme activity      167—168
Equations of motion      46 61—62

Equations of motion, numerical integration      173—180
Experimental methods reviews      5
Extended atoms      58 182
Flash photolysis      123
Fluorescence depolarization      104
Fluorescence depolarization, hinge bending motions      144—145
Fluorescence depolarization, simulation      146
Fluorescence quenching      104
Free energy calculations      66—73
Free energy calculations, ligand binding      166
Free energy calculations, normal mode analysis      67
Free energy calculations, perturbation theory      69—70
Free energy calculations, potential of mean force      69
Free energy calculations, solvation      70
Free energy calculations, thermodynamic integration      72
Free energy calculations, umbrella sampling      68 120
Friction coefficient      26 77
Friction coefficient, effect on reaction rate      131
Gated process      133—134 170
Gated process, ligand binding      123 136 155—156 166 169
Gated process, ring rotations      133
Gated process, tyrosine ring flip      121
Gear method      176
Gibbs free energy      67
Grid search      48 53
GROMOS      181
Haemoglobin, function      1
Haemoglobin, ligand binding      154 165
Haemoglobin, protein exchange      103
harmonic oscillator      59
Harmonic oscillator, Langevin equation      92—93 110 140
Harmonic oscillator, multidimensional      59
Helmholtz free energy      67 70
Hexokinase, hinge bending      145
Hydration, ionic      10 25—26
Hydration, ligand binding      171
Hydration, nonpolar solutes      8—9
Hydration, nucleic acids      19
Hydration, potential functions      42—43
Hydration, proteins      14
Hydrodynamic models      76—77
Hydrogen bond      7 182—184 186
Hydrogen bond in proteins      15
Hydrogen bond, geometry      182
Hydrogen bond, motions      103—104 110—111
Hydrogen bond, potential function      41 186
Hydrogen exchange, DNA      125—126
Hydrogen exchange, models      103
Hydrogen exchange, nucleic acids      33
Hydrogen exchange, proteins      102—104
Hydrophobic effect      10—11 13 16 19
Ice, structure      8
Immunoglobulins, hinge bending      145
Infrared absorption spectroscopy      57
Intercalation      34 130
Internal coordinates      45 49 182
Internal energy, normal mode analysis      67
Internal energy, umbrella sampling      69
Ions, hydration      10 25—26
Lac repressor      163
Lac repressor, hinge bending      169—170
Langevin equation      27
Langevin equation, Brownian dynamics, relationship      139
Langevin equation, effective friction constant, calculation      94
Langevin equation, harmonic oscillator      92—93 110 140
Langevin equation, internal motions      35 55 92—94 138 140
Langevin equation, stochastic boundary conditions      64
Leapfrog method      174
Ligand binding      67 117 165—166
Ligand binding, hydration effects      171
Ligand binding, perturbation theory      72
Ligand binding, proteins      2—3
Liquid structure      116
Lysozyme, hinge bending      90 140—144
Mean square displacement matrix      81
Minimum image convention      63
Models, phenomenological      27—28 91—95 165
Molecular association      22—24 33—34 168—170
Molecular association, dynamics      151—156
Molecular association, hydration changes      34
Molecular association, protein-DNA interactions      23
Molecular association, reviews      24
Molecular association, solvent effects      43
Molecular Dynamics      6 36—37 60—66
Molecular dynamics, activated molecular dynamics      73—75 117
Molecular dynamics, activated molecular dynamics, oxygen in myoglobin      165—166;
Molecular dynamics, activated molecular dynamics, tyrosine ring flip      118—123
Molecular dynamics, activated processes      37
Molecular dynamics, active site      37 64—65
Molecular dynamics, constant pressure      64 188—189 191—193
Molecular dynamics, constant temperature      64 188—191
Molecular dynamics, constrained      38 176—180
Molecular dynamics, crystal environment      84
Molecular dynamics, crystallographic refinement      65 162—163
Molecular dynamics, DNA      146
Molecular dynamics, DNA, instability      105
Molecular dynamics, DNA, table      106
Molecular dynamics, energy conservation      62
Molecular dynamics, energy minimization      65
Molecular dynamics, energy minimization, relationship      44—47
Molecular dynamics, equilibration      187
Molecular dynamics, history      62
Molecular dynamics, large scale deformations      57 139
Molecular dynamics, ligand binding      165—166
Molecular dynamics, limitations      65—66 157
Molecular dynamics, low temperature      65 163
Molecular dynamics, Monte Carlo, comparison      38 66
Molecular dynamics, periodic boundary conditions      45 63 160
Molecular dynamics, quantum corrections      38—39
Molecular dynamics, rare events      37
Molecular dynamics, solvent      62 159
Molecular dynamics, solvent, effects      84—85 107;
Molecular dynamics, solvent, mobility      85—86
Molecular dynamics, stochastic boundary conditions      65 160
Molecular dynamics, structure refinement      65 161—164
Molecular dynamics, thermodynamic considerations      47
Molecular dynamics, thermodynamic ensembles      64 188—189
Molecular dynamics, warmup      187
Molecular mechanics      39 44 58
Monte Carlo method      6 38
Monte Carlo method, efficiency      38 66
Monte Carlo method, molecular dynamics, comparison      38 66
Monte Carlo method, normal modes      161
Mossbauer spectroscopy      102
Motions, intramolecular, amplitude      80—82 87 107 115
Motions, intramolecular, amplitude, solvent effects      85—86
Motions, intramolecular, amplitude, table      29;
Motions, intramolecular, amplitude, time-dependence      84 87
Motions, intramolecular, anharmonicity      36 59 72 82—84 99 107 109—110 116 162
Motions, intramolecular, anharmonicity, quasiharmonic approximation      67—68
Motions, intramolecular, anisotropy      81 84 107—109
Motions, intramolecular, antigenicity, relationship      169
Motions, intramolecular, base pair melting      33
Motions, intramolecular, charge effects      32
Motions, intramolecular, collective      87—91 115—116
Motions, intramolecular, comparison of proteins and nucleic acids      32
Motions, intramolecular, correlations      84 88—89 98 110—112 116
Motions, intramolecular, damping      30—31 75 80 93 115—117 137 149—150
Motions, intramolecular, damping, DNA bending      146
Motions, intramolecular, damping, lysozyme hinge bending      141
Motions, intramolecular, damping, tRNA      149
Motions, intramolecular, elastic      30—32 137—138 140 144 146 149
Motions, intramolecular, experimental comparisons      96—105 115 142 144—145 147
Motions, intramolecular, global      30—32 137—150
Motions, intramolecular, global, biological significance      137
Motions, intramolecular, global, nucleic acids      145—149;
Motions, intramolecular, global, proteins      139—145
Motions, intramolecular, helix-coil transition      31 142—144
Motions, intramolecular, hinge bending      29—32 139—145
Motions, intramolecular, hinge bending, arabinose-binding protein      141 144 169

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