Fersht A. — Structure and Mechanism in Protein Science :: Электронная библиотека попечительского совета мехмата МГУ

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Fersht A. — Structure and Mechanism in Protein Science

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Название: Structure and Mechanism in Protein Science

Автор: Fersht A.

Аннотация:

By concentrating on fundamental principles and the physical and chemical processes behind them, Structure and Mechanism in Protein Science makes the basic formulas, Kinetics, and thermodynamics of protein engineering easier to understand and apply. Up-to-date, authoritative, and full of relevant examples, it provides a solid introduction to a sprawling, still-growing field.

Язык:

Рубрика: Физика/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Год издания: 1999

Количество страниц: 630

Добавлена в каталог: 30.11.2005

Операции: Положить на полку | Скопировать ссылку для форума | Скопировать ID

Предметный указатель

Intramolecular catalysis, entropy and      68—69
Intramolecular catalysis, versus intermolecular catalysis      69—70
Intrinsic binding energy      341
Intron      25 26
Ionization constants of acids and bases      169—173
Ionization constants of acids and bases, extraction of $pK_{a}$ from equations      173
Ionization constants of acids and bases, kinetic $pK_{a}$       179
Ionization constants of acids and bases, macroscopic $pK_{a}$       179
Ionization constants of acids and bases, microscopic $pK_{a}$       179
Ionization constants of groups in enzymes      170 468
Ionization constants of groups in enzymes, determination from rates of chemical modification      187
Ionization constants of groups in enzymes, determination from rates of irreversible inhibition      187 278
Ionization constants of groups in enzymes, determination from steady state kinetics      174—176 182—184
Ionization constants of groups in enzymes, direct determination      184—187
Ionization constants of groups in enzymes, effect of surface charge      179—180
Ionization constants of groups in enzymes, effects of environment      187—189
Ionization constants of groups in enzymes, highly perturbed      188 189
Isocitrate dehydrogenase      294 459
Isoleucyl-tRNA synthetase      237—239 378 379 385 387—389
Isoleucyl-tRNA synthetase, molecular mechanism of editing      388 389
Isomorphous replacement      4
Isosteric      378 425 427
Isothermal titration calorimetry (ITC)      207
Isotope exchange kinetics      47 235 236 240 563—569
Isotope incorporation      489
Isozyme      461—465
Jellyroll      20 21
Jigsaw model      576 583
K system      294
K system, structural explanation      311
Kallikrein      475
kinesin      317 318
Kinetic $pK_{a}$       178
Kinetic equivalence      94—96 482 555
Kinetic isotope effects      96—99 235 284 490 498
Kinetic isotope effects, hydride transfer reactions      97 98 463—465
Kinetic proofreading      398
Klenow enzyme      405 413
Koshland — Nemethy — Filmer mechanism      295—297
Label-free optical detection      199
Lactate dehydrogenase      465—469 472
Lattice simulations      597
Leaving group      81 86 88—93
Levinthal’s paradox      575 576 598 599 600
Linear free-energy relationships      58 62—65 86 87 599
Linear free-energy relationships, protein engineering of enzymes and      442—444
Linear free-energy relationships, protein folding and      579 581 582
Lineweaver — Burk plot      111 112 114 120
Linked assays      196
Linked equilibria      127—129
Lipoic acid      37
Liver alcohol dehydrogenase      see “Alcohol dehydrogenase”
Lock-and-key hypothesis      354 369
Loops      20 51
Loops, kinetics of formation      541 569
Lysozyme      23 32 33 43 44 50 497—500
Lysozyme, $pK_{a}$ ’s of groups at active site      186 189
Lysozyme, affinity labeling      282
Lysozyme, association rate constants      154 165
Lysozyme, crystal and solution structure      50
Lysozyme, electrostatic effects      60 61 499—500
Lysozyme, enzyme-substrate complex      44
Lysozyme, evolution      33
Lysozyme, exons      33
Lysozyme, kinetic isotope effects      99
Lysozyme, kinetics of ligand binding to      154 165
Lysozyme, lack of accumulation of intermediates      374
Lysozyme, nonproductive binding      113—116 371
Lysozyme, oxocarbenium ion      57 58 60 359 498
Lysozyme, pH dependence of catalysis      497—500
Lysozyme, stereochemistry of reaction      255 497
Lysozyme, strain      358 372—374 497—500
Lysozyme, subsites      44 371
Lysozyme, substrate distortion      358 372—374 497—500
Lysozyme, tertiary structure      23
Lysozyme, transition stage analogues      358 359
Lysozyme, transition state of reaction      60 61
Lysozyme, van der Waals binding energy of D subsite      329
Macroscopic $pK_{a}$       179
Malate dehydrogenase      465—469
Malate synthase      258
Mass action ratio      308
Mass spectroscopy      242—243
Meander      20
Mechanism, definition      216
Mechanism-based inhibitors      see “Suicide inhibitors”
Metabolite concentrations in vivo      366 367
Metal ion catalysis      74—77
Metal ion catalysis, electrophilic      74—77 92 392—394 462 463 483—486
Metal ion catalysis, metal-bound hydroxyl (alkoxide) ion      76 77 392—394 483
Metalloenzymes      74—77 460—463 473 483—486
Metaphosphate      259
Methionyl-tRNA synthetase      387
Methyl-methylene transformations      256—260
Methylene group (prochiral)      256 257
Michael addition reactions      272 277 284 285
Michael is complex      106
Michaelis constant ( $K_{M}$ )      105—109
Michaelis constant ( $K_{M}$ ), evolution of      363—368
Michaelis constant ( $K_{M}$ ), meaning of      109
Michaelis constant ( $K_{M}$ ), pH dependence of      169 174—176
Michaelis — Menten equation      104—109
Michaelis — Menten equation, affinity labels      277
Michaelis — Menten equation, breakdown      119
Michaelis — Menten mechanism      105—107
Michaelis — Menten mechanism, pH dependence      173—175
Michaelis — Menten mechanism, specificity      380—383
Michaelis — Menten mechanism, thermodynamic analysis      349—355
Microscopic $pK_{a}$       179
Microscopic reversibility      93 94 493 500
Minichaperones      606 607 609 610
Modular structure of proteins      33 34
Module      33 577 596 602
Molecular chaperones      603—610
Molecular clock      315
Molecular dynamics simulation      537 574 583 584 589 591 592 597
Molecular isotope exchange      266
Molecular tumbling      46
Molten globule state      520 599 600
Monoamine oxidases      284 285
Monod — Wyman — Changeux mechanism      292—296 300—304
Monod — Wyman — Changeux mechanism, versus Koshland — Nemethy — Filmer mechanism      303—304
Monte Carlo methods      597
Motif      9
Motor proteins      317—321
mRNA      26 404 413 415
Multi-point attachment theory      248
Multienzyme complexes      34—38
Multiproduct analogue      360 361
Multisubstrate analogue      360 361
Multisubstrate systems      119—122
Mutagenesis      413—416
Mutagenesis, deletion      445
Mutagenesis, oligodeoxynucleotide-directed      413 414
Mutagenesis, PCR      413 414
Mutagenesis, random      415 416 418
Mutagenesis, site-specific      413—415
Mutations, choosing      425—427
Mutations, isosteric substitution      427
Mutations, mutator strain of T4 phage      390 391
Mutations, nondisruptive deletion      426 560
Myoglobin      11 22 51 289 290 305—307
myosin      317 318
NAD-pyruvate      467
NAD-pyruvate, stereochemistry of oxidation-reduction      249 250 548 459
NAD-pyruvate, structure      249
NADH extinction coefficient      192
NAG, NAM      43
Negative cooperativity      296 297
Net rate constants      122—125

Neutron diffraction      6 47
Nicotinamide adenine dinucleotide      see “ $NAD^{+}$ ”
Nitrocellulose filters      205
Non-Arrhenius kinetics      555 598
Nonbonded interactions      325—332
Nondisruptive deletion      426 560
Nonequilibrium dialysis      202
Nonproductive binding      114—118 371—372
Nonproductive binding, effect on equilibria on enzyme surface      118
Nonproductive binding, effect on ionization constants      177
Nonproductive binding, effect on specificity      372 381
Nonproductive binding, effect on steady state kinetics      114—118
Normal distribution      210
Nuclear magnetic resonance (NMR), $^{15}N-NMR$ relaxation      49
Nuclear magnetic resonance (NMR), chemical shift      7
Nuclear magnetic resonance (NMR), determination of chirality      251 259 265 266
Nuclear magnetic resonance (NMR), determination of dissociation rate constants      138
Nuclear magnetic resonance (NMR), determination of intracellular pH      186
Nuclear magnetic resonance (NMR), determination of ionization constants      185 186
Nuclear magnetic resonance (NMR), determination of rotational correlation times      46
Nuclear magnetic resonance (NMR), determination of structure      7
Nuclear magnetic resonance (NMR), exchange broadening      138
Nuclear magnetic resonance (NMR), line-width analysis      138 541
Nuclear magnetic resonance (NMR), Nuclear Overhauser Effect (NOE)      7
Nuclear magnetic resonance (NMR), protein mobility and      46—49
Nuclear magnetic resonance (NMR), rotation of amino acid side chains and      47 48
Nucleation mechanism      575 576 583 586
Nucleation-collapse      see “Nucleation-condensation mechanism”
Nucleation-condensation mechanism      583 585—588
Nucleophilic attack on carbonyl group      86—90
Nucleophilic attack on phosphoryl and sulfuryl groups      89 90 260—266
Nucleophilic attack on saturated carbon      90 91
Nucleophilic catalysis      61 84 85
Nucleophilic catalysis, examples with enzymes      45 85 100 101 311
Nucleophilic catalysis, stereochemistry      254—256
Nucleophilic groups on enzymes      76 84 85 274—276
Nucleophilicity      85—92
Nucleotide binding fold      32 459
Off-lattice simulation      597
Oligomer      24
Operon      35
Ordered mechanism      119 120
Oxocarbenium ion      57 58 60 359 498
P-loop      see “Walker consensus sequence”
Packing density      24
Papain      482
Parallel reactions      149
Parallel reactions, versus single in folding      579—582
Parkinson’s Disease      285
Partitioning of products      225—234
PCR      408—410 412—416
PCR, error prone      415
Penicillinopepsin      486
Pepsin      486—491
Pepsin, affinity labeling of carboxylates      280 487
Pepsin, binding energies of subsites      356 357
Pepsin, kinetic constants for peptide hydrolysis      357
Pepsinogen      490
Pepstatin      489 490
Peptide bond      9 10
Peptides, kinetics of folding      569 570
Peptidyl-proline bond isomerization      541 542 591
Peptidyl-prolyl isomerase      454 603
Peptidyl-prolyl isomerase, protein engineering to cyproase      1 454
pH dependence of enzyme catalysis      173—180 460 462 473 474 480 486 490 493 494 498 499
pH dependence of irreversible inhibition and affinity labeling      187 278 279 468 487
pH-jump method      222
Phage display      see “Bacteriophage”
Phosphofructokinase      309—312
Phosphofructokinase, anomeric specificity      252 253
Phosphoglycerate kinase      23 32 268
Phosphoglycerate kinase, double-mutant cycle $\Phi$ -value analysis      594
Phosphoglycerate mutase      119 120
Phosphoramidon      484
Phosphorothioate group      264
Phosphory lase kinase      312—314
Phosphory lation/dephosphorylation for control      312—315
Phosphoryl transfer reactions      259—261
Phosphoryl transfer reactions, stereochemistry      259—266 267 268
Phosphorylases      45 312—315
Photoaffinity labeling      280
PI3 kinase SH3 domain, folding kinetics      552
Picket fence model for heme      307
Ping-pong kinetics      119—121
Plasmid      412
Plasmid, pBR322      412
Plasminogen activator inhibitor      33
Plotting kinetic and binding data      199—201 207—209
Plotting kinetic and binding data, $pK_{a}$ ’s      181 182
Plotting kinetic and binding data, computer fitting      209
Plotting kinetic and binding data, first order reactions      199 200
Plotting kinetic and binding data, Michaelis — Menten kinetics      201
Plotting kinetic and binding data, second order reactions      200
Poisson distribution      212 410
Polarizability      328 329
Polymerase chain reaction      see “PGR”
Polymerization kinetics      124 390—392
Positional isotope exchange      265 266
Pre-steady state      103
Pre-steady state kinetics      132—158
Pre-steady state versus steady-state kinetics      216 217
Primary structure      3 4
Principle of maximization of $K_{M}$ at constant $k_{cat}/K_{M}$       363 364
Procarboxypeptidase      486
Procarboxypeptidase A2 activation domain, $\Phi$ -value analysis      594
Procarboxypeptidase A2 activation domain, folding kinetics      552 594
Processive polymerisation      410
Prochirality      245 247 250 257 262—266
Proflavin      220 221
Proline cis-trans equilibrium      9 10
Proline racemase      359
Promoter      412
Proofreading      see “Editing”
Protease A (Streptomyces griseus)      28 475 477
Protease G (Streptomyces albus)      483
Proteases      472—491
Protein disulfide isomerase      603
Protein engineering      401 420—456
Protein engineering, $pK_{a}$       180 327
Protein engineering, $\Phi$ -value analysis      558—563
Protein engineering, Bronsted equation and catalysis      442—444
Protein engineering, Bronsted equation and protein folding      579—582 590
Protein engineering, changing specificity      452—454 465 468 469 481 482
Protein engineering, construction of hetero-oligomers      446—449
Protein engineering, determination of energetics of protein structure      523—533
Protein engineering, differential and uniform binding energy changes      438 439
Protein engineering, dissection of catalytic triad of serine proteases      450—452
Protein engineering, domain structure analysis      445—449
Protein engineering, evidence for enzyme-intermediate state complementarity      430—432
Protein engineering, evidence for enzyme-transition state complementarity      362 428—430
Protein engineering, evolution of activity      438—442
Protein engineering, examples      180 297 310 339 480 481 496
Protein engineering, half-of-the-sites activity      448
Protein engineering, hydrogen exchange kinetics      566
Protein engineering, increasing protein stability      532
Protein engineering, kinetic isotope effects      465
Protein engineering, linear free energy relationships with binding energy changes      442—444
Protein engineering, protein stability changes      523
Protein engineering, reverse genetics      438—442
Protein engineering, surface charge      180 327
Protein kinases      312 314
Protein stability, $\alpha$ helix      523—532
Protein stability, $\beta$ sheet      528 529 532
Protein stability, engineering increases in      532 535 536
Protein stability, stability and activity      536
Protein, biosynthesis, errors in      385 424
Protein, determination of concentration      214
Protein, diversity      25
Protein, flexibility      32—39
Protein-protein recognition      308—309

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