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

$3_{10}$ helix      13 18
$Biacore^{TM}$       see “Label-free optical detection”
$Delphi^{TM}$       326 327
$F_{0}F_{1}$ -atpase      318—321
$F_{1}$ -ATPase      318—321
$k_{cat}$       see “Catalytic constant”
$k_{cat}$ inhibitors      see “Suicide inhibitors”
$k_{cat}/K_{M}$       see “Specificity constant”
$K_{M}$       see “Michaelis constant”
$NAD^{+}$ , $NADP^{+}$       249 250 458—472
$NAD^{+}$ , $NADP^{+}$ , $S-lac-NAD^{+}$       466
$NAD^{+}$ , $NADP^{+}$ , $\mathrm{H_{2}NADH}$       394
$NAD^{+}$ , $NADP^{+}$ , binding energy and $K_{M}$       365
$NAD^{+}$ , $NADP^{+}$ , fluorescence      458
$NAD^{+}$ , $NADP^{+}$ , kinetic isotope effects and hydride transfer      97 98 463—465
$pK_{a}$       see “Ionization constants”
$S_{N}1$ , $S_{N}2$ reactions      235 254 255 498
$\alpha$ helix      10—13 18 22—24
$\alpha$ helix, amphipathic      13
$\alpha$ helix, caps      12 525—527
$\alpha$ helix, circular dichroism      195
$\alpha$ helix, dipole      13
$\alpha$ helix, kinetics of formation      541 569 570
$\alpha$ helix, stability      see “Protein stability”
$\alpha$ -effect      89
$\alpha$ -Lytic protease      357
$\alpha$ -Spectrin SH3 domain, $\Phi$ -value analysis      594
$\alpha$ -Spectrin SH3 domain, folding kinetics      552 586
$\alpha$ -value      see “Bronsted”
$\beta$ Bend      13 16
$\beta$ Hairpin      20
$\beta$ Hairpin, kinetics of formation      541 570
$\beta$ sheet      10 13 15 19
$\beta$ value      see “Bronsted Tanford”
$\beta$ -Aspartate decarboxylase      81 285
$\beta$ -Galactosidase      233—235 243 255
$\beta$ -Hydroxy-decanoyl dehydrase      283
$\beta-\alpha-\beta$ Hairpin      22
$\lambda$ -repressor folding kinetics      551
$\mathrm{RD_{2}O}$ , solvent effects on kinetics      99
$\mathrm{RD_{2}O}$ , solvent effects on pKa      185
$\mathrm{^{18}O/^{16}O}$ tracer experiments      262—266 488—490
$\Phi$ -value analysis      558—563 574 590 593
$\Phi$ -value analysis, compared with Bronsted $\beta$       562
$\Phi$ -value analysis, fractional values      579—582
$\Phi$ -value analysis, implicating intermediate on pathway      556
$\Phi$ -value analysis, introduction      558—563
$\Phi$ -value analysis, molecular dynamics simulation      583 591
$\Phi$ -value analysis, nucleation-condensation mechanism      583
$\Phi$ -value analysis, versus quenched-flow hydrogen exchange      568 569
$\pi$       see “Hydrophobicity constant”
$\pi$ Helix      18
$^{10}FNIII$ domain, $\Phi$ -value analysis      594
$^{9}FNIII$ domain, folding kinetics      552
(-)Deprenyl      286
1,2-Anhydro-D-mannitolphosphate      279
2,5-Anhydro-D-glucitolphosphate      254
2,5-Anhydro-D-mannitolphosphate      254
Absolute configuration      246
Abzyme      see “Catalytic antibody”
Acetoacetate decarboxylase      78 189 298
Acetyl coenzyme A: arylamine acetyl-transferase      121
Acetylcholinesterase      84 108 166
Acid phosphatase      233 374
Acid proteases      see “Carboxyl proteases” “Pepsin”
Acid-base catalysis      see “General-acid-base catalysis”
Actinidin      482
Activation energy      56 58 546 547
Activation energy, interconversion of activation and binding energies      350—355
Active-site directed irreversible inhibitors      see “Affinity labels”
Active-site titration      155—158 423
Acylbinding proteins, $\Phi$ -value analysis      594
Acylbinding proteins, folding kinetics      551
Acylphosphatase (muscle), folding kinetics      552
Adair equation      290 291
Adjacent mechanism      260 263 267
Affinity labels      277—280 474
AGADIR      529 530 532
Alanine racemase      285
Alcohol dehydrogenase      23 32 40 61 86 97 460—465
Alcohol dehydrogenase, protein engineering of specificity      465
Alcohol dehydrogenase, stereospecificity      250
Aldolase      79 296 366
Aldose-ketose isomerases      251 252
Alkaline phosphatase      225 231—233
Allosteric interactions      289—315 604—606
Allosteric interactions, activators and inhibitors      290 293 300 310—315
Allosteric interactions, feedback      290 309
Amino acids      2 3
Amino acids, absolute configuration      247
Amino acids, chemical reactivity of side chains      273—277
Aminoacyl-tRNA synthetases      92 235—242
Aminoacyl-tRNA synthetases, determination of binding energies by      341 342
Aminoacyl-tRNA synthetases, editing mechanism      239—242
Amyloidosis      1 575
Angiotensin converting enzyme      483
Anilinyl-naphthalene sulfonic acid (ANS)      520
Annealing mechanism      607
Anti-cooperativity      see “Negative cooperativity”
Anti-Hammond effect      591
Antimutator strain of T4 phage      390 391
Apical position      260
Apoenzyme      458
Apparent $pK_{a}$       173 175 177 178 180 183
Apparent binding energies      428
Apparent binding energies, relationship with incremental binding energies      435
Apparent equilibrium constants      109 110
Arc repressor (dimer), $\Phi$ -value analysis      595
Arc repressor (single chain), $\Phi$ -value analysis      594
Arc repressor (single chain), folding kinetics      552
Arom complex      36 37
Arrhenius equation      544—555
Arrhenius equation, breakdown      555
Aspartate aminotransferase      284 285
Aspartate transcarbamoylase      298 360
Aspartyl proteases      see “Carboxyl proteases”
Aspirin      66 67
Association rate constants, collision theory      54 158 159
Association rate constants, electrostatic enhancement      159—161
Association rate constants, examples      153 164—166
Association rate constants, kinetic analysis      143 144 152 153
Associative mechanism      259
Asymmetry      245
ATP synthase      318—321
Automatic titration      196
Bacteriophage, $\phi X174$       391
Bacteriophage, fd      414 416
Bacteriophage, M13      414 416
Bacteriophage, phage display      416—418
Bacteriophage, phagemid      416
Barnase, $\alpha/\beta$ Barrel      30—32
Barnase, association kinetics with barstar      159—161
Barnase, crystal structure      588
Barnase, electrostatic interactions in      326
Barnase, folding kinetics      544 550 589
Barnase, folding pathway      588—592
Barnase, fragments      589 595
Barnase, GroEL binding      604—606
Barnase, helix stability      524—529
Barnase, helix structure      12
Barnase, hydrogen exchange      566
Barnase, hydrophobic core stability      533 544
Barnase, kinetics of folding      550 551
Barnase, mechanism      492—496
Barnase, solution structure      8
Barnase, solvent denaturation      515 516
Barnase, structure      588
Barnase, subsites and binding energies      495 496
Barnase, thermal denaturation      512
Barstar, association kinetics with barnase      159—161

Barstar, mechanism of folding      591—593
Beer’s law      191 192
Bequerel      196
Binding energy versus specificity      339
Bohr effect      305
Borohydride reduction      78 274 276
Bovine seminal ribonuclease      33
Bradford assay      214
Breathing motion      47
Briggs — Haldane kinetics      106—108 166 167 183
Briggs — Haldane kinetics, evolutionary aspects      368
Briggs — Haldane kinetics, pH dependence      178 179
Briggs — Haldane kinetics, specificity and      166 167 384
Bromelain      482
Bronsted $\alpha$ and $\beta$       58
Bronsted $\alpha$ and $\beta$ , compared with $\Phi$       562
Bronsted $\alpha$ and $\beta$ , general-acid-base catalysis and      62—65
Bronsted $\alpha$ and $\beta$ , interpretation of      58 87 88
Bronsted $\alpha$ and $\beta$ , kinetic equivalence and      95
Bronsted $\alpha$ and $\beta$ , nucleophilic catalysis and      86—89
Bronsted $\alpha$ and $\beta$ , protein engineering of binding energy changes and      442—444
Bronsted equation      58
Bronsted equation in protein folding      579—582 590
Burst kinetics      155—158 218
Caged ATP or GTP      137
Calorimetry      see “Differential scanning calorimetry isothermal
Capillarity      598
Carbonic anhydrase      10 108 163 166
Carbonic anhydrase, chemical models      76 77
Carbonic anhydrase, substrate concentrations in vivo      365
Carboxyl proteases      486—491
Carboxypeptidases      23 30 75 482—486
Carboxypeptidases, chemical modification      420
Catalase      108 162—164 166
Catalysis, binding energy factors      349—375
Catalysis, catalytic power of enzymes      59 60
Catalysis, chemical      54—102
Catalysis, classical factors in enzyme catalysis      100 101
Catalytic antibody      60 361
Catalytic constant ( $k_{cat}$ )      105—109
Catalytic constant ( $k_{cat}$ ), meaning of      108 109
Catalytic constant ( $k_{cat}$ ), pH dependence of      169 174 175 180
Cathepsin D      486
CD2 domain      1
CD2 domain, $\Phi$ -value analysis      594
CD2 domain, folding kinetics      552
Central complex      120
Cerenkov radiation      197
Chair conformation      359
Chaperonins      604
Chelate effect      345 346
Chemical modification of proteins      273—288
Chemical modification of proteins, pH dependence      187 278 279 468 487
Chemiosmotic hypothesis      318 319
Chevron plot      543
CheY protein      596
CheY protein, $\Phi$ -value analysis      594
Chiral methyl group      256—259
Chiral phosphate group      259—266
Chirality      245
Chirality, rules for RS designation      246 247
Chymosin      473 486
Chymostatin      479
Chymotrypsin      4 26—30 60 100 218—231 472—482
Chymotrypsin inhibitor 2 (CI2), folding kinetics      544—577 577
Chymotrypsin inhibitor 2 (CI2), fragments      577 578 587 588 595
Chymotrypsin inhibitor 2 (CI2), GroEL binding      605
Chymotrypsin inhibitor 2 (CI2), mechanism of folding      576—588
Chymotrypsin inhibitor 2 (CI2), structure      576 577
Chymotrypsin, $pK_{a}$ of active site      182—184
Chymotrypsin, active-site titration      157
Chymotrypsin, activity in crystal      45
Chymotrypsin, acylenzyme      37—40 107 218—231
Chymotrypsin, affinity labeling      278 279
Chymotrypsin, association rate constants with substrates      165
Chymotrypsin, binding energies of subsites      342 343 356—358
Chymotrypsin, catalytic factors      100
Chymotrypsin, catalytic triad      474 475
Chymotrypsin, enzyme-substrate complex      40—44
Chymotrypsin, estimation of binding energies      341
Chymotrypsin, hydrophobicity of active site      342
Chymotrypsin, indolylacryloyl-chymotrypsin      40 45
Chymotrypsin, intermediates      218—231
Chymotrypsin, kinetic constants for substrate hydrolysis      224 228 357 358 477
Chymotrypsin, kinetic equations for      107 110 116 226 227
Chymotrypsin, pH dependence of catalysis      182—184
Chymotrypsin, pre-steady state kinetics      146 148 149
Chymotrypsin, primary structure      5
Chymotrypsin, product partitioning      225—229
Chymotrypsin, reaction mechanism      41 100
Chymotrypsin, redesigning specificity by protein engineering      481 482
Chymotrypsin, rotational correlation time      46
Chymotrypsin, secondary structure      23
Chymotrypsin, specificity      27 40 481
Chymotrypsin, steady state kinetics      107 108 223—230
Chymotrypsin, stereochemical specificity      248
Chymotrypsin, stereoelectronic effects on mechanism      270
Chymotrypsin, tertiary structure      27 29
Chymotrypsin, tetrahedral intermediate      13 40 86
Chymotrypsin, zymogen      480
Chymotrypsin, “charge-relay system”      475
Chymotrypsinogen      480 481
Circular dichroism (CD)      193—195
Circular dichroism (CD), optimal absorbance for signal to noise      212—214
Circularly permuted proteins      586 587
Cloning genes      410—415
Clostripain      482
Cold-shock $\beta$ -barrel proteins, folding kinetics      551
Collision theory of kinetics      54 158 159
Competing substrates      116 117
Complementarity      332 334 354
Complementarity in enzyme-substrate interactions      356—362
Complementarity, analysis by transition state theory      354—356
Complementarity, base pairing in DNA      401—403
Complementarity, base pairing in RNA      345
Complementarity, basis of molecular recognition      332
Complementarity, lock-and-key      354
Complementation assay      412
Computer fitting of data      209
Configuration      246 249
Conformation      249
Conformational change      44
Conformational change, detection      242
Conformational mobility of proteins      44—51
Contact order      602
Continuous-flow method      133 134 541
Control analysis      308
Control enzymes      290
Control enzymes, allosteric interactions      293—296
Convergent evolution      29 30
Coomassie blue      214
Cooperativity, ligand binding      289—307
Cooperativity, nested      296
Coordinate expression      35 38
Coordinate regulation      3 8
Cost-selectivity equation      395—399
Coupled assays      196
Covalent catalysis      62 77—85
Creatine kinase      264 266
Crotonase      108 166
Cryoenzymology      40
Crystalline enzymes, activity      45
Crystalline enzymes, water content      39
Curie      196
Cyclophilin      see “Peptidyl-prolyl isomerase”
Cysteine proteases      482
Cytidine deaminase      359
Cytidine triphosphate synthetase      298
Cytochrome c, folding kinetics      551
Debye — Hueckel theory      159

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