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

Proton transfer rates      162 163
Pseudorotation      260
Pulsed quenched flow      136 567—569
Pyridoxal phosphate chemistry      62 79—82
Pyridoxal phosphate chemistry, stereoelectronic control      267
Pyridoxal phosphate chemistry, suicide inhibition      284 285
Pyruvate dehydrogenase complex      37
Pyruvate kinase      267 294
Quaternary structure      9 24
Quenched flow      136 567—569
R state      292 293
Radioactive procedures      196—198
Ramachandran diagram      1—4 18 19 524 526
Raman scattering      192
Random mechanism      120
Rapid equilibrium mechanism      120
Rapid mixing techniques      133—136
Rapid quenching techniques      135—136
Ras protein      45 315 316
Rate limiting step of metabolic pathway      308
Rayleigh scattering      192
Re      247
Recombinant DNA technology      401—419
Reductive methylation      274
Regulation of enzymes and metabolic pathways      308—315
Relaxation methods      137 138
Relaxation methods, kinetics      139—155
Relaxation time      138
Renin      486
Rennin      see “Chymosin”
Repertoire selection      415—418
Reporter group      276
Resonance Raman spectra      476
Restriction endonucleases      406—408
Restriction fragment      408
Retention of stereochemical configuration      253 254
Reverse genetic s      438—442
Reverse transcriptase      38
Rhizopus-pepsin      486 490
Ribonucease T1      492 495 528 529
Ribonuclease A      9
Ribonuclease A, stereochemistry of reaction      262
Ribonucleases      490—496
Ribozyme      26
RNA polymerase, “two-metal-ion” mechanism      393
Rotational correlation time      46
RS notation      246 247
S notation      246 247
S-Adenosyl methionine      90 91
Salt bridges      304 335 337—339 344 530—532
Saturation kinetics      104
Scatchard plot      208 303
Schiff bases      77—82
Second-order transition      521
Secondary structure      9 13 14 20—23
Secondary structure, $\alpha+\beta$       23 24
Secondary structure, $\alpha/\beta$       23 24
Secondary structure, all $\alpha$       23
Selectivity      397
Sequence identity      33 34
Sequential mechanism      119
Sequestration of reactive intermediates      432
Serine dehydratase      284
Serine proteases      7 26—30 40—43 473—482
Serine proteases, Protein engineering of specificity      452—454 481 482
SH3 domain of $\alpha$ -spectrin      552 586 594
Shear motion      48
Shikimate pathway      36 37
Si      247
Sigmoid binding curves      289
Single-turnover kinetics      139 146 147 219—222 242
Site-directed mutagenesis      see “Mutagenesis and protein engineering”
Slater — Kirkwood equation      328
Small angle x-ray scattering      520 521
Sofa conformation      358 496 500
Sofa conformation, structure      359
Solvation energies      336 337
Solvation energies, ions      74 344 426
Specific acid or base catalysis      61
Specific heat      510 511 513 545—547
Specific heat, activation      546 548 578 579
Specific heat, transition state      578 579
Specificity      372 377—400
Specificity constant ( $k_{cat}/K_{M}$ )      104 105 116
Specificity constant ( $k_{cat}/K_{M}$ ), binding energy and      350—355
Specificity constant ( $k_{cat}/K_{M}$ ), Briggs — Haldane kinetics and      166 167 384
Specificity constant ( $k_{cat}/K_{M}$ ), diffusion control and      106 368
Specificity constant ( $k_{cat}/K_{M}$ ), evolution of      362—364 368
Specificity constant ( $k_{cat}/K_{M}$ ), limits from Haldane equation      368
Specificity constant ( $k_{cat}/K_{M}$ ), meaning of      110
Specificity constant ( $k_{cat}/K_{M}$ ), pH dependence of      169 174—176
Specificity in protein-protein interactions      347
Specificity, competing substrates      117 377
Specificity, editing mechanisms      see “Editing mechanisms”
Specificity, induced fit      372 381
Specificity, intermediates      117 381 385
Specificity, nonproductive binding      116—117 372
Specificity, strain      372 377 379 384
Specificity, versus binding      339 340
Spectrofluorimetry      192 193 195
Spectrofluorimetry, determination of ionization constants by      186
Spectrophotometry      191 192 195
Spectrophotometry, optimal absorbance for signal to noise      212—214
Spin glass theory      598
Spliceosomal protein U1A, folding kinetics      552
splicing      26
Src SH3 domain, $\Phi$ -value analysis      594
Src SH3 domain, folding kinetics      552
Staphylococcal IgG binding protein GB1 domain      529
Staphylococcal nuclease      23 47
Statistics      209—214
Statistics, combining errors      211 212
Statistics, standard deviation      210
Statistics, standard error      210
Steady state      103
Steady state approximation      106
Steady state kinetics      103—125 173—179 199—200 216 223—231
Steady state kinetics, induced fit, nonproductive binding, strain and      114—118 372 373
Stereochemistry      245—272
Stereoelectronic control      266 267 270 271

Stereospecificity      247—250
Stopped-flow methods      134 135 243 520 541
strain      369—374 (see also “Transition state stabilization”)
Strain, electrostatic effects on protein stability      74
Strain, equilibria on enzyme surface and      118
Strain, specificity and      372 380
Strain, versus stress      372—374
Streptococcal proteinase      482
Stress      372—374
Structure of proteins-prediction      536—537
Structure-activity relationships      58 59 85—92
Structure-activity relationships, inductive effects on substrate      86
Structure-activity relationships, structural changes of enzyme      362 420—454
Structure-activity relationships, structural changes of substrate      356—358
Substrate channeling      38
Substrate concentrations in vivo      362—368
Subtilisin      27 28 30 450—454 476
Subtilisin, prosequence      540
Subtilisin, protein engineering specificity of      452—454
Subtilisin, protein engineering surface charge and $pK_{a}$ of      180 327
Subtiloloigase      453 454
Subunits      24 289—297
Subunits, construction of hetero-oligomers by protein engineering      446—449
Succinates      66 67
Suicide inhibitors      280—286
Superoxide dismutase      166
Supersecondary structure      9 20
Surface charge of protein      179—180 327
Surface plasmon resonance      see “Label-free optical detection”
T state      292 293
T4 lysozyme      33 497
T4 lysozyme, helix stability of      528 529
T4 lysozyme, hydrophobic core stability of      533 544
Tanford $\beta$ value      544 555 578 582
Temperature jump      137 138 541
Temperature jump, protein folding      593
Terminal transferase      408 410
Ternary complex      120
Tertiary structure      22
Theorell — Chance mechanism      120
Thermodynamic cycles      125—131
Thermodynamic cycles, acid denaturation      516 517
Thermodynamic cycles, double mutant cycles      129—131 594
Thermodynamic cycles, mutant cycles      129
Thermodynamic cycles, specificity      381 383
Thermodynamic cycles, “alchemical” steps      129
Thermolysin      22 30 483—486
Thiamine pyrophosphate      62 83—84
Thiol proteases      473 482
Thionesters      478
TNfn3 domain, $\Phi$ -value analysis      594
TNfn3 domain, folding kinetics      552
Torsion angle      16—18
Tos-L-phenylalanine chloromethyl ketone (TPCK)      278 475
Trans aldolase      79
Transit time      123—125
Transition state      47—49
Transition state analogues      49 317 356 358—361 474 495
Transition state in protein folding      556—558 573—575 578—583
Transition state stabilization      353 369 439
Transition state theory      54—61 86
Transition state theory, analysis of enzyme catalysis      349—355
Transition state theory, analysis of protein folding      545 558
Transition state theory, application to chemical catalysis      57—61
Transition state theory, application to enzyme specificity      380—383
Transition state, definition      55
Transition state, ensemble      600
Transketolase      83
Transmission coefficient      56 558
Triosephosphate isomerase      23 30 31 39 41 108 167
Tritium tracer experiments      47 257—259
Trojan horse inhibitors      see “Suicide inhibitors”
Trypsin      26—30 42 43 474 476 480 482
Trypsin inhibitor (basic pancreatic)      286 575
Trypsin, specificity      28
Trypsinogen      480 481
Tryptophan synthase      35
Tunneling      97 98
Turnover number      see “Catalytic constant”
TWIg18 domain, folding kinetics      552
Two-state transitions      517 518
Two-state transitions, apparent      518 547
Two-state transitions, kinetics      543—553
Tyransducin- $\alpha$       315—317
Tyrosyl-tRNA synthetase      51 118 242 296 297 420—450
Ubiquitin, folding kinetics      552
Ultracentrifugation      204 205
Unfolding of proteins      see “Denaturation”
Uniform binding energy change      351 352
Uniform binding energy change, protein engineering and      438 439
Uracil glycosidase      394
V system      294
Valyl-tRNA synthetase      239—242 379 386 389
Van der Waals contact distance      328
Van der Waals energies      329 331
Van der Waals forces      327—329
Van der Waals radii      328—329
Vanadate      495
Van’t Hoff enthalpy      512 513 517
Van’t Hoff equation      513
Vector      411 412
Walker consensus sequence      316 320
Warwicker — Watson algorithm      326
Watson — Crick base pairing      401—403
X-ray diffraction methods      4—7
X-ray diffraction methods, difference Fourier      39
X-ray diffraction methods, isomorphous replacement      4 5
X-ray diffraction methods, molecular replacement      6 39
X-ray diffraction methods, resolution      6
X-ray diffraction methods, static disorder and real motion      49 50
X-ray diffraction methods, time resolved      39
X-ray diffraction methods, von Laue method      39
Zero-point energy      96
Zinc proteases      482—486
“Effective concentration”      65—72
“Effective concentration” in general-acid-base catalysis      66
“Effective concentration” in nucleophilic catalysis      66
“Effective concentration”, entropy and      68—72
“Orbital steering”      72 73
“Ridges-into-grooves”      22
“Rollover”      550

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