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Fersht A. Structure and Mechanism in Protein Science
Fersht A.  Structure and Mechanism in Protein Science









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: Structure and Mechanism in Protein Science

: Fersht A.

:

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.


: en

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ed2k: ed2k stats

: 1999

: 630

: 30.11.2005

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$3_{10}$ helix      13 18
$Biacore^{TM}$      see Label-free optical detection
$Delphi^{TM}$      326 327
$F_{0}F_{1}$-atpase      318321
$F_{1}$-ATPase      318321
$k_{cat}$      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 458472
$NAD^{+}$, $NADP^{+}$, $S-lac-NAD^{+}$      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 463465
$pK_{a}$      see Ionization constants
$S_{N}1$, $S_{N}2$ reactions      235 254 255 498
$\alpha$ helix      1013 18 2224
$\alpha$ helix, amphipathic      13
$\alpha$ helix, caps      12 525527
$\alpha$ 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      233235 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      262266 488490
$\Phi$-value analysis      558563 574 590 593
$\Phi$-value analysis, compared with Bronsted $\beta$      562
$\Phi$-value analysis, fractional values      579582
$\Phi$-value analysis, implicating intermediate on pathway      556
$\Phi$-value analysis, introduction      558563
$\Phi$-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      350355
Active-site directed irreversible inhibitors      see Affinity labels
Active-site titration      155158 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      277280 474
AGADIR      529 530 532
Alanine racemase      285
Alcohol dehydrogenase      23 32 40 61 86 97 460465
Alcohol dehydrogenase, protein engineering of specificity      465
Alcohol dehydrogenase, stereospecificity      250
Aldolase      79 296 366
Aldose-ketose isomerases      251 252
Alkaline phosphatase      225 231233
Allosteric interactions      289315 604606
Allosteric interactions, activators and inhibitors      290 293 300 310315
Allosteric interactions, feedback      290 309
Amino acids      2 3
Amino acids, absolute configuration      247
Amino acids, chemical reactivity of side chains      273277
Aminoacyl-tRNA synthetases      92 235242
Aminoacyl-tRNA synthetases, determination of binding energies by      341 342
Aminoacyl-tRNA synthetases, editing mechanism      239242
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      544555
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      159161
Association rate constants, examples      153 164166
Association rate constants, kinetic analysis      143 144 152 153
Associative mechanism      259
Asymmetry      245
ATP synthase      318321
Automatic titration      196
Bacteriophage, $\phi X174$      391
Bacteriophage, fd      414 416
Bacteriophage, M13      414 416
Bacteriophage, phage display      416418
Bacteriophage, phagemid      416
Barnase, $\alpha/\beta$ Barrel      3032
Barnase, association kinetics with barstar      159161
Barnase, crystal structure      588
Barnase, electrostatic interactions in      326
Barnase, folding kinetics      544 550 589
Barnase, folding pathway      588592
Barnase, fragments      589 595
Barnase, GroEL binding      604606
Barnase, helix stability      524529
Barnase, helix structure      12
Barnase, hydrogen exchange      566
Barnase, hydrophobic core stability      533 544
Barnase, kinetics of folding      550 551
Barnase, mechanism      492496
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      159161
Barstar, mechanism of folding      591593
Beers 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      106108 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      6265
Bronsted $\alpha$ and $\beta$, interpretation of      58 87 88
Bronsted $\alpha$ and $\beta$, kinetic equivalence and      95
Bronsted $\alpha$ and $\beta$, nucleophilic catalysis and      8689
Bronsted $\alpha$ and $\beta$, protein engineering of binding energy changes and      442444
Bronsted equation      58
Bronsted equation in protein folding      579582 590
Burst kinetics      155158 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      486491
Carboxypeptidases      23 30 75 482486
Carboxypeptidases, chemical modification      420
Catalase      108 162164 166
Catalysis, binding energy factors      349375
Catalysis, catalytic power of enzymes      59 60
Catalysis, chemical      54102
Catalysis, classical factors in enzyme catalysis      100 101
Catalytic antibody      60 361
Catalytic constant ($k_{cat}$)      105109
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      273288
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      256259
Chiral phosphate group      259266
Chirality      245
Chirality, rules for RS designation      246 247
Chymosin      473 486
Chymostatin      479
Chymotrypsin      4 2630 60 100 218231 472482
Chymotrypsin inhibitor 2 (CI2), folding kinetics      544577 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      576588
Chymotrypsin inhibitor 2 (CI2), structure      576 577
Chymotrypsin, $pK_{a}$ of active site      182184
Chymotrypsin, active-site titration      157
Chymotrypsin, activity in crystal      45
Chymotrypsin, acylenzyme      3740 107 218231
Chymotrypsin, affinity labeling      278 279
Chymotrypsin, association rate constants with substrates      165
Chymotrypsin, binding energies of subsites      342 343 356358
Chymotrypsin, catalytic factors      100
Chymotrypsin, catalytic triad      474 475
Chymotrypsin, enzyme-substrate complex      4044
Chymotrypsin, estimation of binding energies      341
Chymotrypsin, hydrophobicity of active site      342
Chymotrypsin, indolylacryloyl-chymotrypsin      40 45
Chymotrypsin, intermediates      218231
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      182184
Chymotrypsin, pre-steady state kinetics      146 148 149
Chymotrypsin, primary structure      5
Chymotrypsin, product partitioning      225229
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 223230
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)      193195
Circular dichroism (CD), optimal absorbance for signal to noise      212214
Circularly permuted proteins      586 587
Cloning genes      410415
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      356362
Complementarity, analysis by transition state theory      354356
Complementarity, base pairing in DNA      401403
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      4451
Contact order      602
Continuous-flow method      133 134 541
Control analysis      308
Control enzymes      290
Control enzymes, allosteric interactions      293296
Convergent evolution      29 30
Coomassie blue      214
Cooperativity, ligand binding      289307
Cooperativity, nested      296
Coordinate expression      35 38
Coordinate regulation      3 8
Cost-selectivity equation      395399
Coupled assays      196
Covalent catalysis      62 7785
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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