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| Ïîèñê ïî óêàçàòåëÿì |
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| Branden C., Tooze J. — Introduction to protein structure |
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| Ïðåäìåòíûé óêàçàòåëü |
Amino acid sequence in interpretation of NMR spectra 390
Amino acid sequence,  -crystallin 76
Amino acid sequence, assignment to three-dimensional folds 353—354
Amino acid sequence, calcium-binding motif 26F
Amino acid sequence, calculation of possible number 352
Amino acid sequence, DNA binding domain of glucocorticoid receptor 182F
Amino acid sequence, Fos and Jun 192F
Amino acid sequence, GCN4 192F 193 194F
Amino acid sequence, heptad, in coiled-coil  helix 35—37 36F
Amino acid sequence, HLH region 201F
Amino acid sequence, homeodomains 160 162 162F
Amino acid sequence, homologous from different species 21
Amino acid sequence, homologous proteins 348
Amino acid sequence, Max protein 192F
Amino acid sequence, photosynthetic reaction center 247F
Amino acid sequence, protein structure prediction from 352—353
Amino acid sequence, retinol-binding protein (RBP) 69—70 70F
Amino acid sequence, Rop 369T
Amino acid sequence, similar three-dimensional structures 352
Amino acid sequence, TATA box-binding protein 153
Amino acid sequence, transmembrane a helices prediction 244—245
Amino acid sequence, Zif 268 protein 177F 368T
Amino acids in  barrels 48 50T
Amino acids, basic, in helix-loop-helix region 196
Amino acids, classes 5
Amino acids, D- and L- forms 5 9
Amino acids, handedness 5
Amino acids, nomenclature 7F
Amino acids, preferred in a helix 16—18
Amino acids, role of individual residues 391
Amino acids, side chains see “Side chains”
Amino acids, structures 4 4F
Amino groups 4 4F
Aminoacyl-tRNA synthetases, domains 59—60 59F 60F
Ammonium ions 211 213
Amplitude, diffracted beams 370F 379 380 380F
Amyloid  -protein precursor inhibitor, Alzheimer’s (APPI) 361 362 362T
Amyloid fibers 289 297
Amyloid fibrils 288—289
Amyloidosis 288
Antenna pigment proteins 235 240—241
Antenna pigment proteins, ring in LH1 light-harvesting complex 242—244 243F
Antennapedia 159 160 162 162F
Antibodies 299
Antibodies, antigen-binding sites see “Antigen-binding sites”
Antibodies, catalytic 207 309
Antibodies, catalytic, production 309
Antibodies, chimeric 306
Antibodies, diversity 302—303
Antibodies, membrane protein solubilization 224—225
Antibodies, polypeptide chains 300—301 (see also “Immunoglobulin(s)”)
Antigen, recognition in MHC molecules 314—315 315F 316
Antigen-binding sites 21
Antigen-binding sites for antigens 308—311
Antigen-binding sites for haptens 308—309 309F
Antigen-binding sites for lysozyme 309—310 310F
Antigen-binding sites of immunoglobulins 21 306—308 306F 308—311
Antigen-binding sites of immunoglobulins, modeling 349—350
Antigen-binding sites of MHC class I molecule 314
Antigen-binding sites of T-cell receptors (TCR) 317F
Antigen-presenting cells 315
Antigenic determinants 299
Antiparallel barrels, chymotrypsin 210—211 210F
Antiparallel barrels, cyclophilin 99 99F
Antiparallel barrels, GroES 102
Antiparallel barrels, p53 DNA-binding domain 168—169 168F
Antiparallel barrels, porins 229—230 230F
Antiparallel barrels, viruses 335 335F
Antiparallel hairpin see “Hairpin motif”
Antiparallel sandwich, TFIIA 159
Antiparallel sheets 18F 19 67 67F
Antiparallel sheets in domains 31
Antiparallel sheets, bacteriophage MS2 subunits 339
Antiparallel sheets, DNA-binding site of TATA box-binding protein 154
Antiparallel sheets, Greek key motifs 27
Antiparallel sheets, immunoglobulin fold 304—305 3041"
Antiparallel sheets, lambda Cro protein 132
Antiparallel sheets, MHC class I molecule 314
Antiparallel sheets, neuraminidase 71—72 71F
Antiparallel sheets, p53 domain 167
Antiparallel sheets, serpin fold 111
Antiparallel sheets, SH2 domain 273
Antiparallel sheets, topology diagram 24F
Antiparallel strands in up-and-down barrel 68F 69—70 70F
Antiparallel strands, active site of carboxypeptidase 62
Antiparallel strands, GroEL 102
Antiparallel strands, jelly roll barrel formation 77—78 77F
Antiparallel strands, variable domain of immunoglobulin 306 308
Antiparallel structures 67—84
Antiparallel structures, -crystallin 74 74F
Antiparallel structures, Greek key motifs 72—74 (see also “Greek key motif proteins”
Antiparallel structures, included 67
Antiparallel structures, SH3 domain 274 275F
Antiparallel structures, up-and-down barrels (sheets) see “Up-and-down barrels” “Up-and-down
Antithrombin 111 112 113
Antiviral compounds, design for common cold 337—338 337F 338F
AP1 complex 192
AP1 complex, pseudo-symmetric binding site 194 194F 196
Aphthoviruses 333
APPI (Alzheimer’s amyloid P-protein precursor inhibitor) 361 362 362T
Arabidopsis thaliana 154
Arabinose 63F
Arabinose, transport 62
Arabinose-binding protein, domains 62—63 62F
Area detectors 377
Arginine, p53 binding to DNA 170 170F 171
Arginine, recognition helix of glucocorticoid receptor 184—185
Arginine, structure 7F
Arginine, zinc finger interaction with DNA 179 179F 181
Aromatic residues, hydrophobicity in porins 231
Asparagine, structure 6F
Asparagine, TATA box and TBP binding 157—158
Aspartate transcarbamoylase 24F
Aspartic acid in Gp subunit 263
Aspartic acid in parvalbumin calcium-binding motif 25
Aspartic acid in serine proteinases 209
Aspartic acid, mutation in trypsin 215
Aspartic acid, structure 6F
Aspartic acid, substrate-assisted catalysis 218
Aspartic proteinases 205
Asymmetric units, definition 328
Asymmetric units, icosahedron 328 328F
AT sequence, p53 binding to DNA 170
ATP, binding to phosphofructokinase 116
ATP, cyclin A and CDK2 binding 108 109F
ATP, depletion in rigor mortis 295 296
ATP, GroEL-GroES complex 101F 103
ATP, hydrolysis, GroEL-GroES binding 103
ATP, hydrolysis, swinging cross-bridge model 292F
ATP, role in muscular contraction 296—297
B cells (B lymphocytes) 299
B cells (B lymphocytes), antibody formation 300
B cells (B lymphocytes), numbers produced 302
B-DNA see “DNA”
b/HLH transcription factors 175 196F 197 202
b/HLH transcription factors, amino acid sequences 201F
b/HLH transcription factors, consensus sequence recognized 197 199 201
b/HLH transcription factors, homodimer and heterodimers 196—197 196F
b/HLH transcription factors, structure 197 200
b/HLH/zip transcription factors 196F 199—200
b/HLH/zip transcription factors, amino acid sequences 201F
b/HLH/zip transcription factors, motif structure 200
b/HLH/zip transcription factors, Myc 199
b/zip family, Fos and Jun 199
b/zip transcription factor 196F 197
Bacillus amyloliquefaciens 215
Bacillus subtilis, PRA-isomerase and IGP-synthase 52
Bactenophage, filamentous 359—361 360F
Bactenophage, gene control 129—130
Bactenophage, helper 360
| Bactenophage, lytic-lysogeniccycle switch 130—131 130F 133
Bactenophage, repressors see “Repressor proteins” “Specific
Bactenophage, T-even 326F
Bactenophage, temperate 130
Bacteria, antibody-tagged 299 300
Bacteria, antibody-tagged, disulfide bridge formation 96
Bacteria, antibody-tagged, lysogenic strains 129—130
Bacteria, antibody-tagged, lytic strains 130
Bacteria, antibody-tagged, outer membrane proteins see “Porins”
Bacteria, antibody-tagged, photosynthetic reaction center see “Photo synthetic reaction center”
Bacteria, antibody-tagged, protein A 363 363F
Bacteria, antibody-tagged, purple 242 (see also “Specific genera”)
Bacteriochlorophyll 236 236F
Bacteriochlorophyll, LH2 light-harvesting complex 241 242F
Bacteriophage 434
Bacteriophage display 359—363
Bacteriophage display, applications 361—365
Bacteriophage display, binding specificity of proteinase inhibitors 362—363
Bacteriophage display, DNA shuffled libraries 366
Bacteriophage display, Kunitz domains 362 362T
Bacteriophage display, libraries of erythropoietin receptor agonists 364—365
Bacteriophage display, procedures 360
Bacteriophage display, protein linked to DNA by 359—361
Bacteriophage display, proteinase inhibitor optimization 361—363
Bacteriophage display, sorting of libraries 360F
Bacteriophage lambda, Cro protein 129
Bacteriophage lambda, Cro protein, dimer 132 132F
Bacteriophage lambda, Cro protein, DNA-binding motif 133—134 134F
Bacteriophage lambda, Cro protein, structure 131—132
Bacteriophage lambda, Cro-DNA interactions model 134—135
Bacteriophage lambda, Cro-DNA interactions model, genetic studies supporting 135
Bacteriophage lambda, dimers 132 132F 133 133F
Bacteriophage lambda, DNA-binding domain 132—133 133F
Bacteriophage lambda, DNA-binding motif 133—134
Bacteriophage lambda, genetic switch region 130—131 130F
Bacteriophage lambda, N-terminal domain 133F
Bacteriophage lambda, operator regions, nucleotide sequences 130 131—132 131T
Bacteriophage lambda, POU region structure similarity 164
Bacteriophage lambda, repressor 129 161F
Bacteriophage M13 359—361
Bacteriophage MS2 339—340
Bacteriophage MS2, dimer recognizing RNA packaging signal 339—340 339F 340F
Bacteriophage MS2, polypeptide chain fold 339
Bacteriophage MS2, subunit structure 339 339F
Bacteriophage P22 130—131 130F
Bacteriophage P22, repressor, DNA-binding surface 135 136F
Bacteriophage P22, tailspike protein 84—85
Bacteriophage replicase 339
Bacteriophage T4 325
Bacteriophage T4, lysozyme 354
Bacteriophage T4, lysozyme,  type 355F
Bacteriophage T4, lysozyme, cavities in hydrophobic core 358
Bacteriophage T4, lysozyme, dipoles of helices 357 357F
Bacteriophage T4, lysozyme, glycine and proline effect on stability 356—357
Bacteriophage T4, lysozyme, melting temperatures 356F
Bacteriophage T4, lysozyme, mutations to increase proline 356—357
Bacteriophage T4, lysozyme, polypeptide chain 355F
Bacteriophage T4, lysozyme, stability increased by disulfide bridges 355—356
Bacteriophage, Cro protein, DNA complex structure 136—137
Bacteriophage, Cro protein, DNA distortion after binding 138 138F
Bacteriophage, Cro protein, operator region binding 138—139 138F 139F
Bacteriophage, Cro protein, repressor DNA-binding domain similarity 137
Bacteriophage, genetic switch region 130—131 130F
Bacteriophage, operator regions 137T
Bacteriophage, operator regions, base pair 4 140
Bacteriophage, operator regions, central region and overwinding 140—141
Bacteriophage, repressor 137 137F
Bacteriophage, repressor, DNA complex structure 136—137
Bacteriophage, repressor, DNA distortion after binding 138 138F
Bacteriophage, repressor, DNA-binding surface 135 136F
Bacteriophage, repressor, sequence-specific OR interactions 138—139 138F 139F 140
Bacteriorhodopsin, light-driven proton pump 227—228 229F
Bacteriorhodopsin, retinal binding site 227
Bacteriorhodopsin, transmembrane helices 226—227 226F
Ball-and-stick diagram 22
Ball-and-stick diagram, antiparallel sheet 18F
Ball-and-stick diagram, collagen model 284F
Ball-and-stick diagram, parallel sheet 19F
Banner, David 39
Barnase 357—358
Barnase, destabilizing mutants 358
Barnase, folding 94—95 94F
Barnase, stability increased by histidine 357—358
Bax, Ad 110
Bence — Jones protein 304
Benzoate, mandelate conversion to 54—55 54F
Berman, Helen 285
Biliverdin 70
Biochemical studies 391
Biopolymers, fiber diffraction 386—387
Bjorkman, Pamela 312
Blake, Colin 288
Blow, David 59 210
Bluetongue virus 326
Blundell, Tom 74 76
Bovine pancreatic trypsin inhibitor (BPTI) 26 26F 96—97 96F
Bovine pancreatic trypsin inhibitor (BPTI), folding pathway 96—97 96F
Bovine pancreatic trypsin inhibitor (BPTI), NMR and x-ray crystallography comparison 390—391
Bragg, Lawrence 378
Bragg, W.L. 13
Bragg’s law 378 379F
Braisted, Andrew 363
Branden, Carl 20F 49F 53F 59 97
Breathing, proteins 105
Brennan, Richard 143
Bugg, Charles 109
Burley, Stephen 154 159 199—200
Calcium 25F
Calcium-binding domain 29F
Calcium-binding motif 24 25F
Calcium-binding motif, amino acid sequences 26F
Calcium-binding proteins 25
Calmodulin 24 26 109—110
Calmodulin, calcium binding 26
Calmodulin, domains and structure 110 110F
Calmodulin, peptide binding 109—110 110F
Campbell, Ian 274
Canonical loop structures 311
CAP see “Catabolite gene activating protein (CAP)”
Capsid 325 326
Capsid, bacteriophage MS2 339—340 (see also “Specific viruses”)
Carbon atoms 4
Carbonyl groups, GAL4 binding to DNA 188 189F
Carboxyl groups 4 4F
Carboxypeptidase, protein with mixed sheet 60—62 61F
Carboxypeptidase, active site 62F
Carboxypeptidase, zinc environment 62F
Cardioviruses 333
Carrel, Robin 111
Caspar, Don 330 342
Catabolite gene activating protein (CAP) 132
Catabolite gene activating protein (CAP), cAMP-DNA complex 146 146F
Catabolite gene activating protein (CAP), DNA bending 146—147 156
Catabolite gene activating protein (CAP), helix-turn-helix motif 146 146F
Catalysis 205
Catalysis without catalytic triad in subtilisin 217—218 (see also “Serine proteinases”)
Catalysis, reactions, barrels in 51
Catalysis, substrate-assisted 218—219 218F
Catalytic triad 209
Catalytic triad, alphavirus coat protein protease 341
Catalytic triad, catalysis without 217—218
Catalytic triad, chymotrypsin 211 211F 212F
Catalytic triad, subtilisin 216 217
CCG triplets 191
CCG triplets, GAL4 binding 188 189
CCG triplets, zinc-containing motifs binding to 190 191
CD4 168 319 319F
Cdk see “Cyclin-dependent protein kinases (CDKs)”
CDR see “Complementarity determining regions”
Cell cycle 105—106 106F
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