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Lesk A.M. — Introduction to Protein Architecture
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Название: Introduction to Protein Architecture
Автор: Lesk A.M.
Аннотация: Written in a clear and engaging style, and profusely illustrated with superb computer graphics, Introduction to Protein Architecture is a textbook for second and third year undergraduate students and beginning post-graduate students, and will be of interest to all biological and medical scientists whose work touches on proteins.
The structures and functions of proteins unlock the secrets inherent in genomes, including the human genome. The emphasis of this book is on protein architecture, on proteins as three-dimensional patterns. A new field, bioinformatics, has grown up around gene and protein sequences and structures. It has captured the interest of many scientists for its intellectual challenges, its potential for useful applications, and promising scope for careers. This book introduces the use of the World Wide Web in bioinformatics.
Written by one of the leaders in this field, Introduction to Protein Architecture explains the general characteristics of proteins that underlie the very great variety of folding patterns observed in nature. For specialists in structural biology, it contains the core of what they need to know. For students and workers in related disciplines, undergraduates or beginning graduate students in biology, chemistry, medicine, bioinformatics, and related fields it contains what they will be able to apply to their own work. Topics treated include: Pattern and form in protein structure; The building blocks; The relationship between amino acid sequence and protein structure; Secondary, supersecondary and tertiary structure; Classifications and hierarchies of protein folding patterns; Protein evolution; How proteins change conformation (and why).
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Рубрика: Биология /
Статус предметного указателя: Готов указатель с номерами страниц
ed2k: ed2k stats
Год издания: 2001
Количество страниц: 347
Добавлена в каталог: 16.03.2007
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Предметный указатель
, -hydroxysteroid dehydrogenase, NAD-binding domain (Streptomyces hydrogenans) [2HSD] 222
helix 62 64 195 201
transition (serpins) 291
transition (haemoglobin) 284ff
lysozyme, effect of mutation 182
-Helix 33 60—63 67
-lactalbumin (baboon) [1ALC] 326
-antitrypsin (human) [2PSI] 293 296
-barrel 70 74 152ff 207ff 213 217
-barrel packing of interior 154—157 213—216
-barrel topology 154ff 163
-bulge 70 74 79
-cryptogein (Phytophthora cryptogea) [1BEO] 115 116
-hairpin 76 240 246
-hairpin sequence-structure relationships 97ff 184
-hydroxydecanoyl thiol ester dehydrase (Escherichia coli) [1MKA] 328
-sandwich 143ff 233
-sheet 9 34 59—61 67—69 71—73 233
unit 77
-crystallin domain (cow) [1AMM] 146
cro-DNA complex 108
-helix 62 65—66
17E8, L3 canonical structure (mouse) [1EAP] 243
434 repressor, N-terminal domain (phage 434) [1R69] 309
6-phosphogluconate dehydrogenase (sheep), NAD-binding domain [1PGO] 221 224
Ab1 tyrosine kinase (mouse) / peptide complex [1ABO] 82
Accessible surface area 27 56
Actinidin 183
Actinidin (kiwi fruit) [2ACT] 178
Actinidin (kiwi fruit) [2ACT], Type I’ hairpin loop 97
Acy1 phosphatase (cow) [2acy] 91
Adenylate kinase (pig) [3adk] 332
Alanine racemase (Bacillus stearothermophilus), N-terminal domain [1SFT] 84
Alanine scan 19
Alcohol dehydrogenase (Horse liver), NAD-binding domain [6ADH, 2OHX] 27 218 223 224
Alignment 88
Alignment table, globins 168—169
Alignment table, insulins 171
Allumwandlung (replacement of an amino acid by all 19 others) 19 182
Amino acids 20—22
AN02 (mouse), L3 canonical structure [1BAF] 243
Anti-gp41 monoclonal antibody (human), L3 canonical structure [1DFB] 243
Anti-hypertensive, anti-viral protein (sea anemone) [1BDS] 316
Antibody, B1—B8 245
Antibody, B1—B8, catalytic 19
Antibody, B1—B8, HyHEL-5 238—239
Antibody, B1—B8, McPC603 238—239
Antibody, B1—B8, therapeutic 19
Antigen-binding 236
Antithrombin (human) [1AZX] 294
Apopain (human) [1PAU] 332
Ark clam globin (Scapharca inaequivalvis) [4SDH] 136
Ascorbate oxidase (Escherichia coli) [1ASA] 148
Aspartate carbamoyltransferase (aspartate transcarbamylase) (Escherichia coli) [8ATC] 328
ATPase 3 302
Avian pancreatic (turkey) [1PFI] 322
Azurin 183ff
Azurin (Alcaligenes denitrificans) [2AZA] 179
B-factor 38
B1—B8, antibody 245
B35, class I MHC protein (human) [1A1N] 251 254
B53, class I MHC protein (human) [1A1O] 255 257 258
Bacteriochlorophyll 10
Bacteriochlorophyll a protein (Prosthecochloris aestuarii) [4BCL] 327
Bacteriorhodopsin (Halobacterium halobium) [1BRD] 139
Barley chymotrypsin inhibitor [2CI2] 83
Barnase (Bacillus amyloliquefaciens) [1BRN] 87
Barrel see “ -barrel”
Barstar (Bacillus amyloliquefaciens), , [1BRS] 68 71
Binding change mechanism of ATPase 302—303
Bioinformatics 16
Bovine liver phosphotyrosine protein phosphatase [1PHR| 190—191
Bovine pancreatic trypsin inhibitor (and trypsin) [1TPA] 108
Bovine pancreatic trypsin inhibitor [5PTI] 82
C-Ha-ras encoded p21 (human), catalytic domain [4Q21] and [6Q21] 87
Caenorhabditis elegans genome 16 94
Canonical structures, immunoglobulin 240ff
Canonical structures, T-cell receptor 262
Carboxypeptidase a (cow) [5CPA] 327
Carboxypeptidase a (cow) [5CPA], helix 142
Carboxypeptidase a (cow) [5CPA], helix-helix contact 163 164
Carboxypeptidase a (cow) [5CPA], IIbcellobiose (Escherichia coli), A chain [1IIB] 190—191
CASP (Critical Assessment of Structure Prediction) 90
Catalytic antibody 19
Catalytic triad (Ser-His-Asp) 204 207
CATH (class, architecture, topology, homologous superfamily) 43 127 129ff
CDR see “Complementarity-determining region”
Chaperone 3 297
Chemical shift 41
Chymotrypsin (cow) [8GCH] 204
Chymotrypsin (cow) [8GCH], specificity pocket 213
Chymotrypsin inhibitor 2 (barley) [2CI2] 323
Citrate synthase 281ff
Citrate synthase (chicken) [3CTS, 5CTS] 138 283
Cleaved -antitrypsin (human) [7API] 292 296
Complementarity-determining region (CDR) 233 236 240ff
Complementarity-determining region (CDR), T-cell receptor 262
Concanavalin A (jackbean) [3CNA] 147
Conformation 31-32
Conformational angles 31—32 35
Core of protein structure 18 50 88 180—181
Cow mitochondrial F1-ATPase [1BMF] 304
Crambin (Crambe abyssinica) [1CRN] 24
Critical Assessment of Structure Prediction (CASP) 90
Cryo-EM 42
Crystal-packing forces, effect on structure 180
Cytochrome (cow) [3B5C] 324
Cytochrome (Desulfovibrio vulgaris Miyazaki) [2CDV] 310
Cytochrome (Desulfovibrio vulgaris Miyazaki) [2CDV], hairpin loop 103
Cytochrome c (rice) [1CCR] 26 138
Cytochrome c (tuna) [5CYT] 138
Cytokine: glycosylation-inhibiting factor (human) [1GIF] 329
D-ribose-binding protein (Escherichia coli) [2DRI] 333
D1.3 (mouse) binding hen egg white lysozyme [1VFB] 86
DALI 43 88 127 131
Dali Domain Dictionary 131
Databanks 45—46
Death domain of p75 low affinity neurotrophin receptor (rat) [1NGR] 312
Denaturation 37
Dihydropteridine reductase (rat), NAD-binding domain [1DHR] 221 223
Direct methods of phase determination 38
Discs large protein, PDZ3 domain, DHR3 domain (human) [1PDR] 318
Disulphide bond 23
DNA 61
DNA complex of transcription factor Skn-1 (Caenorhabditis elegans) [1SKN] 120
DNA polymerase (rat), catalytic domain [1RPL] 113
Domain 75
Domain swapping 175-176
Drosophila melanogaster genome 16 94 204
Drug design 19
Elastase (pig) [3EST] 215
Elastase (pig) [3EST], type II’ hairpin loop 98
Engrailed homeodomain (Drosophila melanogaster) [1ENH] 80
Enolase 173—174
Erythrocruorin (Chironomus thummi), B/G helix contact [1ECD] 198
Erythrocruorin (Chironomus thummi), B/G helix contact [1ECD], loop 104—105
Exon, proposed relation to protein structural unit 166
F1-ATPase see “ATPase”
Fab J539 (mouse), H1 loop [2FBJ] 241
Fab J539 (mouse), H1 loop [2FBJ], H3 loop 246
Fab KOL (human), CH1 domain [2FB4] 234
Fab KOL (human), VL domain 234
Fab McPC603 (mouse), H3 loop [1MCP] 246
Fab McPC603 (mouse), H3 loop [1MCP], antigen-binding site 238
Fab McPC603 (mouse), H3 loop [1MCP], VH domain 244
Fab TE33 (mouse), antigen-binding site [1TET] 245
Farnesyl diphosphate synthase (chicken) [1FPS] 315
Fatty acid binding protein (human) [1HMS] 320
Ferredoxin (Azotobacter vinelandii) [6FD1] 159
Ferredoxin reductase (spinach) [1FNB] 134
Fibre diffraction 36
FK506-binding protein (human) [2FKE] 86
FK506-binding protein (yeast) [1YAT] 86
Flavodoxin (Clostridium beijerinckii) [5NLL] 29 128 133
Fold recognition 90
Folding pathway 23
Formate dehydrogenase (Pseudomonas sp. 101) [2NAD] 219
Four-helix bundle 132 135ff
Fructose permease subunit IIb (Escherichia coli) [1BLE] 331
FSSP (Fold classification based on Structure-Structure alignment of Proteins) 88
Fv D1.3 (mouse) [1VFB] 86
GCN4-bZIP, DNA complex (yeast) [2DGC] 139
Gene duplication 173
genetic code 17
Genomics 12 15—16 94
Globin (Aplysia limacina) [1MBA] 202
Globin (Glycera dibranchiata) [1HBG] 136
Glucoamylase fragment (Aspergillus awamori) [1GAI] 316
Glutathione peroxidase (cow) [1GP1] 333
Glyceraldehyde-3-phosphate dehydrogenase (Bacillus stearothermophilus), NAD-binding domain [1GD1] 220
Glycolate oxidase (spinach) [1GOX] 75 153 156—157
Glycosyl-asparaginase domain (Flavobacterium meningosepticum) [1PGS] 145
Green fluorescent protein (Aequorea victoria) [1EMA] 321
GroEL (Escherichia coli) [1DER] 298
GroEL-GroES 3 297
GroEL-GroES complex (Escherichia coli) [1AON] 300 301
Haemoglobin (horse), -chain, B/G helix contact [1EHB] 198
Haemoglobin (human) [1HHO] 285 288 289
Haemoglobin (human) [1HHO], a-chain, haem pocket 200
Haemoglobin (human) [4HHB] 137
Haemoglobin S 182
Haemoglobin, transition 284ff
Haemoglobin, alignment table 168—169
Haemoglobin, allosteric change 284ff
Haemoglobin, evolution 166ff 195ff
Haemoglobin, oxygen binding 285
Hairpin see “ -hairpin”
Haplotype 249
Haptoglobin 174
Helical wheel 67
Helices 9 59
Helix cap 66
Helix capping 62 66
Helix hairpin 78
Helix interface see “Helix-helix packing”
Helix, 62 64 195
Helix, 33 60—63 67
Helix, , 62 65—66
Helix, conformational parameters 67
Helix, polyproline II 62 67 68
Helix-helix packing 141ff 163—164 201 203
Helix-interface-shear mechanism of conformational change 277ff
Hinge motion 274
HLA-B53, MHC protein (human) [1A1M] and [1A1O] 250
Homology modelling 18 90 184ff
Human genome 16 94
Hydrogen bond pattern 59
Hydrogen bond pattern, effect of proline 62
Hydrogen bond pattern, helix 59ff
Hydrogen bond pattern, NAD-binding domains 218ff
Hydrogen bond pattern, serine proteinases 210 215
Hydrogen bond pattern, sheet 68ff
Hydrogen bonding 23 27
Hydrophobic effect 21 49 62
Hydrophobicity scale 21 22
HyHEL-5 (mouse), hen egg white lysozyme complex [1BQL] 239
HyHEL-5 (mouse), hen egg white lysozyme complex [1BQL], L3 canonical structure [3HFL] 242
HyHEL-5, antibody 238—239
I-Ak, class II MHC protein (human) [1IAK] 252-254 260
Immunoglobulin D1.3 Fv fragment (mouse) [1FVB] 86
Immunoglobulin G MAB231 (mouse) [1IGT] 232
Immunoglobulin HyHEL-5 Fab fragment (mouse), hen egg white lysozyme complex [1BQL] 239
Immunoglobulin HyHEL-5 Fab fragment (mouse), hen egg white lysozyme complex [1BQL], L3 canonical structure [3HFL] 242
Immunoglobulin J539, Fab fragment (mouse) [2FBJ] 86
Immunoglobulin McPC603, Fab fragment (mouse) [1MCP] 102
Immunoglobulin McPC603, Fab fragment (mouse) [1MCP], hairpin loop 101 104
Immunoglobulin structure 231ff
Immunoglobulin superfamily 230
Immunoglobulin TE33, Fab fragment (mouse) [1TET] 86 245
Immunoglobulin TE33, Fab fragment (mouse) [1TET], CL domain 69 72
Immunoglobulin, antigen-binding by 236 245
Immunoglobulin, B1-B8 244
Immunoglobulin, canonical structures 240ff
Immunoglobulin, gene assembly 229 244
Immunoglobulin, HyHEL-5 238—239
Immunoglobulin, McPC603 238—239
Immunoglobulin, TE33 245
Induced fit 258
Influenza haemagglutinin [3HMG] 149
Insulin (pig) [1ZNI] 24
Insulin (pig), 2-zinc form, dimer [3INS] 278 282
Insulin (pig), 2-zinc form, hexamer 279
Insulin (pig), 2-zinc form, monomer 280
Insulin (pig), 4-zinc form, dimer [1ZRO] 24 278
Insulin (pig), 4-zinc form, hexamer 279
Insulin (pig), 4-zinc form, monomer 280
Insulin, alignment table 171
Insulin, conformational change 277
Insulin, zinc binding sites 105ff
Interleukin-5 (human) [1HUL] 176
Internet 16
Irregular structures 158
Isocitrate dehydrogenase (Escherichia coli) [5ICD] 54
J539 (mouse) [2FBJ] 86
J539 (mouse) [2FBJ], H3 loop 246
J539 (mouse) [2FBJ], L3 canonical structure 242
Keratin 9 15
Lactate dehydrogenase 174
Lactate dehydrogenase (pig), NAD-binding domain [9LDT] 223
Lactoferrin (human) [1LFG] and [1LFH] 274
Lactoferrin, hinge motion 274
Leghaemoglobin (lupin) [2LH7] 177 196
Leghaemoglobin (lupin) [2LH7], F/H helix contact 198
Leghaemoglobin (lupin) [2LH7], haem pocket 200
Lens crystallins 173
Light-harvesting protein: peridinin-chlorophyll protein (Amphidimum carterae) [1PPR] 314
Lithostatine: pancreatic stone inhibitor (human) [1LIT] 323
Lock and key model of enzyme specificity 36
Loops 95ff
Loops, classification 96
Loops, sequence-structure relationships 97ff 184
Low temperature electron microscopy 42
Lysozyme (hen egg white) [1HEW] 106
Lysozyme (hen egg white), HyHEL-5 (human) complex [1BQL] 239
Lysozyme (phage ) [3LZM, 1LYD] 81 130 326
Lysozyme (phage ) [3LZM, 1LYD], wild type and mutant [3LZM] and [1L18] 183
MAD (multiwavelength anomalous dispersion) 38
Major histocompatibility complex (MHC) proteins 247 263ff
Major histocompatibility complex (MHC) proteins, binding of peptides 25lff 255ff
Major histocompatibility complex (MHC) proteins, interaction with TCR 263ff
Malate dehydrogenase 174
Malate dehydrogenase (Escherichia coli), NAD-binding domain [1EMD] 220 223
Malate dehydrogenase (pig), NAD-binding domain [1MLD] 84
Mannose-specific agglutinin (snowdrop) [1JPC] 319
Max protein, DNA-binding domain (mouse) [1AN2] 313
McPC603 (mouse), H3 loop [1MCP] 246
McPC603 (mouse), H3 loop [1MCP], antigen-binding site [2MCP] 238
McPC603 (mouse), H3 loop [1MCP], hairpin loop 101ff
McPC603 (mouse), H3 loop [1MCP], VH domain 244
McPC603, antibody 238—239
MHC see “Major histocompatibility complex”
MHC protein/T-cell receptor complex (mouse) [2CKB] 263—265
Modular protein 75
Molecular clock 170
Molecular replacement 38
Monellin (african serendipity berry) [4MON] 325
Motif 95 218
Motif, canonical structures of antigen-binding loop 243
Multiwavelength anomalous dispersion (MAD) 38
Murine/human ubiquitin-conjugating enzyme ubc9 [1U9B] 150
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