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Lesk A.M. — Introduction to Protein Architecture
Lesk A.M. — Introduction to Protein Architecture

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Название: Introduction to Protein Architecture

Автор: Lesk A.M.


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).

Язык: en

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

Операции: Положить на полку | Скопировать ссылку для форума | Скопировать ID
Предметный указатель
$3\alpha$, $20\beta$-hydroxysteroid dehydrogenase, NAD-binding domain (Streptomyces hydrogenans) [2HSD]      222
$3_{10}$ helix      62 64 195 201
$S\rightarrowR$ transition (serpins)      291
$T\rightarrowR$ transition (haemoglobin)      284ff
$T_{4}$ lysozyme, effect of mutation      182
$\alpha$-Helix      33 60—63 67
$\alpha$-lactalbumin (baboon) [1ALC]      326
$\alpha_{1}$-antitrypsin (human) [2PSI]      293 296
$\beta$-barrel      70 74 152ff 207ff 213 217
$\beta$-barrel packing of interior      154—157 213—216
$\beta$-barrel topology      154ff 163
$\beta$-bulge      70 74 79
$\beta$-cryptogein (Phytophthora cryptogea) [1BEO]      115 116
$\beta$-hairpin      76 240 246
$\beta$-hairpin sequence-structure relationships      97ff 184
$\beta$-hydroxydecanoyl thiol ester dehydrase (Escherichia coli) [1MKA]      328
$\beta$-sandwich      143ff 233
$\beta$-sheet      9 34 59—61 67—69 71—73 233
$\beta-\alpha-\beta$ unit      77
$\gamma$-crystallin domain (cow) [1AMM]      146
$\lambda$ cro-DNA complex      108
$\pi$-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 “$\beta$-barrel”
Barstar (Bacillus amyloliquefaciens), $C40\rightarrowA$, $C82\rightarrowA$ [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 $\alpha_{1}$-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 $b_{5}$ (cow) [3B5C]      324
Cytochrome $c_{3}$ (Desulfovibrio vulgaris Miyazaki) [2CDV]      310
Cytochrome $c_{3}$ (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$\beta$ (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), $\alpha$-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, $T\rightarrowR$ transition      284ff
Haemoglobin, alignment table      168—169
Haemoglobin, allosteric change      284ff
Haemoglobin, evolution      166ff 195ff
Haemoglobin, oxygen binding      285
Hairpin      see “$\beta$-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, $3_{10}$      62 64 195
Helix, $\alpha$      33 60—63 67
Helix, $\pi$,      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 $T_{4}$) [3LZM, 1LYD]      81 130 326
Lysozyme (phage $T_{4}$) [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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