Branden C., Tooze J. — Introduction to protein structure :: Электронная библиотека попечительского совета мехмата МГУ

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Branden C., Tooze J. — Introduction to protein structure

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Название: Introduction to protein structure

Авторы: Branden C., Tooze J.

Аннотация:

Introduction to Protein Structure gives an up-to-date account of the principles of protein structure, with examples of key proteins in their biological context generously illustrated in full colour to illuminate the structural principles described in the text. The first few chapters introduces the general principles of protein structure both for novices and for non-specialists needing a primer. Subsequent chapters use specific examples of proteins to show how they fulfil a wide variety of biological functions. The book ends with chapters on the experimental approach to determining and predicting protein structure, as well as engineering new proteins to modify their functions.

Язык:

Рубрика: Биология/

Статус предметного указателя: Готов указатель с номерами страниц

ed2k: ed2k stats

Издание: 2nd edition

Год издания: 1999

Добавлена в каталог: 29.03.2006

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Предметный указатель

NMR, homeodomain binding to DNA      162
NMR, interpretation of spectra      390
NMR, limitations      390 391
NMR, NOE      388 388F 389 389F
NMR, one-dimensional spectra      387F 388
NMR, radio frequency (RF)      387
NMR, SH2 domain      273
NMR, silk fibroins      290
NMR, two-dimensional spectra      388 388F 390F
NMR, two-dimensional spectra, sequential assignment      389—390
NMR, x-ray crystallography results comparisons      390—391
NOE (nuclear Overhauser effect) spectrum      388 388F 389 389F
NOE NMR      38h 388F 389 389F
Nuclear lamins      287F
Nuclear magnetic resonance      see “NMR”
Nuclear receptors      181 191 202
Nyborg, Jens      255
Oct-1      164F 165
Octylglucoside      224
Oligonucleotide-directed mutagenesis      359F
Omega loop      22
Operator regions (OR)      130
Operator regions (OR), bacteriophage 434      137T
Operator regions (OR), bacteriophage lambda      130 131—132 131T
Operator regions (OR), bacteriophage, overwinding      140—141
Operator regions (OR), bacteriophage, repressor recognition      135 136
Operator regions (OR), differential binding of Cro and repressor, DNA conformation changes      140—141
Operator regions (OR), differential binding of Cro and repressor, sequence-specific      138—139
Operator regions (OR), palindromic sequences      131—132 131T 135
Operator regions (OR), sequence-specific protein-DNA, interactions      138—139 139F
Ovalbumin      111 111F
Overwinding, operator region, phage 434      140—141
Oxidation, disulfide bridge formation      5
Oxidizing agents      98
Oxyanion hole      209
Oxyanion hole, chymotrypsin      211 211F
Oxyanion hole, subtilisin      216—217
Oxygen, binding to myoglobin      105
Oxygen, ion selectivity filter of channel      234
P hairpin      see “Hairpin $\beta$ motif”
P2 family      70
p21      166 254F
p21, transcription activation by p53      166
p53      166
p53, Arg mutations      170 170F 171
p53, DNA binding      169—170 169F
p53, DNA-binding domain      167 167F
p53, DNA-binding domain, antiparallel $\beta$ barrel      168—169 168F
p53, DNA-binding domain, mutations      167 170—171 170F 171F
p53, DNA-binding domain, nucleotide sequence of DNA      169F
p53, domains      167 167F
p53, function      166
p53, loop regions      169—170 171 171F
p53, mutations, regions      170—171 170F 171F
p53, oligomerization domain      167—168 167F
p53, tetramers      167
p53, tetramers, formation      167—168 167F
Pabo, Carl      133 160 165 177 197
Palindromic sequences      131—132 131T 135
Palindromic sequences, glucocorticoid receptor binding      185 191
Palindromic sequences, MyoD recognition sequence      198F
Papain      304F
Papovavirus family      341
Paracelsus challenge      368—370 369F 369T
Parvalbumin, motif      24 25
Parvoviruses      326
Patterson maps      380 380F
Pauling, Linus      14 43 205 285
Pavletich, Nikola      107 167 177
Pectate lyase, $\beta$ helix structure      84 84F 86F
Peptide bonds, cleavage by serine proteinases      208 208F
Peptide bonds, formation      4 4F
Peptide bonds, hydrolysis      208 208F
Peptide inhibitor, binding to chymotrypsin      211
Peptide units      8
Peptide units, dipole moment      16 16F
Peptide, binding to MHC molecules      314—315 315F 316
Peptidyl prolyl isomerases      98
Periplasmic space      228 231
Perutz, Max      14 44F 113 370F 379—381 380F
Petsko, Greg      54
PH domain      272
pH, hemagglutinin structural change      81—84
Phage      see “Bacteriophage”
Phage display      see “Bacteriophage display”
Phage replicase      339
Phase determination, diffracted beams      370F 379—381 380F
PHD program      351
Phenylalanine, insertion in TATA box      156
Phenylalanine, structure      6F
Pheophytin      238 239
Phi ( $\phi$ ) angle      8 9 14
Phi ( $\phi$ ) angle, Ramachandran plot      9 9F 10
Phillips, David      23F 95F
Phosducin      265—266
Phosducin, binding to $G_{\beta\gamma}$       265—266 266F
Phosducin, C-terminal domain      265 266
Phosducin, structure and domains      265—266 265F
Phosducin, thioredoxin homology      265—266
Phosphate in $\alpha$ helix      16F
Phosphate, Ras and $G_{\alpha}$ binding to GTP      255 257 259
Phosphoenolpyruvate (PEP)      115 117
Phosphofructokinase (PFK)      114—117
Phosphofructokinase (PFK), allosteric properties      114—117
Phosphofructokinase (PFK), ami no acids      115—116
Phosphofructokinase (PFK), dimers and packing of      116
Phosphofructokinase (PFK), Escherichia coli      115—116 115F
Phosphofructokinase (PFK), quaternary structure      116F
Phosphofructokinase (PFK), R and T states      115 116—117 117F
Phosphofructokinase (PFK), reaction      114F
Phosphofructokinase (PFK), subunit structure      115
Phosphofructokinase (PFK), subunit structure, catalytic sites      116
Phosphoglycerate mutase      58F
Phosphoribosyl anthranilate (PRA) isomerase      52—53 53F
Phosphorylation, Src tyrosine kinase      275 276
Phosphorylcholine      308—309 309F
Phosphotyrosine (pTyr)      272—273
Phosphotyrosine (pTyr), binding to SH2 domain      273—274 278
Photoisomerization, retinal      227 228 229F
Photon absorption, photosynthesis      239—240 243
Photon absorption, rhodopsin      265
Photosynthesis, energy flow and mechanisms      243—244 244F
Photosynthesis, process      239—240
Photosynthetic pigments      234—236 235 236 236F
Photosynthetic pigments in photosynthetic reaction center      235 236 236F
Photosynthetic pigments, arrangement      238F
Photosynthetic pigments, bound to L and M subunits      237—239
Photosynthetic reaction center      234—236
Photosynthetic reaction center, amino acid sequences      247F
Photosynthetic reaction center, definition      235
Photosynthetic reaction center, Fe atom      236 238
Photosynthetic reaction center, hydropathy plots, correlation with crystal structure data      246
Photosynthetic reaction center, L, M and H subunits      235
Photosynthetic reaction center, L, M and H subunits, transmembrane $\alpha$ helices      236—237 237F
Photosynthetic reaction center, light energy converted to electrical energy      239—240
Photosynthetic reaction center, light-harvesting (LH1 and LH2) complexes surrounding      240—241 243F
Photosynthetic reaction center, modeling      244
Photosynthetic reaction center, pigments      see “Photosynthetic pigments”
Photosynthetic reaction center, polypeptide chains      234—236
Photosynthetic reaction center, three-dimensional structure      237F
Photosynthetic reaction center, transmembrane $\alpha$ helices      244—245 (see also “Light-harvesting complexes”)
Picornaviruses      326 326F 333—335 333F
Picornaviruses, antibody binding sites      333
Picornaviruses, capsid      333
Picornaviruses, capsid, subunit arrangement      334—335 334F
Picornaviruses, jelly roll structure      335 336F
Picornaviruses, structural proteins (VP1-VP4)      334 336
Picornaviruses, T=3 plant virus relationship      337 (see also “Human rhinovirus”)
Pigments, photosynthetic      see “Photosynthetic pigments”
Plasma membrane proteins      228

Plasminogen      29F
Plasminogen activator inhibitor (PAI)      111 113
Plastocyanin      24F
Plastocyanin, NMR and x-ray crystallography comparison      391
Pleated $\beta$ sheets      19 19F
Pleckstrin      272
Pleckstrin-homology (PH) domain      272
Point mutations      366
Poliovirus      336F
Poljak, Roberto      304 309
Polyalanine repeats      290
Polymerase chain reaction (PCR), random mutagenesis method      359F
Polyomavirus      326 341—343
Polyomavirus, structure      342
Polypeptide chains (subunits)      4 29
Polypeptide chains (subunits) in hemagglutinin      78F 79 79F
Polypeptide chains (subunits), antibodies      300—301
Polypeptide chains (subunits), large, domains      29—30
Polypeptide chains (subunits), main-chains      4
Polypeptide chains (subunits), organization      29F
Polypeptide chains (subunits), unfolded and folded states      90F
Polypeptide chains (subunits), virus capsid      325
Polyproline type II helix      274
Porins      228—231
Porins, channels      230—231 231F
Porins, channels, eyelet      230 231F
Porins, channels, up and down $\beta$ barrels      229—230 230F
Porins, transmembrane channels formed by $\beta$ strands      228—229
Positive control protein      146
Potassium channels      232
Potassium channels, ion pore      232F 233
Potassium channels, ion selectivity filter mechanism      233—234 233F
Potassium channels, selectivity filter structure      233F
Potassium channels, tetrameric molecule      232—233 232F
POU homeodomain      162F
POU regions      164—166 175
POU regions, binding to DNA by helix-turn-helix motifs      164—166 164F 165F
POU regions, domains      164F
POU regions, structure      164 164F
PPR1 transcription factor      190—191 190F
PRA-isomerase, IGp-synthase, double barrels      52—53 52F
Prealbumin      69
Prediction of structure      348—354
Prediction of structure from amino acid sequences      352—353
Prediction of structure, $\alpha$ helix (helices)      352
Prediction of structure, active sites in $\alpha/\beta$ barrels      57 59
Prediction of structure, CDR regions      350F
Prediction of structure, complementarity determining regions      350 350F
Prediction of structure, loop regions      21
Prediction of structure, secondary structure      see “Secondary structure of proteins”
Prediction of structure, side chain conformation      349
Prediction of structure, tertiary structure, secondary structure, knowledge needed      350—351
Prediction of structure, threading methods      353—354
Prediction of structure, three-dimensional, in homologous proteins      349—350
Prediction of structure, transmembrane $\alpha$ helix from, amino acid sequence      244—245
Primary structure of proteins      3F 4 28 29
Prion diseases      283
Prion proteins      290
Prion proteins, model system for      370
Procollagen      284
Prolactin receptor      267
Prolactin receptor, extracellular domain      269
Prolactin receptor, growth hormone complex      269—270 269F 270F 271F
Proline $\alpha$ helix      16—17
Proline $\alpha$ helix in collagen      284
Proline $\alpha$ helix, cis-trans isomerization      98—99 98F
Proline $\alpha$ helix, effect on protein stability      356—357
Proline $\alpha$ helix, structure      7F
Proline-rich regions, binding to SH3 domain      273 274—275
Prolyl hydroxylase      284
Promoter elements      130
Promoter elements, core (basal)      151 151F
Promoter elements, enhancer element distance from      152
Promoter elements, proximal      151 151F
Pronase      71
Protein Data Bank      353
Protein design from first principles      367—368
Protein design, $\beta$ structure conversion to a structure      368—370 369F 369T
Protein design, definition      347
Protein design, zinc finger not stabilized by zinc      367—368 368F 368T
Protein disulfide isomerase (PDI)      96 97
Protein engineering      347—354
Protein engineering, combinatorial methods      358—359
Protein engineering, definition      347
Protein engineering, goal      367
Protein engineering, protein folding studies      93—95
Protein engineering, specificity pockets      213—215
Protein engineering, stability increased      354—358
Protein engineering, stability increased, disulfide bridges      354—356
Protein engineering, stability increased, increasing proline residues      356—357
Protein engineering, stability increased, stabilizing dipoles of $\alpha$ helices      357—358 387F lysozyme”)
Protein engineering, subtilisin      215 217 219
Protein fold assignments (threading)      353—354
Protein fold, database      353
Protein folding      4 89—120
Protein folding in GroEL-GroES complex      104
Protein folding, assignment of amino acid sequences (threading)      353—354
Protein folding, blocked, prevention      91
Protein folding, definition      89
Protein folding, disulfide bond formation      96—98
Protein folding, enzymes role in      89 96—98
Protein folding, hydrophobic side chain burying      93
Protein folding, inside chaperonins      99—100
Protein folding, intermediates      93 94
Protein folding, intermediates, accumulation      113
Protein folding, intermediates, disulfide-bonded      96—97
Protein folding, intermediates, unstable      91
Protein folding, inverse folding problem      353
Protein folding, isomerization of proline residues      98—99 98F
Protein folding, kinetic factors      91—92
Protein folding, molten globule as intermediate      93 94
Protein folding, multiple pathways      95F
Protein folding, problem in protein engineering      348
Protein folding, rate limiting step      98—99 98F
Protein folding, single pathway      93—95
Protein folding, single-site mutations and energetics      93—95
Protein folding, temperature-dependent fluctuations      104—105 (see also “Conformational changes”)
Protein G      369—370 369F
Protein kinase      106
Protein kinase, conformational changes      105—109
Protein kinase, cyclin-dependent (CDKs)      see “Cyclin-dependent protein kinases (CKDs)”
Protein kinase, domains of enzyme-linked receptors      271
Protein structure      see “Specific entries”
Protein(s), aggregation      99
Protein(s), breathing      105
Protein(s), classes      283
Protein(s), conformational state changes      see “Conformational changes”
Protein(s), denatured state      90
Protein(s), folded      90F 92F
Protein(s), folded, flexible structure      104—105
Protein(s), folding      see “Protein folding”
Protein(s), functions      3
Protein(s), homologous      see “Homologous proteins”
Protein(s), membrane      see “Membrane proteins”
Protein(s), molten globules      see “Molten globular proteins”
Protein(s), native state      89 90
Protein(s), native state, secondary structure      92
Protein(s), native state, stability      90
Protein(s), techniques to determine structure      373—392 (see also “x-ray crystallography” “NMR”)
Protein(s), unfolded      90F 92F
Protein(s), unfolded as ensemble of interconverting structures      92 94F
Protein(s), unfolding, in chaperonins      99—100
Protein-DNA interactions, carbonyl groups of GAL4 in      188—189 189F
Protein-DNA interactions, glucocorticoid receptor      184
Protein-DNA interactions, Max and MyoD      201 201F
Protein-DNA interactions, water mediating      162 (see also “Other specific proteins”)
Protein-protein interactions, cytochrome subunit of photosynthetic reaction center      236
Protein-protein interactions, Mat $\alpha$ 2-Mat al binding      163—164
Protein-protein interactions, transcription activation      152—153 159
Proteinase inhibitors      110—111

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