Introduction to protein science: architecture, function, and genomics
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Oxford
Oxford University Press
[2016]
|
| Ausgabe: | Third edition |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xxii, 466 Seiten Illustrationen, Diagramme |
| ISBN: | 9780198716846 |
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| 245 | 1 | 0 | |a Introduction to protein science |b architecture, function, and genomics |c Arthur M. Lesk, the Pennsylvania State University |
| 246 | 1 | 3 | |a Protein science |
| 250 | |a Third edition | ||
| 264 | 1 | |a Oxford |b Oxford University Press |c [2016] | |
| 300 | |a xxii, 466 Seiten |b Illustrationen, Diagramme | ||
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| 650 | 4 | |a Genomics | |
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Datensatz im Suchindex
| _version_ | 1804174864588734464 |
|---|---|
| adam_text | CONTENTS
Preface to the first edition xvii
Preface to the second edition xx
Preface to the third edition xxi
1 introduction 1
Proteins in their biological context 2
The amino acids 4
Dogmas—central and peripheral 5
The relationship between amino acid sequence and
protein structure is robust 6
Disorder in proteins 7
Regulation 10
The genetic code 11
With life so dependent on proteins, there is ample
opportunity for things to go wrong 12
Genome sequences 15
Gene sequence determines amino acid sequence 16
Protein synthesis: the ribosome is the point of contact
between genes and proteins—it is the fulcrum of genomics 17
Ribosomes were implicated in protein synthesis very early on 18
Structural studies of ribosomes by X-ray crystallography and electron microscopy 18
Protein stability, dénaturation, aggregation, and turnover 19
Protein turnover 19
Description of protein structures 20
Primary structure 21
Secondary structure: helices and sheets are favourable conformations
of the chain that recur in many proteins 21
Tertiary and quaternary structure 23
Folding patterns in native proteins—themes and variations 23
Modular proteins, and ‘mixing and matching as a mechanism of evolution 25
How do proteins develop new functions? 27
The study of proteins: in the laboratory, in the cell, in the computer 29
Spectroscopic methods of characterizing proteins in solution 30
Absorbance and fluorescence of proteins 32
Fluorescence is sensitive to the environment and dynamics
of the chromophore 34
Fluorescence resonance energy transfer (FRET) 34
Circular dichroism 34
Protein expression patterns in space and time: proteomics 35
Subcelfular localization 35
The transcriptome 36
DNA microarrays 37
Mass spectrometry 38
Computing In protein science 38
Computer—instrument partnerships in the laboratory 38
Simulations, including molecular dynamics 39
Bioinformatics 40
Introduction to databanks for protein science 40
Information**retrieval tools 41
Web access to the scientific literature 41
Useful websites 42
Recommended reading 42
Exercises and Problems 43
2 Protein structure 46
Introduction 47
Structures of the amino acids 47
Protein conformation 50
Conformational angles and the
Sasisekharan-Ramakrishnan-Ramachandran plot 51
Sidechain conformation 53
Rotamer libraries 53
Stabilization of the native state 54
Conformational change 59
Protein folding patterns 60
Supersecondary structures 60
An album of small structures 62
Comparison of the folding patterns of acyl phosphatase
and a fungal toxin 64
Classification of protein structures 67
Databanks of protein structure classifications 68
SCOP 68
SCOP2 70
CATH 71
The DALI Database 72
A survey of protein structures and functions 73
Fibrous proteins 73
Enzymes—proteins that catalyse chemical reactions 76
Antibodies 77
Inhibitors 77
Carrier proteins 77
Membrane proteins 78
Receptors 80
Regulatory proteins 81
Motor proteins 81
Control of protein activity 81
Regulation of tyrosine hydroxylase illustrates several control
mechanisms common to many proteins 84
Control cascades 84
Recommended reading 85
Exercises and Problems 85
Protein structure determination 92
Introduction 93
X-ray crystallography 94
X-ray structure determination 95
X-ray crystallography of proteins 96
Interpretation of the electron density: model building and improvement 100
The endgame—refinement 102
How accurate are the structures? 102
X-ray crystallography—the theoretical background 104
Nuclear magnetic resonance spectroscopy in structural biology 110
NMR spectra of proteins 111
Measurement of NMR spectra 113
Protein structure determination by NMR 113
Assignment of the spectrum 114
Transverse relaxation optimized spectroscopy 117
From the data to the structure 117
Solid-state NMR: magic angle spinning 118
Near atomic-resolution low-temperature electron microscopy (cryo-EAA) 119
Octameric pyruvate-ferredoxin oxidoreductase from
Desulfovibrio vulgaris Hildenborough 120
Conformational change in activation of human integrin aVfB 120
Trajectories of conformational change 124
The elastic network model accounts for conformational
change in Mycobacterium tuberculosis thioredoxin reductase 125
The relationship between structure determinations of
isolated proteins, and protein structure and function in vivo 127
Protein structure prediction and modelling 127
A priori methods of protein structure prediction 128
Empirical, or knowledge-based , methods of protein structure prediction 129
Secondary structure prediction 131
Homology modelling 133
Fold recognition 135
Antibody modeling 137
Prediction of special categories of structures 139
Conformational energy calculations and molecular dynamics 140
ROSETTA 142
Protein structure prediction from contact maps derived
from correlated mutations in multiple sequence alignments 144
Critical Assessment of Structure Prediction (CASP) 146
CAPRI 153
Recommended reading 153
Exercises and Problems 154
Bioinformatics of protein sequence and structure 160
Introduction 160
Databases and information retrieval 161
Amino acid sequence databases 162
Protein databases at the U.S. National Center for
Biotechnology Information 163
Specialized, or boutique , databases 164
Nucleic acid sequence databases 165
Genome databases and genome browsers 166
Ensembl 166
Expression and proteomics databases 166
Databases of macromolecular structure 168
Organization of wwPDB entries 169
Retrieval of sequences and structures 170
Retrieval of amino acid sequences by keyword 171
The Protein Information Resource (PIR) and associated databases 171
Retrieval of structures by keyword 172
Probing databanks with sequence information 173
Sequence alignment 174
The dotplot 175
Dotplots and alignments 176
BLAST and PSI-BLAST 177
Significance of alignments 179
Multiple sequence alignment 181
A multiple sequence alignment of thioredoxins shows the
importance of conservation patterns 182
Analysis of structures 184
Superposition of structures 184
Structural alignment 185
Multiple structure alignment 187
Database searching for structures or fragments 187
Databases of protein families 188
Classifications of protein structures 189
Classification and assignment of protein function
189
The Enzyme Commission 189
The Gene Ontology™ Consortium protein function classification 190
The ENZYME database and PROSiTE 192
Databases of metabolic networks 193
Recommended reading 194
Exercises and Problems 195
Proteins as catalysts: enzyme structure,
kinetics, and mechanism 197
Introduction 197
What are the crucial features of enzymes? 198
Reaction rates and transition states 201
The activated complex 203
Measurement of reaction rates 204
Slow the reaction down 205
Fast methods of data collection 205
Active sites 206
Cofactors 206
Protein-ligand binding equilibria 207
The Scatchard plot 207
Catalysis by enzymes 208
Enzyme kinetics 209
Derivation of KM and Vmax from rate data 210
Measures of effectiveness of enzymes 211
Inhibitors 212
Irreversible inhibitor binding 212
Multisubstrate reactions 213
Enzyme mechanisms 214
The mechanism of action of thymidylate synthase 216
Computational approaches to enzyme mechanisms 218
The mechanism of action of chymotrypsin 220
The evidence from kinetics 221
The evidence from crystallography 221
Blood coagulation 222
Thrombosis 222
Serpins: serine proteinase inhibitors-conformational disease 226
Several conformational states of serpins are known 227
Mechanism of proteinase inhibition by serpins 228
Evolutionary divergence of enzymes 229
The mechanism of action of malate and lactate dehydrogenases 229
Enolase, mandeiate racemase, and muconate lactonizing
enzyme catalyse different reactions but have related mechanisms 230
The structure and mechanism of E. coh topoisomerase III 231
Motor proteins 233
The sliding filament mechanism of muscle contraction 233
ATP synthase 234
Membrane transport 238
Specificity of the potassium channel from Streptomyces
lividans—room to swing a cation? 238
Allosteric regulation of protein activity 239
The allosteric structural change of haemoglobin 242
Recommended reading 246
Exercises and Problems 246
Proteins with partners 252
Introduction 252
General properties of protein-protein interfaces 254
Burial of protein surface 254
The composition of the interface 254
Complementarity 254
Specific interactions at protein-protein interfaces 25^
Phage M13 gene III protein and E. cofi TolA 255
Multisubunit proteins 256
Diseases of protein aggregation 257
Amyloidoses 2^8
Alzheimer s disease 258
Prion diseases—spongiform encephalopathies 259
The immune system 260
Antibody structure 26^
Antibody maturation 26^
Catalytic antibodies— abzymes 267
Proteins of the major histocompatibility complex 2^8
T-cell receptors 273
Virus structures 274
Tomato bushy stunt virus 270
Bacteriophage HK97: protein chain-mail 278
Photosynthetic reaction centres 279
Protein-DNA interactions 280
Structural themes in protein-DNA binding and sequence recognition 28^
Bacteriophage T7 DNA polymerase 282
Some protein-DNA complexes that regulate gene transcription 283
Recommended reading 287
Exercises and Problems 288
7 Evolution of protein structure and function
291
Introduction 291
Protein structure classification 294
A case study: superpositions and alignments of pairs of proteins with
increasingly more-distant relationships 296
Structural relationships among homologous domains 298
Changes in proteins during evolution give clues to the
roles of residues at different positions 302
To what constraints are pathways of protein evolution subject? 302
Closed /3-barrel structures 303
The TIM barrel 303
Evolution of the globins 307
Mammalian globins 308
What determines the globin folding pattern? 310
Truncated globins 312
Expansion of the globin family 313
Classification of the globins 313
Globin functions 316
Phycocyanins and the globins 316
Evolution of NAD-binding domains of dehydrogenases 318
Comparison of NAD-binding domains of dehydrogenases 320
The sequence motif G * G * *G 323
Structure and evolution of serine proteinases of the Chymotrypsin family 324
Structures of individual domains 324
The domain/domain interface 326
The specificity pocket 327
The ß-barrels in serine proteinase domains and the packing of
residues in their interiors 328
Evolution of visual pigments and related molecules 331
Selection has tuned vertebrate opsins so that the absorption
maximum varies with the light environment 335
How do proteins evolve new functions? 338
Pathways and limits in the divergence of sequence, structure and function 339
Evolution of functional change in the enoiase superfamily 342
Protein evolution at the level of domain assembly 345
Domain swapping is a general mechanism for forming an
oligomer from a multidomain protein 345
Directed evolution 346
Directed evolution of subtifisin E 347
Enhancement of thermal stability 347
Activity in organic solvents 348
Affinity selectivity by phage display 349
Recommended reading 350
Exercises and Problems 350
8 Protein folding and design 356
introduction 356
Why is protein folding so fast? 357
Thermodynamics—key concepts 358
Entropy 359
Spontaneity and equilibrium 359
Kinetics 360
Thermodynamics of protein folding 360
Thermodynamics of mutated proteins 361
Experimental characterization of events in protein folding 362
The molten globule 363
Folding funnels 364
The effect of dénaturants on rates of folding and unfolding:
chevron plots 365
The kinetics of folding of mutated proteins gives clues to the
structure of the transition state for folding 365
Comparison of folding pathways of a natural protein and a
circular permutant 366
Relationship between native structure and folding 369
The hierarchical model of protein folding 371
How fast could a protein fold? 372
Protein misfolding and the GroEL-GroES chaperone protein 373
The GroEL-GroES conformational change 375
Protein engineering 376
Protein design 376
ab initio design of a hyperstable variant of Streptococcal
protein G, ]31 domain 376
Expanding and contracting the genetic code 378
Expansion of the genetic code 378
Contraction of the genetic code 381
Understanding the contents and layout of the common
genetic code 382
Recommended reading 382
Exercises and Problems 383
9 Proteomics and systems biology 387
Introduction 388
Separation and analysis of proteins 389
Polyacrylamide gel electrophoresis 38^
Two-dimensional polyacrylamide gel electrophoresis 39®
Difference gel electrophoresis 3^°
Mass spectrometry 393
Identification of components of a complex mixture 393
Protein sequencing by mass spectrometry 395
Quantitative analysis of relative abundance 395
Measuring deuterium exchange in proteins 398
Ome, ome, on the range—environmental genomics
and proteomics 398
Metagenomics 398
Metaproteomics 398
Dynamic proteomics of the response to cadmium challenge 399
Microarrays 401
Microarray data are semi quantitative 401
Applications of DNA microarrays 403
Analysis of microarray data 404
Expression patterns in different physiological states 406
Expression pattern changes in development: the life cycle of
Drosophila melanogaster 406
RNAseq 408
RNAseq v. microarrays 409
Systems biology 411
Two parallel networks: physical and logical 411
Networks and graphs 412
Robustness and redundancy 413
Connectivity in networks 414
Dynamics, stability, and robustness 416
Protein complexes and aggregates 417
Protein interaction networks 417
Regulatory networks 421
Structures of regulatory networks 422
Structural biology of regulatory networks 423
Gene regulation 424
The transcriptional regulatory network of E. coli 424
Regulation of the lactose operon in E. coli 427
The genetic regulatory network of Saccharomyces cerevisiae 429
Adaptability of the yeast regulatory network 430
Recommended reading 433
Exercises and Problems 434
Epilogue 437
List of Abbreviations 438
Glossary 440
Index 453
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| spelling | Lesk, Arthur M. Verfasser (DE-588)1047454270 aut Introduction to protein science architecture, function, and genomics Arthur M. Lesk, the Pennsylvania State University Protein science Third edition Oxford Oxford University Press [2016] xxii, 466 Seiten Illustrationen, Diagramme txt rdacontent n rdamedia nc rdacarrier Genomics Proteins Proteins Structure Proteine (DE-588)4076388-2 gnd rswk-swf 1\p (DE-588)4151278-9 Einführung gnd-content 2\p (DE-588)4123623-3 Lehrbuch gnd-content Proteine (DE-588)4076388-2 s DE-604 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028105430&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 2\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Lesk, Arthur M. Introduction to protein science architecture, function, and genomics Genomics Proteins Proteins Structure Proteine (DE-588)4076388-2 gnd |
| subject_GND | (DE-588)4076388-2 (DE-588)4151278-9 (DE-588)4123623-3 |
| title | Introduction to protein science architecture, function, and genomics |
| title_alt | Protein science |
| title_auth | Introduction to protein science architecture, function, and genomics |
| title_exact_search | Introduction to protein science architecture, function, and genomics |
| title_full | Introduction to protein science architecture, function, and genomics Arthur M. Lesk, the Pennsylvania State University |
| title_fullStr | Introduction to protein science architecture, function, and genomics Arthur M. Lesk, the Pennsylvania State University |
| title_full_unstemmed | Introduction to protein science architecture, function, and genomics Arthur M. Lesk, the Pennsylvania State University |
| title_short | Introduction to protein science |
| title_sort | introduction to protein science architecture function and genomics |
| title_sub | architecture, function, and genomics |
| topic | Genomics Proteins Proteins Structure Proteine (DE-588)4076388-2 gnd |
| topic_facet | Genomics Proteins Proteins Structure Proteine Einführung Lehrbuch |
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