Introduction to protein science: architecture, function, and genomics
Gespeichert in:
1. Verfasser: | |
---|---|
Format: | Buch |
Sprache: | English |
Veröffentlicht: |
Oxford [u.a.]
Oxford Univ. Press
2010
|
Ausgabe: | 2. ed. |
Schlagworte: | |
Online-Zugang: | Inhaltsverzeichnis |
Beschreibung: | XIX, 455 S. Ill., graph. Darst. |
ISBN: | 9780199541300 |
Internformat
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245 | 1 | 0 | |a Introduction to protein science |b architecture, function, and genomics |c Arthur M. Lesk |
250 | |a 2. ed. | ||
264 | 1 | |a Oxford [u.a.] |b Oxford Univ. Press |c 2010 | |
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Datensatz im Suchindex
_version_ | 1804140939306860544 |
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adam_text | CONTENTS
Preface to the first edition
xvii
Preface to the second edition
xx
1
Introduction
1
Proteins in their biological context
2
The
amino
acids
3
Dogmas
—
central and peripheral
5
The relationship between
amino
acid sequence and
protein structure is robust
б
Regulation
7
The genetic code
7
With life so dependent on proteins, there is ample
opportunity for things to go wrong
8
Genome sequences
11
Gene sequence determines
amino
acid sequence
12
Protein synthesis: the ribosome is the point of contact
between genes and proteins
—
it is the fulcrum of genomics
14
Ribosomes were implicated in protein synthesis very early on
14
Structural studies of ribosomes by X-ray crystallography and electron microscopy
15
Protein stability, denaturation, aggregation, and turnover
15
Protein turnover
16
Description of protein structures
17
Primary structure
17
Secondary structure: helices and sheets are favourable conformations
of the chain that recur in many proteins
17
Tertiary and quaternary structure
19
Folding patterns in native proteins—themes and variations
19
Modular proteins, and mixing and matching as a mechanism of evolution
22
How do proteins develop new functions?
25
The study of proteins: in the laboratory, in the cell, in the computer
26
Spectroscopic methods of characterizing proteins in solution
26
Absorbance and fluorescence of proteins
29
Fluorescence is sensitive to the environment and dynamics
of the chromophore
30
Fluorescence resonance energy transfer (FRET)
30
Circular dichroism
30
Protein expression patterns in space and time: proteomics
32
Subcellular localization
32
DNA microarrays 33
Mass spectrometry
34
Computing in protein science
34
Computer-instrumental partnerships in the laboratory
34
Simulations, including molecular dynamics
35
Bioinformatics 36
Databanks for protein science
36
Information-retrieval tools 37
Web access to the scientific literature
38
Useful websites
38
Recommended reading 39
Exercises, Problems, and Weblems
39
2
Protein structure
41
Introduction
42
Structures of the
amino
acids
42
Protein conformation
45
Conformational angles and the
Sasisekharan-Ramakrishnan-Ramachandran plot
45
Sidechain conformation
47
Rotamer libraries
48
Stabilization of the native state
48
Protein folding patterns
52
Supersecondary structures
54
An album of small structures
55
Comparison of the folding patterns of acylphosphatase
and a fungal toxin
60
Classification of protein structures
63
Databanks of protein structure classifications
63
SCOP
64
CATH
64
The
DALI
Database
68
A survey of protein structures and functions
68
Fibrous proteins
68
Enzymes
—
proteins that catalyse chemical reactions
72
Antibodies
74
Inhibitors
74
Carrier proteins
76
Membrane proteins
76
Receptors
78
Regulatory proteins
79
Motor proteins
79
Conformational change
80
Control of protein activity
81
Regulation of tyrosine hydroxylase illustrates several control
mechanisms common to many proteins
82
Control cascades g2
Recommended reading
85
Exercises, Problems, and Weblems
85
3
Protein
structure
determination
95
Introduction
96
X-ray crystallography
97
X-ray structure determination
98
X-ray crystallography of proteins
99
Solving the phase problem in protein crystallography
104
Interpretation of the electron density: model building and improvement
107
The endgame
—
refinement
109
How accurate are the structures?
109
Nuclear magnetic resonance spectroscopy in structural biology
111
NMR spectra of proteins
113
Measurement of NMR spectra
114
Protein structure determination by NMR
114
Assignment of the spectrum
115
Transverse relaxation optimized spectroscopy
118
From the data to the structure
118
Low-temperature electron microscopy (cryo-EM)
119
Octameric pyruvate-ferredoxin oxidoreductase from
Desulfovibrio
vulgáris Hildenborough
119
Conformational change in activation of human
integrin «VÖ3
120
The relationship between structure determinations of
isolated proteins, and protein structure and function in vivo
121
Protein structure prediction and modelling
121
A priori methods of protein structure prediction
123
Empirical, or knowledge-based , methods of protein structure prediction
124
Critical assessment of structure prediction
126
Secondary structure prediction
129
Homology modelling
130
Fold recognition
132
Prediction of special categories of structures
134
Conformational energy calculations and molecular dynamics
137
ROSETTA
139
LINUS
140
Conformational change
141
The elastic network model accounts for conformational change in
Mycobaăerium
tuberculosis thioredoxin reductase
143
Recommended reading
144
Exercises, Problems, and Weblems
145
4
Bioinformatics of protein sequence and structure
149
Introduction
149
Databases and information retrieval
150
Amino
acid sequence databases
151
Protein databases at the U.S. National Center for
Biotechnology Information
152
Specialized, or boutique ,
databases
153
Nucleic acid sequence databases
153
Genome databases and genome browsers
154
Ensembl
154
Expression and proteomics databases
155
Databases of macromolecular structure
156
Organization of wwPDB entries
156
Retrieval of sequences and structures
158
Retrieval of
amino
acid sequences by keyword
158
The Sequence Retrieval System (SRS)
159
The Protein Information Resource
(PIR)
and associated databases
159
Retrieval of structures by keyword
160
Probing databanks with sequence information
161
Sequence alignment
162
Thedotplot
163
Dotplots and alignments
164
BLAST and PSI-BLAST
165
Significance of alignments
168
Multiple sequence alignment
170
A multiple sequence alignment of thioredoxins shows the
importance of conservation patterns
170
Analysis of structures
173
Superposition of structures
173
Structural alignment
174
Multiple structure alignment
175
Database searching for structures or fragments
175
Databases of protein families
177
Classifications of protein structures
177
Classification and assignment of protein function
178
The Enzyme Commission
178
The Gene Ontology™ Consortium protein function classification
178
The ENZYME database and
PROSITE
181
Databases of
metabolic
networks
181
Recommended reading
183
Exercises, Problems and Weblems
183
>
Proteins as catalysts: enzyme structure,
kinetics, and mechanism
187
Introduction 1gg
What are the crucial features of enzymes?
188
Reaction rates and transition states
191
The activated complex
^,
Measurement of reaction rates
194
Slow the reaction down
194
Fast methods of data collection
195
Active sites
195
Cof actors
196
Protein-ligand binding equilibria
196
The Scatchard plot
197
Catalysis by enzymes
198
Enzyme kinetics
198
Derivation of KM and Vmax from rate data
200
Measures of effectiveness of enzymes
201
Inhibitors
201
Irreversible inhibitors
202
Multisubstrate reactions
203
Enzyme mechanisms
204
The mechanism of action of thymidylate synthase
205
Computational approaches to enzyme mechanisms
208
The mechanism of action of chymotrypsin
210
The evidence from kinetics
211
The evidence from crystallography
211
Blood coagulation
212
Thrombosis
212
Serpins:
serine
proteinase inhibitors-conformationai disease
216
Several conformational states of serpins are known
217
Mechanism of proteinase inhibition by serpins
219
Evolutionary divergence of enzymes
219
The mechanism of action of
malate
and
lactate
dehydrogenases
219
Enolase,
mandelate racemase,
and muconate lactonizing
enzyme catalyse different reactions but have related mechanisms
220
Enzymes that process
DNA
and
RNA
221
The structure and mechanism of f.
coli topoisomerase
III
221
Motor proteins
224
The sliding filament mechanism of muscle contraction
224
ATPase
224
Membrane transport
227
Specificity of the potassium channel from Streptomyces
lividans
—
room to swing a cation?
228
Allosteric regulation of protein activity
228
The allosteric change of haemoglobin
231
Recommended reading
236
Exercises, Problems, and Weblems
236
б
Proteins
with partners 241
Introduction 2^1
General properties of protein-protein interfaces
243
Burial of protein surface
243
The composition of the interface
243
Complementarity
243
Specific interactions at protein-protein interfaces
244
Phage M13 gene III protein and f.
coli TolA
244
Multisubunit proteins
245
Diseases of protein aggregation
246
Amyloidoses
246
Alzheimer disease
247
Prion diseases
—
spongiform encephalopathies
247
The immune system
249
Antibody structure
249
Antibody maturation
256
Catalytic antibodies
—
abzymes
256
Proteins of the major histocompatibility complex
258
Т
-cell
receptors
263
Virus structures
264
Tomato bushy stunt virus
269
Bacteriophage HK97: protein chain-mail
269
Photosynthetic reaction centres
270
Protein-DNA interactions
271
Structural themes in protein-DNA binding and sequence recognition
272
Bacteriophage T7
DNA polymerase 274
Some protein-DNA complexes that regulate gene transcription
274
Recommended reading
280
Exercises, Problems, and Weblems
281
7
Evolution of protein structure and function
285
Introduction
285
Protein structure classification
288
Superpositions and alignments of pairs of proteins with
increasingly more distant relationships
291
Structural relationships among homologous domains
294
Changes in proteins during evolution give clues to the
roles of residues at different positions
298
To what constraints are pathways of protein evolution subject?
298
Closed
í
barrel structures
299
The TIM barrel
300
Evolution of the globins
304
Mammalian globins
305
What determines the globin folding pattern?
308
Truncated globins
310
Phycocyanins and the globins
311
Evolution of NAD-binding domains of dehydrogenases
313
Comparison of NAD-binding domains of dehydrogenases
315
The sequence motif CCO
320
Structure and evolution of
serine
proteinases
of the chymotrypsin family
321
Structures of individual domains
322
The domain/domain interface
324
The specificity pocket
324
The ¿(-barrels in
serine proteinase
domains and the packing of
residues in their interiors
324
Evolution of visual pigments and related molecules
330
Selection has tuned vertebrate opsins so that the absorption
maximum matches the light environment
333
How do proteins evolve new functions?
335
Protein evolution at the level of domain assembly
337
Domain swapping is a general mechanism for forming an
oligomer from a multidomain protein
337
Directed evolution
338
Directed evolution of subtilisin
E
339
Enhancement of thermal stability
339
Recommended reading
341
Exercises, Problems, and Weblems
341
8
Protein folding and design
347
Introduction
347
Why is protein folding so fast?
348
Thermodynamics
—
key concepts
349
Entropy
350
Spontaneity and equilibrium
350
Kinetics
351
Thermodynamics of protein folding
351
Thermodynamics of mutated proteins
352
Experimental characterization of events in protein folding
353
The molten globule
354
Folding funnels
355
The effect of
dénaturants on
rates of folding and unfolding:
chevron plots
356
The kinetics of folding of mutated proteins gives clues to the
structure of the transition state for folding
356
Comparison of folding pathways of a natural protein and a
circular
permutant
357
Relationship between native structure and folding
360
The hierarchical model of protein folding
362
How fast could a protein fold?
363
Protein misfolding and the GroEL-GroES chaperone protein
364
The GroEL-CroES «informational change
365
Protein engineering
368
Protein design 368
ab
initio design of a hyperstable variant of Streptococcal
protein G,
Л
domain
368
Expanding and contracting the genetic code
370
Expansion of the genetic code
370
Contraction of the genetic code
371
Understanding the contents and layout of the common genetic code
375
Recommended reading
375
Exercises, Problems, and Weblems
375
9
Proteomics and systems biology
380
Introduction
381
Separation and analysis of proteins
382
Polyacrylamide gel electrophoresis
382
Two-dimensional polyacrylamide gel electrophoresis
383
Difference gel electrophoresis
383
Mass spectrometry
386
Identification of components of a complex mixture
386
Protein sequencing by mass spectrometry
388
Quantitative analysis of relative abundance
388
Measuring deuterium exchange in proteins
391
Ome, ome,
on the range
—
environmental genomics
and proteomics
391
Metagenomics
391
Metaproteomics
391
Dynamic proteomics of the response to cadmium challenge
393
Microarrays
394
Microarray data are
semiquantitative 396
Will high-throughput sequencing replace microarrays?
396
Applications of
DNA
microarrays
396
Analysis of microarray data
397
Expression patterns in different physiological states
400
Expression pattern changes in development: the life cycle of
Drosophila
melanogaster
400
Systems biology
402
Two parallel networks: physical and logical
403
Networks
and graphs
404
Robustness and redundancy
405
Connectivity in networks
405
Dynamics, stability, and robustness
407
Protein complexes and aggregates
408
Protein interaction networks
409
Regulatory networks
413
Structures of regulatory networks
414
Structural biology of regulatory networks
414
Gene regulation
415
The transcriptional regulatory network of
£
coli
415
Regulation of the lactose operon in
E. coli
418
The genetic regulatory network of Saccharomyces cerevisiae
420
Adaptability of the yeast regulatory network
422
Recommended reading
425
Exercises, Problems, and Weblems
425
Epilogue
429
List of Abbreviations
430
Glossary
432
Index
443
|
any_adam_object | 1 |
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indexdate | 2024-07-09T22:07:56Z |
institution | BVB |
isbn | 9780199541300 |
language | English |
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physical | XIX, 455 S. Ill., graph. Darst. |
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publisher | Oxford Univ. Press |
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spelling | Lesk, Arthur M. Verfasser (DE-588)1047454270 aut Introduction to protein science architecture, function, and genomics Arthur M. Lesk 2. ed. Oxford [u.a.] Oxford Univ. Press 2010 XIX, 455 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Genomics Proteins Proteins Structure Proteine (DE-588)4076388-2 gnd rswk-swf (DE-588)4123623-3 Lehrbuch gnd-content Proteine (DE-588)4076388-2 s DE-604 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018805247&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
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)4123623-3 |
title | Introduction to protein science architecture, function, and genomics |
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 |
title_fullStr | Introduction to protein science architecture, function, and genomics Arthur M. Lesk |
title_full_unstemmed | Introduction to protein science architecture, function, and genomics Arthur M. Lesk |
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 Lehrbuch |
url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=018805247&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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