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Protein Structure and Function : Primers in Biology - Gregory A. Petsko

Protein Structure and Function

Primers in Biology

Paperback

Published: 1st April 2004
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Published by New Science Press and distributed in the U.S. and Canada by Oxford University Press

This text introduces general principles of protein structure, folding, and function, then goes beyond these basics to tackle the conceptual basis of inferring structure and function from genomic sequence. It is the first book in a series, Primers in Biology, employing a modular design in which chapters are divided into topics, each occupying one two-page spread that includes the relevant text, illustrations (in full color), definitions, and references.

The book has five chapters. The first is an introduction to the principles of protein structure and folding, with emphasis on proteins' biophysical properties. The second describes the principles of the main biochemical functions of proteins, namely binding and catalysis, with a short section on the properties of structural proteins. Chapter 3 covers the regulation of protein function, containing concise descriptions of all the regulatory mechanisms that operate on proteins, from pH to phosphorylation, with several sections on protein switches based on nucleotide hydrolysis. Chapter 4 introduces the principles whereby structure and function are deduced from sequence, with illustrative examples. The final chapter addresses how data on protein structure is gathered, interpreted, and presented.

Written for upper-level undergraduates and beginning graduate students, Protein Structure and Function is also be for working scientists needing an up-to-date introduction to the field.


I have not encountered a book better than this one for students interested in learning more about structure-function relationships in proteins." * B. Williams, Choice *

From Sequence to Structure
Overview: Protein Function and Architecturep. 2
Amino Acidsp. 4
Genes and Proteinsp. 6
The Peptide Bondp. 8
Bonds that Stabilize Folded Proteinsp. 10
Importance and Determinants of Secondary Structurep. 12
Properties of the Alpha Helixp. 14
Properties of the Beta Sheetp. 16
Prediction of Secondary Structurep. 18
Foldingp. 20
Tertiary Structurep. 22
Membrane Protein Structurep. 24
Protein Stability: Weak Interactions and Flexibilityp. 26
Protein Stability: Post-Translational Modificationsp. 28
The Protein Domainp. 30
The Universe of Protein Structuresp. 32
Protein Motifsp. 34
Alpha Domains and Beta Domainsp. 36
Alpha/Beta, Alpha+Beta and Cross-Linked Domainsp. 38
Quaternary Structure: General Principlesp. 40
Quaternary Structure: Intermolecular Interfacesp. 42
Quaternary Structure: Geometryp. 44
Protein Flexibilityp. 46
From Structure to Function
Overview: The Structural Basis of Protein Functionp. 50
Recognition, Complementarity and Active Sitesp. 52
Flexibility and Protein Functionp. 54
Location of Binding Sitesp. 56
Nature of Binding Sitesp. 58
Functional Properties of Structural Proteinsp. 60
Catalysis: Overviewp. 62
Active-Site Geometryp. 64
Proximity and Ground-State Destabilizationp. 66
Stabilization of Transition States and Exclusion of Waterp. 68
Redox Reactionsp. 70
Addition/Elimination, Hydrolysis and Decarboxylationp. 72
Active-Site Chemistryp. 74
Cofactorsp. 76
Multi-Step Reactionsp. 78
Multifunctional Enzymesp. 80
Multifunctional Enzymes with Tunnelsp. 82
Control of Protein Function
Overview: Mechanisms of Regulationp. 86
Protein Interaction Domainsp. 88
Regulation by Locationp. 90
Control by pH and Redox Environmentp. 92
Effector Ligands: Competitive Binding and Cooperativityp. 94
Effector Ligands: Conformational Change and Allosteryp. 96
Protein Switches Based on Nucleotide Hydrolysisp. 98
GTPase Switches: Small Signaling G proteinsp. 100
GTPase Switches: Signal Relay by Heterotrimeric GTPasesp. 102
GTPase Switches: Protein Synthesisp. 104
Motor Protein Switchesp. 106
Regulation by Degradationp. 108
Control of Protein Function by Phosphorylationp. 110
Regulation of Signaling Protein Kinases: Activation Mechanismp. 112
Regulation of Signaling Protein Kinases: Cdk Activationp. 114
Two-Component Signaling Systems in Bacteriap. 116
Control by Proteolysis: Activation of Precursorsp. 118
Protein Splicing: Autoproteolysis by Inteinsp. 120
Glycosylationp. 122
Protein Targeting by Lipid Modificationsp. 124
Methylation, N-acetylation, Sumoylation and Nitrosylationp. 126
From Sequence to Function: Case Studies in Structural and Functional Genomics
Overview: From Sequence to Function in the Age of Genomicsp. 130
Sequence Alignment and Comparisonp. 132
Protein Profilingp. 134
Deriving Function from Sequencep. 136
Experimental Tools for Probing Protein Functionp. 138
Divergent and Convergent Evolutionp. 140
Structure from Sequence: Homology Modelingp. 142
Structure From Sequence: Profile-Based Threading and "Rosetta"p. 144
Deducing Function from Structure: Protein Superfamiliesp. 146
Strategies for Identifying Binding Sitesp. 148
Strategies for Identifying Catalytic Residuesp. 150
TIM Barrels: One Structure with Diverse Functionsp. 152
PLP Enzymes: Diverse Structures with One Functionp. 154
Moonlighting: Proteins With More Than One Functionp. 156
Chameleon Sequences: One Sequence with More than One Foldp. 158
Prions, Amyloids and Serpins: Metastable Protein Foldsp. 160
Functions for Uncharacterized Genes: Galactonate Dehydratasep. 162
Starting From Scratch: A Gene Product of Unknown Functionp. 164
Structure Determination
The Interpretation of Structural Informationp. 168
Structure Determination by X-Ray Crystallography and NMRp. 170
Quality and Representation of Crystal and NMR Structuresp. 172
Glossaryp. 175
Referencesp. 181
Indexp. 189
Table of Contents provided by Rittenhouse. All Rights Reserved.

ISBN: 9780878936632
ISBN-10: 0878936637
Series: Primers in Biology
Audience: Tertiary; University or College
Format: Paperback
Language: English
Number Of Pages: 180
Published: 1st April 2004
Publisher: Oxford University Press Inc
Country of Publication: US
Dimensions (cm): 28.0 x 22.0  x 1.1
Weight (kg): 0.52
Edition Number: 1