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Protein Structure and Function,9780878936632

Protein Structure and Function

by ;
Edition: 1st
Format: Paperback
Pub. Date: 8/1/2003
Publisher(s): Sinauer Associates is an imprint of Oxford University Press
Availability: This title is currently not available.


(New Science Press Ltd.) Brandeis Univ., Waltham, MA. First volume in a series, text provides an up-to-date data of what is known about protein function and structure. Presents some general perspective on the types of strategies used and some of the most important current techniques for exploring protein function. High-quality color illustrations. Softcover.

Author Biography

Gregory A. Petsko studied chemistry and classics as an undergraduate at Princeton University before going to Oxford as a Rhodes scholar to work for his Ph.D. with David Phillips. He then pursued his interest in the mechanism of enzyme catalysis at the Massachusetts Institute of Technology, where he taught courses in chemistry and detective fiction. Currently the Director of the Rosenstiel Center at Brandeis, he has extended his research interests to include the use of yeast genetics to study the unfolded protein response pathway, and the mechanism of action of the ABC transporter proteins.

Dagmar Ringe graduated in chemistry from Barnard College, Columbia, and took her Ph.D. in bioorganic chemistry from Boston University. She then pursued her research interest in the study of enzyme catalysis by X-ray crystallography at the Massachusetts Institute of Technology before moving to Brandeis, where she is Professor of Biochemistry and Chemistry. The principal focus of Dr. Ringe's research is structure-function relationships in enzymes of particular industrial and pharmaceutical importance.

Table of Contents

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.

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