Protein Structure and Function

(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.

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.

From Sequence to Structure
Overview: Protein Function and Architecture	p. 2
Amino Acids	p. 4
Genes and Proteins	p. 6
The Peptide Bond	p. 8
Bonds that Stabilize Folded Proteins	p. 10
Importance and Determinants of Secondary Structure	p. 12
Properties of the Alpha Helix	p. 14
Properties of the Beta Sheet	p. 16
Prediction of Secondary Structure	p. 18
Folding	p. 20
Tertiary Structure	p. 22
Membrane Protein Structure	p. 24
Protein Stability: Weak Interactions and Flexibility	p. 26
Protein Stability: Post-Translational Modifications	p. 28
The Protein Domain	p. 30
The Universe of Protein Structures	p. 32
Protein Motifs	p. 34
Alpha Domains and Beta Domains	p. 36
Alpha/Beta, Alpha+Beta and Cross-Linked Domains	p. 38
Quaternary Structure: General Principles	p. 40
Quaternary Structure: Intermolecular Interfaces	p. 42
Quaternary Structure: Geometry	p. 44
Protein Flexibility	p. 46
From Structure to Function
Overview: The Structural Basis of Protein Function	p. 50
Recognition, Complementarity and Active Sites	p. 52
Flexibility and Protein Function	p. 54
Location of Binding Sites	p. 56
Nature of Binding Sites	p. 58
Functional Properties of Structural Proteins	p. 60
Catalysis: Overview	p. 62
Active-Site Geometry	p. 64
Proximity and Ground-State Destabilization	p. 66
Stabilization of Transition States and Exclusion of Water	p. 68
Redox Reactions	p. 70
Addition/Elimination, Hydrolysis and Decarboxylation	p. 72
Active-Site Chemistry	p. 74
Cofactors	p. 76
Multi-Step Reactions	p. 78
Multifunctional Enzymes	p. 80
Multifunctional Enzymes with Tunnels	p. 82
Control of Protein Function
Overview: Mechanisms of Regulation	p. 86
Protein Interaction Domains	p. 88
Regulation by Location	p. 90
Control by pH and Redox Environment	p. 92
Effector Ligands: Competitive Binding and Cooperativity	p. 94
Effector Ligands: Conformational Change and Allostery	p. 96
Protein Switches Based on Nucleotide Hydrolysis	p. 98
GTPase Switches: Small Signaling G proteins	p. 100
GTPase Switches: Signal Relay by Heterotrimeric GTPases	p. 102
GTPase Switches: Protein Synthesis	p. 104
Motor Protein Switches	p. 106
Regulation by Degradation	p. 108
Control of Protein Function by Phosphorylation	p. 110
Regulation of Signaling Protein Kinases: Activation Mechanism	p. 112
Regulation of Signaling Protein Kinases: Cdk Activation	p. 114
Two-Component Signaling Systems in Bacteria	p. 116
Control by Proteolysis: Activation of Precursors	p. 118
Protein Splicing: Autoproteolysis by Inteins	p. 120
Glycosylation	p. 122
Protein Targeting by Lipid Modifications	p. 124
Methylation, N-acetylation, Sumoylation and Nitrosylation	p. 126
From Sequence to Function: Case Studies in Structural and Functional Genomics
Overview: From Sequence to Function in the Age of Genomics	p. 130
Sequence Alignment and Comparison	p. 132
Protein Profiling	p. 134
Deriving Function from Sequence	p. 136
Experimental Tools for Probing Protein Function	p. 138
Divergent and Convergent Evolution	p. 140
Structure from Sequence: Homology Modeling	p. 142
Structure From Sequence: Profile-Based Threading and "Rosetta"	p. 144
Deducing Function from Structure: Protein Superfamilies	p. 146
Strategies for Identifying Binding Sites	p. 148
Strategies for Identifying Catalytic Residues	p. 150
TIM Barrels: One Structure with Diverse Functions	p. 152
PLP Enzymes: Diverse Structures with One Function	p. 154
Moonlighting: Proteins With More Than One Function	p. 156
Chameleon Sequences: One Sequence with More than One Fold	p. 158
Prions, Amyloids and Serpins: Metastable Protein Folds	p. 160
Functions for Uncharacterized Genes: Galactonate Dehydratase	p. 162
Starting From Scratch: A Gene Product of Unknown Function	p. 164
Structure Determination
The Interpretation of Structural Information	p. 168
Structure Determination by X-Ray Crystallography and NMR	p. 170
Quality and Representation of Crystal and NMR Structures	p. 172
Glossary	p. 175
References	p. 181
Index	p. 189
Table of Contents provided by Rittenhouse. All Rights Reserved.

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Protein Structure and Function

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