Structural Genomics and High Throughput Structural Biology

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ISBN: 9780824753351 | 0824753356
Cover: Hardcover
Copyright: 8/23/2005

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This timely reference contains detailed chapters on the latest developments in the field and provides expert reviews of topics such as protein crystallization, comparative modeling, the retrieval and validation of structural information, challenges in computational structural proteomics, and therapeutically-driven structural genomics.

Overview of Structural Genomics: Landscape, Premises, and Current Direction

(18)

Sung-Hou Kim

Dong Hae Shin

Weiru Wang

Paul D. Adams

John-Marc Chandonia

The Landscape of Sequence Genomics

(2)

Premises of Structural Genomics

(6)

The Protein Fold Space

(1)

Concept

(2)

Representation of the Protein Fold Space

(2)

Fold and Functional Space Coverage

(1)

Family and Fold Space Coverage

(2)

Functional Space Coverage

(1)

International Efforts

(5)

Metrics and Lessons Learned from PSI Pilot Phase

(2)

Prospects

(3)

Acknowledgment

(1)

References

(2)

Purifying Protein for Structural Biology

(10)

Aled M. Edwards

Overview

(1)

Protein Expression

(4)

Escherichia coli: The Consensus Expression System

(1)

Insufficient Protein Expression and Solubility: The Bane of Structural Biologists

(3)

Expression of Eukaryotic Proteins

(1)

Protein Purification

(1)

Perspective

(4)

References

(3)

Protein Crystallization: Automation, Robotization, and Miniaturization

(20)

Naomi E. Chayen

Abstract

(1)

Background

(1)

The Search for Crystallization Conditions (Screening)

(1)

Automation and Miniaturisation of Screening Procedures

(4)

The Microbatch Method

(1)

The Effect of Different Oils

(1)

Diffusion Techniques

(1)

Vapour Diffusion

(1)

Free Interface Diffusion

(1)

Imaging and Monitoring of Crystallization Trials

(1)

Genomics/Proteomics Projects: Current State of the Art

(1)

Automation of Optimisation Experiments Based on the Fundamental Principles of Crystallization

(4)

Utilisation of Crystallization Phase Diagrams

(2)

Dynamic Separation of Nucleation and Growth

(2)

Other Automated Means to Control the Crystallization Environment

(2)

Solubility as a Function of Temperature

(1)

Control of Evaporation

(1)

Heterogeneous Nucleation

(2)

Crystallization in Gels

(1)

Automation and Miniaturisation of the Crystallization of Membrane Proteins

(1)

Crystallization in cubo

(1)

Crystallization Under Oil

(1)

Key Issues and Next Steps

(6)

References

(5)

NMR Spectroscopy in Structural Genomics

(12)

Weontae Lee

Adelinda Yee

Cheryl H. Arrowsmith

Introduction

(1)

The Sample NMR Pipeline

(3)

Recent Development of NMR Techniques for Structural Proteomics

(4)

Ultra High Field Magnet

(1)

Cryogenic/Chilled Probe Technology

(1)

Transverse Relaxation Optimization Spectroscopy (TROSY)

(1)

Residual Dipolar Coupling (RDC)

(1)

Automated Data Analysis

(1)

Isotope Labeling Techniques

(1)

Isotope Labeling of Protein

(1)

Selective Protonation of Methyl Group and Segmental Labeling

(1)

Cell Free System

(1)

NMR-Based Functional Genomics

(4)

References

(3)

High Throughput Protein Crystallography

(44)

Bernhard Rupp

Background and Rationale

(6)

Definition and Scope

(1)

Choosing Crystallography for High Throughput Structure Determination

(2)

Why High Throughput?

(1)

Definition of High Throughput Protein Crystallography

(1)

High Throughput vs. Low Throughput

(1)

Key Developments

(3)

Literature

(1)

Methods of High Throughput Protein Crystallography

(37)

Overview

(1)

Processes Involving Crystal Manipulation

(6)

Selection and Harvesting of Crystals

(1)

Soaking and Derivatization of Crystals

(1)

Cryo-Protection and Loop Mounting

(1)

Robotic Sample Mounting

(1)

Data Collection

(1)

High Throughput Considerations

(2)

Data Collection as a Multi-Level Decision Process

(1)

Initial Assessment of Crystal Quality and Indexing

(2)

Data Collection Strategies for Phasing

(1)

Data Collection for High Resolution Structures

(1)

Single Anomalous Diffraction Data and SAD from Sulfur

(2)

Multiple Anomalous Diffraction Data

(1)

Raw Data Warehousing

(1)

Crystallographic Computing

(1)

Data Reduction and Scaling

(1)

Phasing: General Remarks

(1)

Substructure Solution

(2)

Initial Phase Calculation

(1)

Density Modification Techniques

(16)

From Sequence to Function

105

(4)

Martin Norin

Introduction

105

(1)

Gene and Protein Sequence Databases

106

(1)

Sequence Comparison Methods

107

(1)

Summary

107

(2)

References

107

(2)

Comparative Modeling and Structural Proteomics

109

(28)

Guoli Wang

J. Michael Sauder

Roland L. Dunbrack, Jr.

Introduction

109

(2)

Methods of Comparative Modeling

111

(5)

Template Identification and Sequence Alignment

112

(1)

Structure Modeling

113

(2)

Current Challenges

115

(1)

Impact of Structural Genomics Targets on Modeling of Genome Sequences

116

(4)

Purposes of Comparative Modeling from Structural Proteomics Targets

120

(9)

Analysis of Sequence-Structure-Function Relationships of Orthologues and Paralogues of the Structural Proteomics Template

120

(5)

Inhibitor Design and Off-Target Modeling

125

(1)

Structure-Function Relationships of Mutations

126

(1)

Target Selection

127

(1)

Modeling Used to Facilitate Structure Determination in Structural Proteomics

127

(2)

Industry Experience

129

(1)

Future Prospects

130

(7)

Acknowledgments

130

(1)

References

131

(6)

Ab initio Modeling

137

(26)

Jeffrey Skolnick

Yang Zhang

Andrzej Kolinski

The Importance of Protein Structure in the Postgenomic Era

138

(1)

Overview of Protein Structure Prediction Methods

138

(1)

Ab initio Structure Prediction: Historical Overview

139

(7)

Continuous Space Reduced Models

139

(1)

Lattice Models

140

(1)

Ab initio Folding Using Secondary Structure Restraints

141

(1)

Ab initio Folding Using Secondary and Tertiary Restraints

141

(1)

Representative Conformational Search Methods

142

(1)

ab initio Prediction Results in CASP3 and CASP4

143

(3)

The TOUCHSTONE ab initio Folding Algorithm

146

(8)

Overview

146

(2)

Benchmarking on a Large Test Set

148

(1)

Accuracy of Tertiary Contact and Secondary Structure Prediction

149

(1)

A New Lattice Model for Tertiary Structure Prediction

149

(1)

Selection of the Native Conformation

150

(1)

Universal Similarity Measure for Comparing Protein Structures

150

(1)

How Can One Select Native-Like Clusters?

150

(1)

Relationship Between Cluster Population and Likelihood of Prediction Success

151

(1)

Prediction of Tertiary Structure Using Residual Dipolar Coupling Information

152

(1)

Benchmark Prediction of Tertiary Structure Using a Small Number of Exact Long Range Restraints (Specific Aim 7)

152

(1)

Prediction of the Tertiary Structure All the Small Proteins in the M. genitalium Genome

153

(1)

Summary

154

(9)

Acknowledgment

155

(1)

References

155

(8)

Determining Function from Structure

163

(22)

Roman A. Laskowski

Introduction

163

(2)

Biochemical vs. Biological Function

165

(1)

Protein Fold Comparison

165

(4)

Fold Databases

166

(1)

Fold and Function

166

(3)

Structural Motifs

169

(1)

Common Residue Groupings

169

(1)

Detection of Binding Sites

170

(2)

Identification of Cognate Ligands

172

(1)

Binding Site Comparison

172

(2)

Geometrical Matching

173

(1)

Physicochemical Properties

173

(1)

Nonsurface Methods

173

(1)

Surface and Sequence

174

(1)

Identification of Functionally Important Residues

174

(3)

Residue Conservation

174

(2)

Identification of Residues with ``Unusual'' Properties

176

(1)

3-D Template Methods

177

(3)

Enzyme Catalytic Residues

177

(1)

Automatically Generated Templates

177

(3)

Protein--Protein Interaction Sites

180

(1)

Determining the Biologically Relevant Unit

180

(1)

Concluding Remarks

181

(4)

Acknowledgement

182

(1)

References

182

(3)

Retrieval and Validation of Structural Information

185

(38)

Gerard J. Kleywegt

Henrik Hansson

Introduction

185

(2)

Primary Structural Databases

187

(4)

Protein Data Bank

187

(2)

Other Primary Databases

189

(1)

Search Mechanisms and Front-Ends

190

(1)

Secondary Structural Databases

191

(7)

Structural Classification Databases

191

(2)

Structurally Specialised Structural Databases

193

(1)

Biologically Specialised Structural Databases

194

(2)

Miscellaneous Databases

196

(2)

Validation

198

(16)

Need for Validation

198

(1)

Validation of Crystallographic Models

199

(1)

Errors

200

(1)

Quality Indicators

200

(2)

Global Model Quality

202

(1)

Local Model Quality

202

(3)

Validation of NMR Models

205

(1)

Precision and Accuracy

205

(3)

Data Quality and Quantity

208

(1)

Validation Using Experimental Data

209

(1)

Validation Databases

209

(2)

Validation Servers

211

(3)

Concluding Remarks

214

(9)

Acknowledgements

216

(1)

References

216

(7)

Problems in Computational Structural Genomics

223

(28)

Ruben Abagyan

Introduction and Motivation

224

(1)

Funding

224

(1)

Completing, Improving, and Correcting Experimental Structures

225

(4)

Symmetry and Biological Unit

226

(1)

Adding Missing or Zero-Occupancy Atoms, Resolving Uncertainties

227

(1)

Detecting Errors: Energy Strain

227

(1)

NMR Structures

227

(2)

Modeling by Homology

229

(4)

Predicting Local Model Reliability

231

(1)

How Good are Homology Models?

232

(1)

Annotating Protein Surface

233

(5)

Sequence Conservation

233

(1)

Structural Residue Pattern: Catalytic Triads

234

(1)

Electrostatic Potential Indicates Binding Site for a Charged Ligand

234

(1)

Binding Cleft Identification

235

(1)

Pocketome

236

(1)

Protein-Protein Interaction Interface Prediction

236

(1)

Surface Flexibility Views and Docking

237

(1)

Protein-Protein Docking

238

(5)

Deciding How to Dock

239

(1)

Atoms to Grids

239

(3)

How Successful is Protein Docking?

242

(1)

Grid-to-Grid Docking

242

(1)

Peptide--Protein Docking

243

(1)

Docking Small Molecules

244

(7)

Deorphanization

245

(1)

Acknowledgments

245

(1)

References

246

(5)

Applied Structural Genomics

251

(18)

Michael Sundstrom

Introduction

252

(1)

Completeness of Structural Space

252

(2)

Public Structural Genomic Initiatives

254

(1)

RSGI (Japan)

254

(1)

PSI (United States)

254

(1)

SPINE (European Union)

255

(1)

SGC (Canada and United Kingdom)

255

(1)

Commercial Structural Genomics Operations

255

(2)

Structural GenomiX (United States)

256

(1)

SYRRX (United States)

256

(1)

Affinium Pharmaceuticals (Canada)

256

(1)

Astex Technology (United Kingdom)

257

(1)

Structure Guided Functional Validation

257

(1)

Screening for Natural Ligands to Infer Function

258

(1)

Screening for Enzymatic Activity

258

(1)

The Druggable Genome

259

(1)

Structure Based Drug Discovery

259

(1)

Identification of Chemical Starting Points

260

(1)

Validating Chemical Starting Points

261

(1)

Protein--Protein Interactions

261

(1)

Structure Based Selectivity Design

262

(1)

Drug Metabolism Screens

262

(1)

Structural Mapping of Disease Causing Mutations

263

(1)

Areas for Improvement

263

(1)

Membrane Proteins

263

(1)

``Not Hot'' Targets

264

(1)

Biased Sampling

264

(1)

Promises of Structural Genomics

264

(5)

Acknowledgements

265

(1)

References

265

(4)

Index

269

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Structural Genomics and High Throughput Structural Biology

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Structural Genomics and High Throughput Structural Biology

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