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E-book: Structural Genomics and High Throughput Structural Biology

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  • Format: 304 pages
  • Pub. Date: 23-Aug-2005
  • Publisher: CRC Press Inc
  • Language: eng
  • ISBN-13: 9781040201244
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Structural Genomics and High Throughput Structural BiologyLarger Image
  • Format: 304 pages
  • Pub. Date: 23-Aug-2005
  • Publisher: CRC Press Inc
  • Language: eng
  • ISBN-13: 9781040201244
Other books in subject:

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Researchers in structural genomics continue to search for biochemical and cellular functions of proteins as well as the ways in which proteins assemble into functional pathways and networks using either experimental or computational approaches. Based on the experience of leading international experts, Structural Genomics and High Throughput Structural Biology details state-of-the-art analytical and computational methods used to reveal the three-dimensional structure and function of proteins.

A historical perspective and a detailed guide to the production of protein material for structural determination, a key step in the process, lay the necessary foundation for discussing the most effective structure determination technologies, such as X-ray crystallography and NMR spectroscopy. Encouraging the study of genes and proteins of unknown structure in order to discover new information about folding, specific structural features, or function, Structural Genomics and High Throughput Structural Biology presents the methods used to interpret the sequences of proteins in a structural context, giving insight into their function. It also explains how to extract information from public data repositories and how to account for variability and accuracy in the quality of this data.

The book concludes with a discussion of practical applications of therapeutically driven structural genomics, and presents future directions in the field. Structural Genomics and High Throughput Structural Biology offers a comprehensive guide to the theoretical, technological, and experimental methodologies used to derive structural information from encoded proteins by renowned and world leading scientists in the field.
Overview of Structural Genomics: Landscape, Premises, and Current Direction
1(18)
Sung-Hou Kim
Dong Hae Shin
Weiru Wang
Paul D. Adams
John-Marc Chandonia
The Landscape of Sequence Genomics
1(2)
Premises of Structural Genomics
3(6)
The Protein Fold Space
3(1)
Concept
3(2)
Representation of the Protein Fold Space
5(2)
Fold and Functional Space Coverage
7(1)
Family and Fold Space Coverage
7(2)
Functional Space Coverage
9(1)
International Efforts
9(5)
Metrics and Lessons Learned from PSI Pilot Phase
14(2)
Prospects
16(3)
Acknowledgment
16(1)
References
17(2)
Purifying Protein for Structural Biology
19(10)
Aled M. Edwards
Overview
19(1)
Protein Expression
19(4)
Escherichia coli: The Consensus Expression System
20(1)
Insufficient Protein Expression and Solubility: The Bane of Structural Biologists
20(3)
Expression of Eukaryotic Proteins
23(1)
Protein Purification
24(1)
Perspective
25(4)
References
26(3)
Protein Crystallization: Automation, Robotization, and Miniaturization
29(20)
Naomi E. Chayen
Abstract
30(1)
Background
30(1)
The Search for Crystallization Conditions (Screening)
30(1)
Automation and Miniaturisation of Screening Procedures
31(4)
The Microbatch Method
31(1)
The Effect of Different Oils
32(1)
Diffusion Techniques
33(1)
Vapour Diffusion
33(1)
Free Interface Diffusion
34(1)
Imaging and Monitoring of Crystallization Trials
35(1)
Genomics/Proteomics Projects: Current State of the Art
35(1)
Automation of Optimisation Experiments Based on the Fundamental Principles of Crystallization
36(4)
Utilisation of Crystallization Phase Diagrams
36(2)
Dynamic Separation of Nucleation and Growth
38(2)
Other Automated Means to Control the Crystallization Environment
40(2)
Solubility as a Function of Temperature
40(1)
Control of Evaporation
40(1)
Heterogeneous Nucleation
40(2)
Crystallization in Gels
42(1)
Automation and Miniaturisation of the Crystallization of Membrane Proteins
42(1)
Crystallization in cubo
42(1)
Crystallization Under Oil
43(1)
Key Issues and Next Steps
43(6)
References
44(5)
NMR Spectroscopy in Structural Genomics
49(12)
Weontae Lee
Adelinda Yee
Cheryl H. Arrowsmith
Introduction
49(1)
The Sample NMR Pipeline
50(3)
Recent Development of NMR Techniques for Structural Proteomics
53(4)
Ultra High Field Magnet
54(1)
Cryogenic/Chilled Probe Technology
54(1)
Transverse Relaxation Optimization Spectroscopy (TROSY)
54(1)
Residual Dipolar Coupling (RDC)
55(1)
Automated Data Analysis
55(1)
Isotope Labeling Techniques
56(1)
Isotope Labeling of Protein
56(1)
Selective Protonation of Methyl Group and Segmental Labeling
56(1)
Cell Free System
57(1)
NMR-Based Functional Genomics
57(4)
References
58(3)
High Throughput Protein Crystallography
61(44)
Bernhard Rupp
Background and Rationale
62(6)
Definition and Scope
62(1)
Choosing Crystallography for High Throughput Structure Determination
62(2)
Why High Throughput?
64(1)
Definition of High Throughput Protein Crystallography
65(1)
High Throughput vs. Low Throughput
65(1)
Key Developments
65(3)
Literature
68(1)
Methods of High Throughput Protein Crystallography
68(37)
Overview
68(1)
Processes Involving Crystal Manipulation
69(6)
Selection and Harvesting of Crystals
75(1)
Soaking and Derivatization of Crystals
75(1)
Cryo-Protection and Loop Mounting
76(1)
Robotic Sample Mounting
77(1)
Data Collection
77(1)
High Throughput Considerations
77(2)
Data Collection as a Multi-Level Decision Process
79(1)
Initial Assessment of Crystal Quality and Indexing
79(2)
Data Collection Strategies for Phasing
81(1)
Data Collection for High Resolution Structures
82(1)
Single Anomalous Diffraction Data and SAD from Sulfur
82(2)
Multiple Anomalous Diffraction Data
84(1)
Raw Data Warehousing
85(1)
Crystallographic Computing
85(1)
Data Reduction and Scaling
85(1)
Phasing: General Remarks
86(1)
Substructure Solution
87(2)
Initial Phase Calculation
89(1)
Density Modification Techniques
89(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


Michael Sundström, Martin Norin, Aled Edwards
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