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Structural proteomics : high-throughput methods / edited by Bostjan Kobe, Mitchell Guss, Thomas Huber. — Totowa, N.J. : Humana ; London : Springer [distributor], 2008. – (58.17/M592/v.426) |
Contents
Contents
Preface
Contributors
Section I. Protein Target Selection， Bioinformatic Approaches， and Data Management
1 Target Selection for Structural Genomics: An Overview 3
2 A General Target Selection Method for Crystallographic Proteomics 27
3 Target Selection: Triage in the Structural Genomics Battlefield 37
4 Data Management in Structural Genomics: An Overview 49
5 Data Deposition and Annotation at the Worldwide Protein Data Bank 81
6 Prediction of Protein Disorder 103
7 Protein Domain Prediction 117
8 Protein Structure Modeling with MODELLER 145
Section II. Protein Production
9 High Throughput Cloning with Restriction Enzymes 163
l0 Automated Recombinant Protein Expression Screening in Escherichia coli 175
11 From No Expression to High-Level Soluble Expression in Escherichia coli by Screening a Library of the Target Proteins with Randomized N-Termini 187
12 Application of High-Throughput Methodologies to the Expression of Recombinant Proteins in E. coli 197
13 A High Throughput Platform for Eukaryotic Genes 209
14 High Throughput Production of Recombinant Human Proteins for Crystallography. 221
15 Assembly of Protein Complexes by Coexpression in Prokaryotic and Eukaryotic Hosts: an Overview 247
16 Cell-Free Protein Synthesis for Analysis by NMR Spectroscopy. 257
17 A Medium or High Throughput Protein Refolding Assay 269
18 Structural Proteomics of Membrane Proteins: a Survey of Published Techniques and Design of a Rational High Throughput Strategy 277
Section III. Biophysical and Functional Characterization of Proteins
19 Methods for Protein Characterization by Mass Spectrometry， Thermal Shift (ThermoFluor) Assay， and Multiangle or Static Light Scattering 299
20 High Throughput Methods for Analyzing Transition Metals in Proteins on a Microgram Scale 319
21 High Throughput Screening of Purified Proteins for Enzymatic Activity 331
Section IV. Structural Characterization of Proteins
22 Strategies for Improving Crystallization Success Rates 345
23 Protein Crystallization in Restricted Geometry Advancing Old Ideas for Modern Times in Structural Proteomics 363
24 Fluorescence Approaches to Growing Macromolecule Crystals 377
25 Efficient Macromolecular Crystallization Using Microfluidics and Randomized Design of Screening Reagents 387
26 Increasing Protein Crystallization Screening Success with Heterogeneous Nucleating Agents 403
27 High Throughput pH Optimization of Protein Crystallization 411
28 Automated Structure Solution with the PHENIX Suite 419
29 NMR Screening for Rapid Protein Characterization in Structural Proteomics 437
30 Microcoil NMR Spectroscopy: a Novel Tool for Biological High Throughput NMR Spectroscopy 447
31 Protein Structure Determination Using a Combination of Cross-Linking， Mass Spectrometry， and Molecular Modeling 459
Section V. Structural Proteomics Initiatives Overviews
32 Structural Genomics of Minimal Organisms: Pipeline and Results 477
33 Structural Genomics of Pathogenic Protozoa: an Overview 497
34 High Throughput Crystallography at SGC Toronto: an Overview 515
35 The Structural Biology and Genomics Platform in Strasbourg: an Overview 523
36 Bacterial Structural Genomics Initiative: Overview of Methods and Technologies Applied to the Process of Structure Determination 537
37 High Throughput Protein Production and Crystallization at NYSGXRC 561
38 Overview of the Pipeline for Structural and Functional Characterization of Macrophage Proteins at the University of Queensland 577
39 Structural Genomics of the Bacterial Mobile Metagenome: an Overview 589
Index 597
