Structural Genomics: General Applications

Structural Genomics: General Applications

by Yu Wai Chen (Editor)

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Overview

Structural Genomics: General Applications by Yu Wai Chen

The field of Structural Genomics has produced many technological advances that transform and accelerate structure solution and analysis. Structural Genomics: General Applications emphasizes the benefits to the wider structural research community. It also reflects the current trend in tackling the more ambitious challenges of studying macromolecular machineries and complexes. Divided into three convenient sections, topics include the cloning and production of proteins for structural studies, experimental methods, and computational methods and data analysis. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, Structural Genomics: General Applications aims primarily to channel spin-off technologies to the average structural biologist in a small or medium-sized laboratory.

Product Details

ISBN-13: 9781493960606
Publisher: Springer-Verlag New York, LLC
Publication date: 08/23/2016
Series: Methods in Molecular Biology , #1091
Edition description: Softcover reprint of the original 1st ed. 2014
Pages: 358
Product dimensions: 7.01(w) x 10.00(h) x 0.03(d)

Table of Contents

Part I. Cloning, Expression and Protein Production

1. DisMeta – a Meta Server for Construct Design and Optimization

Yuanpeng Janet Huang, Thomas B. Acton, and Gaetano T. Montelione

2. Stable Expression Clones and Auto-Induction for Protein Production in E. Coli

F. William Studier

3. High-Throughput Expression Screening and Purification of Recombinant Proteins in E. coli

Natalie J. Saez and Renaud Vincentelli

4. Medium Throughput Production of Recombinant Human Proteins: Ligation Independent Cloning

Claire Strain-Damerell, Nicola A. Burgess-Brown, Pravin Mahajan, and Opher Gileadi

5. Medium Throughput Production of Recombinant Human Proteins: Protein Production in E. coli

Nicola A. Burgess-Brown, Pravin Mahajan, Claire Strain-Damerell, Opher Gileadi, and Susanne Gräslund

6. Medium Throughput Production of Recombinant Human Proteins: Protein Production in Insect Cells

Pravin Mahajan, Nicola A. Burgess-Brown, Claire Strain-Damerell, and Opher Gileadi

7. OmniBac: Universal Multigene Transfer Plasmids for Baculovirus Expression Vector Systems

Deepak B. Thimiri Govinda Raj, Lakshmi S. Vijayachandran, and Imre Berger

8. Multiprotein Complex Production in Insect Cells by Using Polyproteins

Yan Nie, Itxaso Bellon-Echeverria, SimonTrowitzsch, Christoph Bieniossek, and Imre Berger

9. Expression Screening in Mammalian Suspension Cells

Susan D. Chapple and Michael R. Dyson

10. Cell-free Expression of Protein Complexes for Structural Biology

Takaho Terada, Takeshi Murata, Mikako Shirouzu, and Shigeyuki Yokoyama

11. Cell-Free Protein Synthesis for Functional and Structural Studies

Shin-ichi Makino, Emily T. Beebe, John L. Markley, and Brian G. Fox

12. Insoluble Protein Purification with Sarkosyl: Facts and Precautions

Ben Chisnall, Courtney Johnson, Yavuz Kulaberoglu, and Yu Wai Chen

Part II. Experimental Structure Determination and Characterisation

13. Estimation of Crystallization Likelihood Through a Fluorimetric Thermal Stability Assay

Vincent Mariaule, Florine Dupeus, and José A. Márquez

14. CrystalDirect™: A Novel Approach for Automated Crystal Harvesting Based on Photoablation of Thin Films

Jose A. Marquez and Florent Cipriani

15. Methods to Refine Macromolecular Structures in Cases of Severe Diffraction Anisotropy

Michael R. Sawaya

16. Applications of NMR-Based PRE and EPR-Based DEER Spectroscopy to Homodimer Chain Exchange Characterization and Structure Determination

Yunhuang Yang, Theresa A. Ramelot, Shuisong Ni, Robert M. McCarrick, and Michael A. Kennedy

17. A Cost-Effective Protocol for the Parallel Production of Libraries of 13CH3-Specifically Labelled Mutants for NMR Studies of High Molecular Weight Proteins

Elodie Crublet, Rime Kerfah, Guillaume Mas, Marjolaine Noirclerc-Savoye, Violaine Lantez, Thierry Vernet, and Jerome Boisbouvier

18. High-Throughput SAXS for the Characterization of Biomolecules in Solution: A Practical Approach

Kevin N. Dyer, Michal Hammel, Robert P. Rambo, Susan E. Tsutakawa, Ivan Rodic, Scott Classen, John A. Tainer, and Greg L. Hura

19. Measuring Spatial Restraints on Native Protein Complexes using Isotope-Tagged Chemical Cross-Linking and Mass Spectrometry

Franz Herzog

Part III. Computational Methods and Structural Data Analyses

20. Modeling of Proteins and Their Assemblies with the Integrative Modeling Platform

Benjamin Webb, Keren Lasker, Javier Velázquez-Muriel, Dina Schneidman-Duhovny, Riccardo Pellarin, Massimiliano Bonomi, Charles Greenberg, Barak Raveh, Elina Tjioe, Daniel Russel, and Andrej Sali

21. The Quality and Validation of Structures from Structural Genomics

Marcin J. Domagalski, Heping Zheng, Matthew D. Zimmerman, Zbigniew Dauter, Alexander Wlodawer, and Wladek Minor

22. Navigating the Global Protein-Protein Interaction Landscape Using iRefWeb

Andrei L. Turinsky, Sabry Razick, Brian Turner, Ian M. Donaldson, and Shoshana J. Wodak

23. Mespeus, A Database of Metal Interactions with Proteins

Marjorie M. Harding and Kun-Yi Hsin

24. High-Quality Macromolecular Graphics on Mobile Devices: A Quick Starter’s Guide

Chin-Pang Benny Yiu and Yu Wai Chen

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