Structural Genomics: General Applications

ISBN-13: 9781627036900 / Angielski / Twarda / 2013 / 358 str.

Yu Wai Chen

Opis

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.

Spis treści

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, Simon Trowitzsch, 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