Structural Genomics: General Applications

ISBN-13: 9781071608944 / Angielski / Miękka / 2021

Chen, Yu Wai

Opis

This updated edition emphasizes the benefits of structural genomics to the wider structural research community with a diverse range of applicable methods. The book opens with an extensive section on protein production, including new methodologies for membrane and metal-binding proteins, as well as high-throughput protein production and screening. It continues with sections on structural analyses and data management, as well as modeling, simulation, and visualization. Overall, the spectrum of topics reflects the trend towards tackling more diverse challenges of studying macromolecular machineries and complexes. Written for the highly successful Methods in Molecular Biology series, chapters include the type of detail and key implementation advice to ensure successful results. 

Authoritative and up-to-date, Structural Genomics: General Applications, Second Edition serves as a vital guide to structural biologists in small to medium-sized laboratories seeking to better utilize this powerful area of study.

Chapter 11 is available open access under a Creative Commons Attribution 4.0 International License via link.springer.com. For further details see license information in the chapter.

Spis treści

Part I: Protein Production

 

1. High-Throughput Protein Engineering by Massively Parallel Combinatorial Mutagenesis

            Yuk Kei Wan, Gigi C.G. Choi, and Alan S.L. Wong

 

2. Rational Design and Construction of Active-Site Labeled Enzymes

            Man-Wah Tsang, Yun-Chung Leung, and Kwok-Yin Wong

 

3. Screening and Production of Recombinant Human Proteins: Ligation Independent Cloning

            Claire Strain-Damerell, Pravin Mahajan, Alejandra Fernandez-Cid, Opher Gileadi, and Nicola Burgess-Brown

 

4. Screening and Production of Recombinant Human Proteins: Protein Production in E. coli

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

 

5. Screening and Production of Recombinant Human Proteins: Protein Production in Insect Cells

            Pravin Mahajan, Claire Strain-Damerell, Shubhashish Mukhopadhyay, Alejandra Fernandez-Cid, Opher Gileadi, and Nicola A. Burgess-Brown

 

6. Expression Screening of Human Integral Membrane Proteins Using BacMam

            Pravin Mahajan, Katherine Ellis, Shubhashish Mukhopadhyay, Alejandra Fernandez-Cid, Gamma Chi, Henry Man, Katharina L. Dürr, and Nicola A. Burgess-Brown

 

7. High-Throughput Expression Screening in Mammalian Suspension Cells

            Susan D. Chapple and Michael R. Dyson

 

8. In Vitro Production of Perdeuterated Proteins in H₂O for Biomolecular NMR Studies

            Lionel Imbert, Rachel Lenoir-Capello, Elodie Crublet, Alicia Vallet, Rida Awad, Isabel Ayala, Celine Juillan-Binard, Hubert Mayerhofer, Rime Kerfah, Pierre Gans, Emeric Miclet, and Jerome Boisbouvier

 

9. Minimizing Heterogeneity of Protein Samples for Metal Transporter Proteins Using SAXS and Metal Radioisotopes

            Shah Kamranur Rahman

 

Part II: Structural Analyses and Data Management

 

10. Hydrogen/Deuterium Exchange-Mass Spectrometry for Probing Changes in Conformation and Dynamics of Proteins

            Pui-Kin So

 

11. BeStSel: From Secondary Structure Analysis to Protein Fold Prediction by Circular Dichroism Spectroscopy

            András Micsonai, Éva Bulyáki, and József Kardos

 

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

            Andrei L. Turinsky, Sam Dupont, Alexander Botzki, Sabry Razick, Brian Turner,

Ian M. Donaldson, and Shoshana J. Wodak

 

13. State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and In Vitro Biochemical Experiments

            David Cooper, Marek Grabowski, Matthew D. Zimmerman, Przemyslaw J. Porebski, Ivan G. Shabalin, Magdalena Woinska, Marcin J. Domagalski, Heping Zheng, Piotr Sroka, Marcin Cymborowski, Mateusz P. Czub, Ewa Niedzialkowska, Barat S. Venkataramany, Tomasz Osinski, Zbigniew Fratczak, Jacek Bajor, Juliusz Gonera, Elizabeth MacLean, Kamila Wojciechowska, Wojciech Wajerowicz, Maksymilian Chruszcz, and Wladek Minor

 

Part III: Modeling, Simulation, and Visualization

 

14. Protein Structure Modeling with MODELLER

            Benjamin Webb and Andrej Sali

 

15. Parameterization of a Dioxygen Binding Metal Site Using the MCPB.py Program

            Pengfei Li and Kenneth M. Merz Jr.

 

16. Parameterization of Large Ligands for Gromacs Molecular Dynamics Simulation with LigParGen

            Yu Wai Chen, Yong Wang, Yun-Chung Leung, and Kwok-Yin Wong

 

17. Simulation of Proteins Modified with a Fluorescent Label

            Zoe Chan and Yun-Chung Leung

 

18. Protocol for Simulations of PEGylated Proteins with Martini 3

            Fabian Grünewald, Peter C. Kroon, Paulo C.T. Souza, and Siewert J. Marrink

 

19. Molecular Data Visualization on Mobile Devices: A Quick Starter’s Guide

            Chin-Pang Bennu Yiu and Yu Wai Chen

 

20. Molecular Data Visualization with Augmented Reality (AR) on Mobile Devices

            Chin-Pang Bennu Yiu and Yu Wai Chen