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Structural Genomics

General Applications

  • Book
  • © 2021
  • Latest edition

Overview

Editors:
  1. Yu Wai Chen

    1. Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Hong Kong

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    You can also search for this editor in PubMed   Google Scholar

  2. Chin-Pang Bennu Yiu

    1. BMI Biotechnology Appraisals & Investments Limited, Wan Chai, Hong Kong

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2199)

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Table of contents (20 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Protein Production

    1. Front Matter

      Pages 1-1
      Download chapter PDF

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

      • Yuk Kei Wan, Gigi C. G. Choi, Alan S. L. Wong
      Pages 3-12

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

      • Man-Wah Tsang, Yun-Chung Leung, Kwok-Yin Wong
      Pages 13-22

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

      • Claire Strain-Damerell, Pravin Mahajan, Alejandra Fernandez-Cid, Opher Gileadi, Nicola A. Burgess-Brown
      Pages 23-43

    5. 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, Susanne Gräslund
      Pages 45-66

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

      • Pravin Mahajan, Claire Strain-Damerell, Shubhashish Mukhopadhyay, Alejandra Fernandez-Cid, Opher Gileadi, Nicola A. Burgess-Brown
      Pages 67-94

    7. Expression Screening of Human Integral Membrane Proteins Using BacMam

      • Pravin Mahajan, Katherine Ellis, Shubhashish Mukhopadhyay, Alejandra Fernandez-Cid, Gamma Chi, Henry Man et al.
      Pages 95-115

    8. High-Throughput Expression Screening in Mammalian Suspension Cells

      • Susan D. Chapple, Michael R. Dyson
      Pages 117-125

    9. 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 et al.
      Pages 127-149

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

      • Shah Kamranur Rahman
      Pages 151-156

  3. Structural Analyses and Data Management

    1. Front Matter

      Pages 157-157
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    2. Hydrogen–Deuterium Exchange Mass Spectrometry for Probing Changes in Conformation and Dynamics of Proteins

      • Pui-Kin So
      Pages 159-173

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

      • András Micsonai, Éva Bulyáki, József Kardos
      Pages 175-189Open Access

    4. Navigating the Global Protein–Protein Interaction Landscape Using iRefWeb

      • Andrei L. Turinsky, Sam Dupont, Alexander Botzki, Sabry Razick, Brian Turner, Ian M. Donaldson et al.
      Pages 191-207

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

      • David R. Cooper, Marek Grabowski, Matthew D. Zimmerman, Przemyslaw J. Porebski, Ivan G. Shabalin, Magdalena Woinska et al.
      Pages 209-236

  4. Modeling, Simulation, and Visualization

    1. Front Matter

      Pages 237-237
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    2. Protein Structure Modeling with MODELLER

      • Benjamin Webb, Andrej Sali
      Pages 239-255

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

      • Pengfei Li, Kenneth M. Merz Jr.
      Pages 257-275

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

      • Yu Wai Chen, Yong Wang, Yun-Chung Leung, Kwok-Yin Wong
      Pages 277-288
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Keywords

About this book

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.

Editors and Affiliations

  • Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Hong Kong

    Yu Wai Chen

  • BMI Biotechnology Appraisals & Investments Limited, Wan Chai, Hong Kong

    Chin-Pang Bennu Yiu

Bibliographic Information

  • Book Title: Structural Genomics

  • Book Subtitle: General Applications

  • Editors: Yu Wai Chen, Chin-Pang Bennu Yiu

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0892-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-0891-3Published: 31 October 2020

  • Softcover ISBN: 978-1-0716-0894-4Published: 01 November 2021

  • eBook ISBN: 978-1-0716-0892-0Published: 30 October 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XIV, 364

  • Number of Illustrations: 16 b/w illustrations, 64 illustrations in colour

  • Topics: Life Sciences, general, Genetics and Genomics, Chemistry/Food Science, general

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