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Protein Engineering Protocols

  • Book
  • © 2007

Overview

Editors:
  1. Katja M. Arndt

    1. Institut für Biologie III, Universität Freiburg, Freiburg, Germany

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    You can also search for this editor in PubMed   Google Scholar

  2. Kristian M. Müller

    1. Institut für Biologie III, Universität Freiburg, Freiburg, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Comprehensive guide
  • a fascinating mixture of molecular biology, protein structure analysis, computation, and biochemistry
  • New methods for DNA shuffling
  • Methods in Molecular Biology™ series format
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 352)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-xi
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  2. Design and Computational Strategies for Protein Engineering

    1. Front Matter

      Pages 1-1
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    2. Combinatorial Protein Design Strategies Using Computational Methods

      • Hidetoshi Kono, Wei Wang, Jeffery G. Saven
      Pages 3-22

    3. Global Incorporation of Unnatural Amino Acids in Escherichia coli

      • Jamie M. Bacher, Andrew D. Ellington
      Pages 23-34

    4. Considerations in the Design and Optimization of Coiled Coil Structures

      • Jody M. Mason, Kristian M. Müller, Katja M. Arndt
      Pages 35-70

    5. Calcium Indicators Based on Calmodulin-Fluorescent Protein Fusions

      • Kevin Truong, Asako Sawano, Atsushi Miyawaki, Mitsuhiko Ikura
      Pages 71-82

    6. Design and Synthesis of Artificial Zinc Finger Proteins

      • Wataru Nomura, Yukio Sugiura
      Pages 83-93

    7. Monobodies

      • Akiko Koide, Shohei Koide
      Pages 95-109

    8. Engineering Site-Specific Endonucleases

      • Peter Friedhoff, Alfred Pingoud
      Pages 111-123

  3. Evolutionary Strategies for Protein Engineering

    1. Front Matter

      Pages 125-125
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    2. Protein Library Design and Screening

      • Michel Denault, Joelle N. Pelletier
      Pages 127-154

    3. Protein Design by Binary Patterning of Polar and Nonpolar Amino Acids

      • Luke H. Bradley, Yinan Wei, Peter Thumfort, Christine Wurth, Michael H. Hecht
      Pages 155-166

    4. Versatile DNA Fragmentation and Directed Evolution With Nucleotide Exchange and Excision Technology

      • Sabine C. Stebel, Katja M. Arndt, Kristian M. Müller
      Pages 167-190

    5. Degenerate Oligonucleotide Gene Shuffling

      • Peter L. Bergquist, Moreland D. Gibbs
      Pages 191-204

    6. M13 Bacteriophage Coat Proteins Engineered for Improved Phage Display

      • Sachdev S. Sidhu, Birte K. Feld, Gregory A. Weiss
      Pages 205-219

    7. Ribosome-Inactivation Display System

      • Satoshi Fujita, Jing-Min Zhou, Kazunari Taira
      Pages 221-236

    8. Compartmentalized Self-Replication

      • Farid J. Ghadessy, Philipp Holliger
      Pages 237-248

    9. Synthesis of Degenerated Libraries of the Ras-Binding Domain of Raf and Rapid Selection of Fast-Folding and Stable Clones With the Dihydrofolate Reductase Protein Fragment Complementation Assay

      • François-Xavier Campbell-Valois, Stephen W. Michnick
      Pages 249-274

    10. A General Method of Terminal Truncation, Evolution, and Re-Elongation to Generate Enzymes of Enhanced Stability

      • Jochen Hecky, Jody M. Mason, Katja M. Arndt, Kristian M. Müller
      Pages 275-304

  4. Back Matter

    Pages 305-312
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Keywords

About this book

Protein engineering is a fascinating mixture of molecular biology, protein structure analysis, computation, and biochemistry, with the goal of developing useful or valuable proteins. Protein Engineering Protocols will consider the two general, but not mutually exclusive, strategies for protein engineering. The first is known as rational design, in which the scientist uses detailed knowledge of the structure and function of the protein to make desired changes. The s- ond strategy is known as directed evolution. In this case, random mutagenesis is applied to a protein, and selection or screening is used to pick out variants that have the desired qualities. By several rounds of mutation and selection, this method mimics natural evolution. An additional technique known as DNA shuffling mixes and matches pieces of successful variants to produce better results. This process mimics recombination that occurs naturally during sexual reproduction. The first section of Protein Engineering Protocols describes rational p- tein design strategies, including computational methods, the use of non-natural amino acids to expand the biological alphabet, as well as impressive examples for the generation of proteins with novel characteristics. Although procedures for the introduction of mutations have become routine, predicting and und- standing the effects of these mutations can be very challenging and requires profound knowledge of the system as well as protein structures in general.

Reviews

From the reviews:

"Whether the research in your laboratory focuses on protein engineering or you wish to adopt a method for engineering a protein of interest, you will find this book, with it up-to-date stepwise protocols and experimentally oriented language, well suited to these goals." -Quarterly Review of Biology

"The chapters of Protein Engineering Protocols have been written by researchers with years of practical experience at the bench. It represents a methodological ‘cook-book’ of high quality. The diverse topics are well written and covered in an up-to-date manner. This makes it a bench-top handbook indispensable for all scientists who either work directly in protein engineering and design or use the described approaches of this field for their own research." (Nediljko Budisa, ChemBioChem, Vol. 8, 2007)

Editors and Affiliations

  • Institut für Biologie III, Universität Freiburg, Freiburg, Germany

    Katja M. Arndt, Kristian M. Müller

Bibliographic Information

  • Book Title: Protein Engineering Protocols

  • Editors: Katja M. Arndt, Kristian M. Müller

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1385/1597451878

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Humana Press 2007

  • Hardcover ISBN: 978-1-58829-072-4Published: 15 September 2006

  • Softcover ISBN: 978-1-61737-338-1Published: 10 November 2010

  • eBook ISBN: 978-1-59745-187-1Published: 26 October 2007

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: 328

  • Number of Illustrations: 64 b/w illustrations, 1 illustrations in colour

  • Topics: Protein Science, Cell Biology, Molecular Medicine, Biochemistry, general

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