Protein Engineering 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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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.

• Activation
• Amino acid
• Calcium
• DNA
• Elongation
• Nucleotide
• biochemistry
• enzymes
• escherichia coli
• genes
• molecular biology
• protein structure
• proteins

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)

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

  Katja M. Arndt, Kristian M. Müller

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