Protein Engineering Protocols

ISBN-13: 9781588290724 / Angielski / Twarda / 2006 / 328 str.

Katja M. Arndt; Kristian M. Muller

Opis

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.

Recenzje

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)

Spis treści

Part I. Design and Computational Strategies for Protein Engineering Combinatorial Protein Design Strategies Using Computational Methods Hidetoshi Kono, Wei Wang, and Jeffery G. Saven Global Incorporation of Unnatural Amino Acids in Escherichia coli Jamie M. Bacher and Andrew D. Ellington Considerations in the Design and Optimization of Coiled Coil Structures Jody M. Mason, Kristian M. Müller, and Katja M. Arndt Calcium Indicators Based on Calmodulin-Fluorescent Protein Fusions Kevin Truong, Asako Sawano, Atsushi Miyawaki, and Mitsuhiko Ikura Design and Synthesis of Artificial Zinc Finger Proteins Wataru Nomura and Yukio Sugiura Monobodies: Antibody Mimics Based on the Scaffold of the Fibronectin Type III Domain Akiko Koide and Shohei Koide Engineering Site-Specific Endonucleases Peter Friedhoff and Alfred Pingoud Part II. Evolutionary Strategies for Protein Engineering Protein Library Design and Screening: Working Out the Probabilities Michel Denault and Joelle N. Pelletier Protein Design by Binary Patterning of Polar and Nonpolar Amino Acids Luke H. Bradley, Yinan Wei, Peter Thumfort, Christine Wurth, and Michael H. Hecht Versatile DNA Fragmentation and Directed Evolution With Nucleotide Exchange and Excision Technology Sabine C. Stebel, Katja M. Arndt, and Kristian M. Müller Degenerate Oligonucleotide Gene Shuffling Peter L. Bergquist and Moreland D. Gibbs. M13 Bacteriophage Coat Proteins Engineered for Improved Phage Display Sachdev S. Sidhu, Birte K. Feld, and Gregory A. Weiss Ribosome-Inactivation Display System Satoshi Fujita, Jing-Min Zhou, and Kazunari Taira Compartmentalized Self-Replication: A Novel Method for the Directed Evolution of Polymerases and Other Enzymes Farid J. Ghadessy and Philipp Holliger Synthesisof 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 and Stephen W. Michnick A General Method of Terminal Truncation, Evolution, and Re-Elongation to Generate Enzymes of Enhanced Stability Jochen Hecky, Jody M. Mason, Katja M. Arndt, and Kristian M. Müller Index

Blurb

Protein engineering is a fascinating mixture of molecular biology, protein structure analysis, computation, and biochemistry, with the goal of developing useful or valuable proteins. Divided into two sections, Protein Engineering Protocols reviews rational protein design strategies and directed evolutionary techniques, and their impact on protein engineering.
The first section presents design and computational strategies for protein engineering focusing on designing a protein with desired properties, including examples covering a wide range of engineering techniques, such as protein-protein interactions, DNA binding, antibody mimics, and enzymatic activity. The second section on evolutionary techniques provides step-by-step instructions on library design and statistical assessment of library quality. New methods for DNA shuffling as well as different selection strategies are also presented.
Following the successful Methods in Molecular Biology™ series format, this volume provides a comprehensive guide to the methods used at every stage of the engineering process. By combining a thorough theoretical foundation with detailed protocols, Protein Engineering Protocols will be invaluable to all research workers in the area, from graduate students to senior investigators.