Protein Engineering Protocols - Mycobacteriology research center

ContentsPreface ..............................................................................................................vContributors ..................................................................................................... ixPART I DESIGN AND COMPUTATIONAL STRATEGIES FOR PROTEIN ENGINEERING1 Combinatorial Protein Design StrategiesUsing Computational MethodsHidetoshi Kono, Wei Wang, and Jeffery G. Saven ............................... 32 Global Incorporation of Unnatural Amino Acids in Escherichia coliJamie M. Bacher and Andrew D. Ellington......................................... 233 Considerations in the Design and Optimizationof Coiled Coil StructuresJody M. Mason, Kristian M. Müller, and Katja M. Arndt.................... 354 Calcium Indicators Based on Calmodulin–Fluorescent Protein FusionsKevin Truong, Asako Sawano, Atsushi Miyawaki,and Mitsuhiko Ikura........................................................................ 715 Design and Synthesis of Artificial Zinc Finger ProteinsWataru Nomura and Yukio Sugiura ................................................... 836 Monobodies: Antibody Mimics Based on the Scaffoldof the Fibronectin Type III DomainAkiko Koide and Shohei Koide............................................................ 957 Engineering Site-Specific EndonucleasesPeter Friedhoff and Alfred Pingoud .................................................. 111PART II EVOLUTIONARY STRATEGIES FOR PROTEIN ENGINEERING8 Protein Library Design and Screening: Working Out the ProbabilitiesMichel Denault and Joelle N. Pelletier ............................................. 1279 Protein Design by Binary Patterning of Polarand Nonpolar Amino AcidsLuke H. Bradley, Yinan Wei, Peter Thumfort, Christine Wurth,and Michael H. Hecht .................................................................. 15510 Versatile DNA Fragmentation and Directed EvolutionWith Nucleotide Exchange and Excision TechnologySabine C. Stebel, Katja M. Arndt, and Kristian M. Müller................ 167vii