Description
This detailed book provides state-of-the-art protocols to facilitate the construction of synthetic protein switches for a variety of applications in biotechnology and basic research. Beginning with general strategies, the volume continues with coverage of peptide switches, fluorescent and bioluminescent sensors, -lactamase sensors, proteolytic sensors, optogenetic switches, as well as cellular signaling switches. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Synthetic Protein Switches: Methods and Protocols serves as a useful reference for life scientists from diverse research fields that range from traditional, discovery-centered disciplines, like cancer research, to newly emerging disciplines, such as synthetic biology. Part I: General Strategies and Considerations 1. Synthetic Protein Switches: Theoretical and Experimental Considerations Viktor Stein 2. Construction of Allosteric Protein Switches by Alternate Frame Folding and Intermolecular Fragment Exchange Jeung-Hoi Ha and Stewart N. Loh 3. Construction of Protein Switches by Domain Insertion and Directed Evolution Lucas F. Ribeiro, Tiana D. Warren, and Marc Ostermeier Part II: Peptide Switches 4. Catalytic Amyloid Fibrils that Bind Copper to Activate Oxygen Alex Sternisha and Olga Makhlynets Part III: Fluorescent and Bioluminescent Sensors 5. Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors Ben E. Clifton, Jason H. Whitfield, Inmaculada Sanchez-Romero, Michel K. Herde, Christian Henneberger, Harald Janovjak, and Colin J. Jackson 6. Method for Developing Optical Sensors Using a Synthetic Dye-Fluorescent Protein FRET Pair and Computational Modelling and Assessment Joshua A. Mitchell, William H. Zhang, Michel K. Herde, Christian Henneberger, Harald Janovjak, Megan L. O’Mara, and Colin J. Jackson 7. Rational Design and Applications of Semi-Synthetic Modular Biosensors: SNIFITs and LUCIDs Helen Farrants, Julien Hiblot, Rudolf Griss, and Kai Johnsson 8. Ultrasensitive Firefly Luminescent Intermediate-Based Protein-Protein Interaction Assay (FlimPIA) Based on the Functional Complementation of Mutant Firefly Luciferases Yuki Ohmuro-Matsuyama and Hiroshi Ueda 9. Quantitative and Dynamic Imaging of ATM Kinase Activity Shyam Nyati, Grant Young, Brian Dale Ross, and Alnawaz Rehemtulla Part IV: -lactamase Sensors 10. Creation of Antigen-Dependent -Lactamase Fusion Protein Tethered by Circularly Permuted Antibody Variable Domains Hiroto Iwai, Miki Kojima-Misaizu, Jinhua Dong, and Hiroshi Ueda 11. Protein and Protease Sensing by Allosteric Derepression Goh Hui Chin, Farid J. Ghadessy, and Saurabh Nirantar 12. DNA-Specific Biosensors Based on Intramolecular -Lactamase-Inhibitor Complex Formation Wouter Engelen and Maarten Merkx Part V: Proteolytic Sensors 13. Engineering and Characterizing Synthetic Protease Sensors and Switches Viktor Stein and Kirill Alexandrov 14. Characterizing Dynamic Protein-Protein Interactions Using the Genetically Encoded Split Biosensor Assay Technique Split TEV Jan P. Wintgens, Moritz J Rossner, and Michael C. Wehr Part VI: Optogenetic Switches 15. Development of a Synthetic Switch to Control Protein Stability in Eukaryotic Cells with Light Christof Taxis 16. Light-Regulated Protein Kinases Based on the CRY2-CIB1 System Wignand W.D. Mhlhuser, Maximilian Hrner, Wilfried Weber, and Gerald Radziwill 17. Yeast-Based Screening System for the Selection of Functional Light-Driven K+ Channels Cristian Cosentino, Laura Alberio, Gerhard Thiel, and Anna Moroni 18. Primer-Aided Truncation for the Creation of Hybrid Proteins Robert Stabel, Birthe Stven, Robert Ohlendorf, and Andreas Mglich Part VII: Cellular Signaling Switches 19. Engineering Small Molecule Responsive Split-Protein Kinases Javier Castillo-Montoya and Indraneel Ghosh 20. Directed Evolution Methods to Rewire Signaling Networks Raphal B. Di Roberto, Benjamin M. Scott, and Sergio G. Peisajovich
