Synthetic Protein Switches: Methods and Protocols

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: β-lactamase Sensors

10. Creation of Antigen-Dependent β-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 β-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