vii
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ix
Part I General StrateGIeS and ConSIderatIonS
1 Synthetic Protein Switches: Theoretical and Experimental Considerations . . . .
3
Viktor Stein
2 Construction of Allosteric Protein Switches by Alternate Frame Folding
and Intermolecular Fragment Exchange . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
27
Jeung-Hoi Ha and Stewart N. Loh
3 Construction of Protein Switches by Domain Insertion
and Directed Evolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
43
Lucas F. Ribeiro, Tiana D. Warren, and Marc Ostermeier
Part II PePtIde SwItCheS
4 Catalytic Amyloid Fibrils That Bind Copper to Activate Oxygen . . . . . . . . . . .
59
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 . . . . . . . . . .
71
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 Modeling and Assessment . . . . . . . . . .
89
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 Semisynthetic Modular
Biosensors: SNIFITs and LUCIDs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Yuki Ohmuro-Matsuyama and Hiroshi Ueda
9 Quantitative and Dynamic Imaging of ATM Kinase Activity . . . . . . . . . . . . . . 131
Shyam Nyati, Grant Young, Brian Dale Ross, and Alnawaz Rehemtulla
Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
v
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
ix
Part I General StrateGIeS and ConSIderatIonS
1 Synthetic Protein Switches: Theoretical and Experimental Considerations . . . .
3
Viktor Stein
2 Construction of Allosteric Protein Switches by Alternate Frame Folding
and Intermolecular Fragment Exchange . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
27
Jeung-Hoi Ha and Stewart N. Loh
3 Construction of Protein Switches by Domain Insertion
and Directed Evolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
43
Lucas F. Ribeiro, Tiana D. Warren, and Marc Ostermeier
Part II PePtIde SwItCheS
4 Catalytic Amyloid Fibrils That Bind Copper to Activate Oxygen . . . . . . . . . . .
59
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 . . . . . . . . . .
71
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 Modeling and Assessment . . . . . . . . . .
89
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 Semisynthetic Modular
Biosensors: SNIFITs and LUCIDs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
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 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
Yuki Ohmuro-Matsuyama and Hiroshi Ueda
9 Quantitative and Dynamic Imaging of ATM Kinase Activity . . . . . . . . . . . . . . 131
Shyam Nyati, Grant Young, Brian Dale Ross, and Alnawaz Rehemtulla
Contents