This project employs a combined experimental and computational approach to develop mechanisms by which ordinary proteins can be converted into molecular switches. Induced domain swapping (INDOS) is a technology that allows the function of a protein or enzyme to be switched on and off by a small molecule drug, metal ion, or change in pH. INDOS will be used to manipulate cellular pathways, in living cells and in real time, to examine their roles in health and disease. Protein fragment exchange (FREX) and alternate frame folding (AFF) are mechanisms by which an arbitrary binding protein can be turned into a fluorescent biosensor. We will generate a family of sensors for detecting a variety of biological targets in vivo and in vitro. The impact of this study lies in that the switching mechanisms being developed: (i) are general and can be applied to many proteins; (ii) are versatile, allowing the resulting switches to perform a variety of new and useful functions; and (iii) will provide insight into their underlying molecular phenomena (domain swapping, fragment complementation, and circular permutation), all of which occur commonly in nature yet are poorly understood.

Public Health Relevance

This project develops new mechanisms for converting proteins to functional switches. These technologies are used to create molecules of biological, biotechnological, and medical significance; specifically, biosensors and proteins and enzymes that can be switched on and off in the cell using small molecules or ions.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Smith, Ward
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Upstate Medical University
Schools of Medicine
United States
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DeGrave, Alex J; Ha, Jeung-Hoi; Loh, Stewart N et al. (2018) Large enhancement of response times of a protein conformational switch by computational design. Nat Commun 9:1013
Karchin, Joshua M; Ha, Jeung-Hoi; Namitz, Kevin E et al. (2017) Small Molecule-Induced Domain Swapping as a Mechanism for Controlling Protein Function and Assembly. Sci Rep 7:44388
Wolfe, Aaron J; Si, Wei; Zhang, Zhengqi et al. (2017) Quantification of Membrane Protein-Detergent Complex Interactions. J Phys Chem B 121:10228-10241
Ha, Jeung-Hoi; Loh, Stewart N (2017) Construction of Allosteric Protein Switches by Alternate Frame Folding and Intermolecular Fragment Exchange. Methods Mol Biol 1596:27-41
Wolfe, Aaron J; Hsueh, Yi-Ching; Blanden, Adam R et al. (2017) Interrogating Detergent Desolvation of Nanopore-Forming Proteins by Fluorescence Polarization Spectroscopy. Anal Chem 89:8013-8020
Woodford, Mark R; Dunn, Diana M; Blanden, Adam R et al. (2016) The FNIP co-chaperones decelerate the Hsp90 chaperone cycle and enhance drug binding. Nat Commun 7:12037
Ha, Jeung-Hoi; Karchin, Joshua M; Walker-Kopp, Nancy et al. (2015) Engineered Domain Swapping as an On/Off Switch for Protein Function. Chem Biol 22:1384-93