With this award, the Chemistry of Life Processes Program in the Chemistry Division is funding Dr. Jeanine Amacher from Western Washington University to investigate how loops that are structurally conserved in various families of proteins affect their binding to other proteins and their functions as catalysts. Dr. Amacher’s group will determine how differences in the amino acid sequences that make up these loops help define the interactions that specifically targets a protein to its binding partner or affect its activity as an enzyme. Results from studies on these structural loops will reveal molecular principles to understand protein interactions that control how cells communicate. This project will train undergraduate and masters level graduate students in protein biochemistry and structural biology. The research and educational components of this project are integrated through specialized training in computational biology for undergraduate students and for their mentor. In addition, students at local primarily undergraduate institutions and community colleges will be connected with PhD students and postdoctoral research associates from regional research-intensive universities for “near-peer” mentoring through a regular Life Sciences Symposium hosted at Western Washington University. The importance of scientific communication in society will be integrated into an upper-level Honors “Bioethics of Emergent Technology in Biomedical Research” elective course to be offered at the host institution.

This project will test the hypothesis that the selectivity and/or activity of catalytic and noncatalytic domains of critical signaling or regulatory proteins are determined by conserved structural loops. The studies will characterize structurally-conserved loops in bacterial sortases, two of which are known to affect specificity, along with site-specific contributions of previously identified specificity-determining loops in SH2 and SH3 domains of the human Src oncogene protein that mediate protein-protein interactions. Natural sequence variation will be applied to design chimeric proteins and other loop variants. The structure-function relationship of these loops with respect to encoding target specificity will be determined using FRET(Fluorescence Resonance Energy Transfer)-based activity assays, X-ray crystallography, and molecular dynamics simulations. In addition, biochemical and computational methods, including the structure prediction program ROSETTA, will be used to trace the evolutionary roots that lead to target specificity of conserved loop sequences. This project will identify common principles that broaden the understanding of the relationship between sequence and specificity in structurally-conserved loops across several protein families. Finally, a better understanding for the specificity of sortases will potentially expand the application of sortase-mediated ligation as a tool for protein engineering.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

National Science Foundation (NSF)
Division of Chemistry (CHE)
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Pui Ho
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Western Washington University
United States
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