Ray Nagatani
Graduate Student
Program in Pharmaceutical Sciences and Pharmacogenomics
Research Summary
Despite recent successes in protein design, inadequate knowledge of governing principles limits our capabilities in engineering enzymes to perform new reactions in a general fashion. My research centers on how we can exploit design solutions already optimized by nature to evolve new reactions by extension from a conserved partial reaction. As the conserved functional capabilities in "mechanistically diverse enzyme superfamilies" are linked to highly-conserved constellations of active site residues ("catalytic modules"), I propose that using catalytic modules that already "know" how to do the basic chemistry required for a new reaction can reduce the protein design problem to engineering substrate specificity. Using the enolase superfamily as a model system, my strategy is to engineer member proteins to perform new reactions that rely on the partial reaction performed by the superfamily catalytic module. My approach relies on a collaborative and iterative design process involving identification of new substrates, re-design of active sites for binding specificity, identification of stability-optimized scaffolds, development of high-throughput screening methods for novel functions and optimization of chemistry through combinatorial generation of mutants. Success using this test system will be extended to other superfamily/catalytic module combinations to enhance the generality of this new approach.
Education
B.S. 2002, Molecular and Cellular Biology
University of California at Berkeley
Publications
Nagatani RA, Gonzalez A, Shoichet BK, Brinen LS, Babbitt PC. Stability for function trade-offs in the enolase superfamily "catalytic module". Biochemistry. 2007 Jun 12;46(23):6688-95.Sonawane ND, Muanprasat C, Nagatani R Jr, Song Y, Verkman AS. In vivo pharmacology and antidiarrheal efficacy of a thiazolidinone CFTR inhibitor in rodents. J Pharm Sci. 2005 Jan;94(1):134-43.
