US-Turkey Cooperative Research Project: Studies on the Folding Dynamics of Proteins

University Of California-Davis, Davis CA

Investigators

Abstract

0352868 Palazoglu Description: This project supports a partnership between the Dr. Ahmet Palazoglu, Department of Chemical Engineering and Material Science, The University of California, Davis, California and a team of Turkish scientists including Dr. Attila Gursoy, Department of Computer Engineering, Koc University, Istanbul, Turkey and Dr. Burak Erman and Dr. Yaman Arkun, both of the Department of Chemical and Biological Engineering at Koc University. The focus of the research is the study of protein folding dynamics, with the emphasis on developing fast simulation platforms that can reliably predict the mechanisms of folding and analyzing the simulated trajectories to understand the fundamental features of how the protein folds to its native state. For simulating the folding dynamics, they plan to use coarse-grained fast-folding algorithms. Specifically, a coarse-grained Go-type model will be utilized. They will explore new directions, based on optimal control theory, in steering the protein to its known native state. Furthermore, they plan to use the principal components analysis (PCA) to characterize the large number of trajectories obtained by the fast-folding Go-type model, and perform wavelet decomposition to provide a multi-resolution analysis of their spatial and temporal features. The coarse-grained Go model will also be complemented by more extensive simulations of rigorous molecular dynamics (MD) for proteins in water and different accuracy levels will be probed. Scope: The proposed research on protein folding dynamics is a field of intense study in structural biology. The PI's expect the results of this research to have significant repercussions in understanding the fundamental mechanisms involved during the evolution of the protein from its denatured state to its native state. The two teams have complementary expertise in the related elements of the proposed work, and there is already a brief history of collaborative work between the two groups. The project will involve a junior researcher from Turkey as the lead PI and graduate students from both institutions. The travel between the U.S. and Turkey by the research teams will be organized in such a way as to provide ample time for interaction and substantial research during the year. The proposed research will help train graduate students and provide a synergistic environment in which they can appreciate the benefits of multi-disciplinary research. The results will be disseminated through scientific literature and will also be available on the Web pages of the leading PIs. The proposed activity will enhance our understanding of how proteins function and will have a direct impact on the well being of the society at large.