Protein Dynamics
The energy landscape theory of protein folding states that proteins are minimally frustrated, their energy landscape is funnel shaped and their folded states are at the bottom of the funnel. Thus, models of proteins that have only the native structure encoded, structure-based models, have had great success in reproducing and predicting protein dynamics. Most models tend to be coarse-grained such as in the most commonly used model where each residue is represented by a bead centered at the location of the Calpha atom and only native interactions are stabilizing. Partitioning geometric and energetic effects is difficult in coarse-grained models since geometry is included implicitly through the energetic interactions. In order to explore the role of geometric specificity in folding, I am working to build and characterize an all-atom structure-based model.

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields, Whitford, P. C., Noel, J. K., Gosavi, S., Schug, A., Sanbonmatsu, K. Y., Onuchic, J. N., Proteins-Structure Function and Bioinformatics, Vol: 75, Iss: 2, pp. 430-441 (2009)