The study of protein folding and its ramifications in biological contexts is at the heart of computational biology. Incorrectly folded proteins resulting from errors during folding are responsible for illnesses such as Creutzfeldt-Jakob disease, Bovine spongiform encephalopathy, Parkinson’s and Alzheimer’s diseases. Due its implications in understanding such diseases, the dynamics of folding has received substantial attention in recent years. The dynamics of protein folding is accessible through molecular dynamics modeling, yet requires prohibitive computational times even to simulate a small protein molecule for a period of several micro seconds. Our group studies a number of tools in systems engineering that would help explain the observed dynamic behavior of the protein, ultimately making the connection between protein structure and functionality.
The specific tools range from control and optimization to principal components analysis, wavelet decomposition and clustering.
Michael Gray, an undergraduate researcher, is currently studying the unfolding/folding pathways of chemotrypsin inhibitor 2 (CI2) to uncover dominant mechanisms that govern the folding dynamics, including the principal residues that play key roles during this process.
Collaborators include Professor R. Faller (UC Davis), Dr. Dirk Reith (Fraunhofer Institute, Germany), Professors B. Erman, Y. Arkun and A. Gursoy (Koc University, Turkey).
Related Publications
A. Palazoglu, A. Gursoy, Y. Arkun, and B. Erman,”Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis,” J. Computational Biology , 11, 1149-1168 (2004).
Funding
National Science Foundation – International Collaboration Grant.