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Dr. Gao
http://www.chem.tamu.edu/rgroup/gao/ Studies of fundamental mechanisms of chemical reactions in complex environments are of great importance in understanding enzymatic reactions as well as in designing new molecules for biomedical applications. We are using quantum mechanical and molecular mechanical calculations to understand chemical reactions including excited energy transfer in chromophores, the phosphodiester cleavage reaction catalyzed by the Zn(II)-N Complexes, and the allosteric interactions of carbamoyl phosphate synthetase, an enzyme that synthesizes carbamoyl phosphate. We are also studying the effects of chemical reactions on their environment. We are developing new methods in molecular dynamic simulations to overcome the conventional computational bottleneck, so that multi-time scale complex processes including protein conformational changes, which are common in many enzymatic reactions, can be studied. Protein conformational changes play essential roles in many biological functions, including ligand binding, chemo-mechanical coupling, allosteric interaction, and signal transduction. Multi-scale approaches are required for a full understanding of these processes that cover many orders of magnitude of time and length scales, with events ranging from local chemical reactions to global protein conformational changes. The proposed research requires the development of a new theoretical framework and computational methodology so that dynamics ranging over many orders of magnitude of time and length scales can be studied and understood. The development in these areas requires integration of theories at different levels of detail, and will not only help to unravel the fundamental mechanisms of protein folding and enzymatic reactions, but also have potential applications in ligand-protein binding, as well as in protein-protein interactions. |
