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Thursday, February 19, 2009
10:00 AM - 11:00 AM
CNLS Conference Room (TA-3, Bldg 1690)


Reweighting-based molecular dynamics in studying long-timescale biomolecular events

Donald Hamelberg
Georgia State University

Molecular dynamics is one of the most widely used techniques in computational chemistry due to its ability to accurately sample the energy landscape. However, for most biomolecules, there is a sub-microsecond timescale limitation; therefore, normal MD cannot explore portions of the landscape separated from the initial configuration by high barriers. We have adopted a method that eases the transition between energy basins by modifying the potential landscape in an efficient accelerated MD approach to study a notoriously slow conformational transition in biology: the cis-trans isomerization of the peptide prolyl bond. The local change of the isomeric state of the prolyl peptide bond acts as a switching mechanism in altering the conformation of proteins. A complete understanding of the mechanism of the catalyzed cis-trans isomerization process is still lacking, and current experimental techniques have not been able to provide a detailed atomistic picture. We have carried out several accelerated molecular dynamics simulations with explicit solvent, and we have provided a detailed description of cis-trans isomerization process with and without the assistance of the enzyme, cyclophilin A.

Host: Tongye Shen, T-6