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Center for Nonlinear Studies |
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