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Computational Study of Protein-Protein Interaction Dynamics at Single Molecule Level


EMSL Project ID
38508

Abstract

The dynamic process of binding occurs in a wide dynamic range, including millisecond to second timescale range. To be able to connect and compare computational simulation results with the results from single molecule binding experiments, long time and multiple trajectories are needed so that reliable statistics can be applied to decipher the properties of physical observable. The traditional molecular dynamics simulations cannot be carried out through such a wide time scale range. We propose to achieve a long-time molecular dynamics simulation by describing the protein interactions in a coarse grained way at the residue or atomic contact level guided by energy landscape theory where effects of water molecules can be included and native interactions are preferred. Therefore, the dynamical processes of protein conformational dynamics in protein-protein interactions can be probed thoroughly in the entire time domain. We plan to study the statistical kinetics and characterize the structural correlations among the complex kinetics and conformational changes, which will reveal the dynamical interplay of binding and conformational changes. It would also serve as an adequate computational template enabling further investigations on mechanisms of binding of different bio-molecular interacting complexes in vitro and in living cells. It would also help the understanding of the complex biological network involving protein-protein interactions in bacterial cells. In this project, we plan to carry out a systematic simulation study on protein-protein interaction dynamics using the new parallel computation facility of EMSL at PNNL.

Project Details

Project type
Exploratory Research
Start Date
2010-01-25
End Date
2011-01-30
Status
Closed

Team

Principal Investigator

Jin Wang
Institution
State University of New York at Stony Brook

Team Members

Suneth Peshala Rajapaksha Rajapaksha Mudiyanselage
Institution
Bowling Green State University

Qiang Lu
Institution
State University of New York at Stony Brook

H. Peter Lu
Institution
Bowling Green State University