Protein-substrate recognition process is highly dynamic in nature. A key approach in deciphering the mechanism underlying the recognition process is to capture the kinetic process of substrate in its act of binding to its designated protein cavity. Towards this end, multi microsecond long atomistic molecular dynamics simulation has recently emerged as crucial method of choice. In this presentation we will demonstrate coarse grained models of protein, when systematically optimized to maintain the tertiary fold, can offer an attractive and inexpensive alternative of all-atom simulation, towards complete capture of protein-ligand binding events, from solvent to protein cavity, within a significantly shortened wall clock time compared to that of all-atom MD simulations. The result is validated against three distinct prototypical protein-ligand systems.

Capturing protein-ligand recognition pathways in coarse-grained simulation

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.