Coarse-graining VISM with MARTINI Forcefield: the Right Way To Go

Dr. Clarisse Ricci
Biochem, UCSD


Solvation plays a fundamental role in many biological processes including biomolecular recognition, protein-protein interactions, membrane assembly and many others. The variational implicit solvation method (VISM) is currently developed to predict solvation free energies for systems of very complex topology, such as proteins. VISM theoretical foundation makes it unique in that i) it couples hydrophobic, dispersion interactions and electrostatic effects into one functional, and ii) it produces the solvation surface as an output of the theory. This allows VISM to capture more subtle solvation effects than do other implicit solvation methods. As we plan to expand VISM applications to more challenging scenarios, coarse-graining the protein seems a good strategy to keep the computational cost low. In this work, we adapted VISM to work with a well established coarse-grain forcefield for proteins and other biomolecules, MARTINI. We then tested how coarse-grained MARTINI-VISM compares with (atomistic) VISM for a set of six proteins that differ in shape, size and charge distribution. Promising results suggest that coarse-graining the protein is indeed the right step to broaden VISM applications in the near future.