Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme

TL;DR

This paper demonstrates the application of the Hamiltonian Adaptive Resolution Scheme (H-AdResS) to simulate proteins with a hybrid solvent model, successfully reproducing structural and dynamic properties comparable to fully atomistic simulations.

Contribution

It is the first to apply H-AdResS to proteins with dual-resolution solvent, enabling open boundary simulations of complex biomolecular systems.

Findings

H-AdResS accurately reproduces protein structures.

The method captures solvent dynamics effectively.

Open boundary simulations are feasible for proteins.

Abstract

The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the Molecular Mechanics/Coarse-Grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Towards this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.