Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as test case for Lattice Boltzmann -- All Atom Molecular Dynamics Coupling

Abstract

Physiological solvent flows surround biological structures triggering therein collective motions. Notable examples are virus/host-cell interactions and solvent-mediated allosteric regulation. The present work describes a multiscale approach joining the Lattice Boltzmann fluid dynamics (for solvent flows) with the all-atom atomistic molecular dynamics (for proteins) to model functional interactions between flows and molecules. We present, as an applicative scenario, the study of the SARS-CoV-2 virus spike glycoprotein protein interacting with the surrounding solvent, modeled as a mesoscopic fluid. The equilibrium properties of the wild-type spike and of the Alpha variant in implicit solvent are described by suitable observables. The mesoscopic solvent description is critically compared to the all-atom solvent model, to quantify the advantages and limitations of the mesoscopic fluid description.

15 pages, 6 figures

References in corpus (3)

• Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore
• Mesoscopic simulations at the physics-chemistry-biology interface
• Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2