Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann — All Atom Molecular Dynamics Coupling
Year: 2023
Author: Marco Lauricella, Letizia Chiodo, Fabio Bonaccorso, Mihir Durve, Andrea Montessori, Adriano Tiribocchi, Alessandro Loppini, Simonetta Filippi, Sauro Succi
Communications in Computational Physics, Vol. 33 (2023), Iss. 1 : pp. 57–76
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.
You do not have full access to this article.
Already a Subscriber? Sign in as an individual or via your institution
Journal Article Details
Publisher Name: Global Science Press
Language: English
DOI: https://doi.org/10.4208/cicp.OA-2022-0046
Communications in Computational Physics, Vol. 33 (2023), Iss. 1 : pp. 57–76
Published online: 2023-01
AMS Subject Headings: Global Science Press
Copyright: COPYRIGHT: © Global Science Press
Pages: 20
Keywords: SARS-CoV-2 biophysics lattice Boltzmann molecular dynamics.