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arXiv · 2305.05025

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

Marco Lauricella·Letizia Chiodo·Fabio Bonaccorso·Mihir Durve·Andrea Montessori·Adriano Tiribocchi·Alessandro Loppini·Simonetta Filippi·Sauro Succi
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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.

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Marco Lauricella, Letizia Chiodo, Fabio Bonaccorso, Mihir Durve, Andrea Montessori, Adriano Tiribocchi, Alessandro Loppini, Simonetta Filippi, Sauro Succi. 2023-05-08. Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as test case for Lattice Boltzmann -- All Atom Molecular Dynamics Coupling. https://doi.org/10.4208/cicp.oa-2022-0046

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