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

M Lauricella and L Chiodo and F Bonaccorso and M Durve and A Montessori and A Tiribocchi and A Loppini and S Filippi and S Succi, COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 33, 57-76 (2023).

DOI: 10.4208/cicp.OA-2022-0046

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 join-ing the Lattice Boltzmann fluid dynamics (for solvent flows) with the all-atom atom-istic 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 sol-vent 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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