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.
Lauricella, M., Chiodo, L., Bonaccorso, F., Durve, M., Montessori, A., Tiribocchi, A., et al. (2023). Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling. COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 33(1), 57-76 [10.4208/cicp.OA-2022-0046].
Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann – All Atom Molecular Dynamics Coupling
Montessori A.;Filippi S.;
2023-01-01
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.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
