Multiscale hybrid modeling of proteins in solvent: SARS-CoV2 spike protein as test case for lattice Boltzmann – all atom molecular dynamics coupling. (English) Zbl 1508.92084
Summary: 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.
MSC:
| 92C40 | Biochemistry, molecular biology |
| 35Q20 | Boltzmann equations |
| 82M37 | Computational molecular dynamics in statistical mechanics |
| 92C05 | Biophysics |
| 92C35 | Physiological flow |
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