Three-stage multiscale modelling of the NMDA neuroreceptor

Palma, Francesco Di; Succi, Sauro; Sterpone, Fabio; Lauricella, Marco; Pérot, Franck; Melchionna, Simone

doi:10.1080/00268976.2021.1928312

Cited by 1 publication

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References 48 publications

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“…A different approach is based on the coupling of different tools, to describe the coexistence of different time-and length-scales in a multiscale perspective. Such multiscale approach could become, once assessed, a powerful biophysical computational tools, with perspective usage in drug design and biomedicine [22][23][24].…”

Section: Introductionmentioning

confidence: 99%

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

Lauricella¹,

Chiodo²,

Bonaccorso³

et al. 2023

CICP

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Physiological solvent flows surround biological structures triggering therein collective motions. Notable examples are virus/host-cell interactions and solventmediated 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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Section: Introductionmentioning

confidence: 99%