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Volume 33, Issue 1
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

DOI: 10.4208/cicp.OA-2022-0046

Commun. Comput. Phys., 33 (2023), pp. 57-76.

Published online: 2023-02

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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.

  • Keywords

SARS-CoV-2, biophysics, lattice Boltzmann, molecular dynamics.

  • AMS Subject Headings

82M37, 92C05, 35Q20

  • Copyright

COPYRIGHT: © Global Science Press

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@Article{CiCP-33-57, author = {Lauricella , MarcoChiodo , LetiziaBonaccorso , FabioDurve , MihirMontessori , AndreaTiribocchi , AdrianoLoppini , AlessandroFilippi , Simonetta and Succi , Sauro}, title = {Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann — All Atom Molecular Dynamics Coupling}, journal = {Communications in Computational Physics}, year = {2023}, volume = {33}, number = {1}, pages = {57--76}, 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.

}, issn = {1991-7120}, doi = {https://doi.org/10.4208/cicp.OA-2022-0046}, url = {http://global-sci.org/intro/article_detail/cicp/21425.html} }
TY - JOUR T1 - Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as Test Case for Lattice Boltzmann — All Atom Molecular Dynamics Coupling AU - Lauricella , Marco AU - Chiodo , Letizia AU - Bonaccorso , Fabio AU - Durve , Mihir AU - Montessori , Andrea AU - Tiribocchi , Adriano AU - Loppini , Alessandro AU - Filippi , Simonetta AU - Succi , Sauro JO - Communications in Computational Physics VL - 1 SP - 57 EP - 76 PY - 2023 DA - 2023/02 SN - 33 DO - http://doi.org/10.4208/cicp.OA-2022-0046 UR - https://global-sci.org/intro/article_detail/cicp/21425.html KW - SARS-CoV-2, biophysics, lattice Boltzmann, molecular dynamics. AB -

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 , MarcoChiodo , LetiziaBonaccorso , FabioDurve , MihirMontessori , AndreaTiribocchi , AdrianoLoppini , AlessandroFilippi , Simonetta and Succi , Sauro. (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. doi:10.4208/cicp.OA-2022-0046
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