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

作　　者：Marco Lauricella Letizia Chiodo Fabio Bonaccorso Mihir Durve Andrea Montessori Adriano Tiribocchi Alessandro Loppini Simonetta Filippi Sauro Succi 

机构地区：[1]Consiglio Nazionale delle Ricerche,Istituto per le Applicazioni del Calcolo IAC-CNR,00185,Rome Italy [2]Engineering Department,Campus Bio-Medico University,00128,Rome,Italy [3]Physics Department and INFN,University of Rome“Tor Vergata”,00133 Rome,Italy [4]Istituto Italiano di Tecnologia,Center for Life Nano-&Neuro-Science@Sapienza-IIT,00161,Rome,Italy [5]Engineering Department,Universit´a degli Studi Roma TRE,via Vito Volterra 62,Rome,00146,Italy

出　　处：《Communications in Computational Physics》2023年第1期57-76,共20页计算物理通讯（英文）

基　　金：funding from the European Research Council under the European Union’s Horizon 2020 Framework Programme(No.FP/2014-2020)ERC Grant Agreement No.739964(COPMAT);support on the HPC CRESCO facility used in the LB/MD simulations,under the initiative Associazione Big Data COVID-19 Fast Track.

摘　　要：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 equilibriumproperties 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.

关 键 词：SARS-CoV-2 BIOPHYSICS lattice Boltzmann molecular dynamics 

分 类 号：O62[理学—有机化学]