title: Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.
abstract: A novel simulation framework that integrates the OPEP coarse-grained (CG) model for proteins with the Lattice Boltzmann (LB) methodology to account for the fluid solvent at mesoscale level is presented. OPEP is a very efficient, water-free and electrostatic-free force field that reproduces at quasi-atomistic detail processes like peptide folding, structural rearrangements, and aggregation dynamics. The LB method is based on the kinetic description of the solvent in order to solve the fluid mechanics under a wide range of conditions, with the further advantage of being highly scalable on parallel architectures. The capabilities of the approach are presented, and it is shown that the strategy is effective in exploring the role of hydrodynamics on protein relaxation and peptide aggregation. The end result is a strategy for modeling systems of thousands of proteins, such as in the case of dense protein suspensions. The future perspectives of the multiscale approach are also discussed.
authors.affiliation: Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot , Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.
authors.forename: Fabio
authors.initials: F
authors.lastname: Sterpone
authors.affiliation: Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot , Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.|IUF, Institut Universitaire de France, Boulevard Saint Michel, 75005 Paris, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Derreumaux
authors.affiliation: CNR-IPCF, Consiglio Nazionale delle Ricerche, Rome, Italy.
authors.forename: Simone
authors.initials: S
authors.lastname: Melchionna
mesh_terms: D016229:Amyloid beta-Peptides / Q000737:chemistry / Q000378:metabolism; D057446:Hydrodynamics; D056004:Molecular Dynamics Simulation; D010446:Peptide Fragments / Q000737:chemistry / Q000378:metabolism; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D014867:Water / Q000737:chemistry
chemical_list: D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; D011506:Proteins; C417223:amyloid beta-protein (16-22); D014867:Water