title: MTS-MD of Biomolecules Steered with 3D-RISM-KH Mean Solvation Forces Accelerated with Generalized Solvation Force Extrapolation.
abstract: We developed a generalized solvation force extrapolation (GSFE) approach to speed up multiple time step molecular dynamics (MTS-MD) of biomolecules steered with mean solvation forces obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model with the Kovalenko-Hirata closure). GSFE is based on a set of techniques including the non-Eckart-like transformation of coordinate space separately for each solute atom, extension of the force-coordinate pair basis set followed by selection of the best subset, balancing the normal equations by modified least-squares minimization of deviations, and incremental increase of outer time step in motion integration. Mean solvation forces acting on the biomolecule atoms in conformations at successive inner time steps are extrapolated using a relatively small number of best (closest) solute atomic coordinates and corresponding mean solvation forces obtained at previous outer time steps by converging the 3D-RISM-KH integral equations. The MTS-MD evolution steered with GSFE of 3D-RISM-KH mean solvation forces is efficiently stabilized with our optimized isokinetic Nosé-Hoover chain (OIN) thermostat. We validated the hybrid MTS-MD/OIN/GSFE/3D-RISM-KH integrator on solvated organic and biomolecules of different stiffness and complexity: asphaltene dimer in toluene solvent, hydrated alanine dipeptide, miniprotein 1L2Y, and protein G. The GSFE accuracy and the OIN efficiency allowed us to enlarge outer time steps up to huge values of 1-4 ps while accurately reproducing conformational properties. Quasidynamics steered with 3D-RISM-KH mean solvation forces achieves time scale compression of conformational changes coupled with solvent exchange, resulting in further significant acceleration of protein conformational sampling with respect to real time dynamics. Overall, this provided a 50- to 1000-fold effective speedup of conformational sampling for these systems, compared to conventional MD with explicit solvent. We have been able to fold the miniprotein from a fully denatured, extended state in about 60 ns of quasidynamics steered with 3D-RISM-KH mean solvation forces, compared to the average physical folding time of 4-9 μs observed in experiment.
authors.affiliation: Department of Mechanical Engineering, University of Alberta , Mechanical Engineering Building 4-9, Edmonton, Alberta T6G 2G8, Canada.|National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada.|Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine , 1 Svientsitskii Street, Lviv 79011, Ukraine.
authors.forename: Igor
authors.initials: I
authors.lastname: Omelyan
authors.affiliation: Department of Mechanical Engineering, University of Alberta , Mechanical Engineering Building 4-9, Edmonton, Alberta T6G 2G8, Canada.|National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada.
authors.forename: Andriy
authors.initials: A
authors.lastname: Kovalenko
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D019281:Dimerization; D004151:Dipeptides / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D011084:Polycyclic Aromatic Hydrocarbons / Q000737:chemistry; D017510:Protein Folding; D012997:Solvents / Q000737:chemistry*; D014050:Toluene / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; D004151:Dipeptides; C034284:IgG Fc-binding protein, Streptococcus; D011084:Polycyclic Aromatic Hydrocarbons; D012997:Solvents; C000592077:asphaltene; D014050:Toluene