Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations.
Simulation of the dynamics of a protein in aqueous solution using an atomic model for both the protein and the many water molecules is still computationally extremely demanding considering the time scale of protein motions. The use of supra-atomic or supra-molecular coarse-grained (CG) models may enhance the computational efficiency, but inevitably at the cost of reduced accuracy. Coarse-graining solvent degrees of freedom is likely to yield a favourable balance between reduced accuracy and enhanced computational speed. Here, the use of a supra-molecular coarse-grained water model that largely preserves the thermodynamic and dielectric properties of atomic level fine-grained (FG) water in molecular dynamics simulations of an atomic model for four proteins is investigated. The results of using an FG, a CG, an implicit, or a vacuum solvent environment of the four proteins are compared, and for hen egg-white lysozyme a comparison to NMR data is made. The mixed-grained simulations do not show large differences compared to the FG atomic level simulations, apart from an increased tendency to form hydrogen bonds between long side chains, which is due to the reduced ability of the supra-molecular CG beads that represent five FG water molecules to make solvent-protein hydrogen bonds. But, the mixed-grained simulations are at least an order of magnitude faster than the atomic level ones.
Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.
Sereina
S
Riniker
Andreas P
AP
Eichenberger
Wilfred F
WF
van Gunsteren
D000595:Amino Acid Sequence; D002826:Chorismate Mutase / Q000737:chemistry; D057773:Cold Shock Proteins and Peptides / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009113:Muramidase / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D014867:Water / Q000737:chemistry
D057773:Cold Shock Proteins and Peptides; D014867:Water; D009113:Muramidase; D002826:Chorismate Mutase