title: Water model tuning for improved reproduction of rotational diffusion and NMR spectral density.
abstract: A water model for molecular simulation was optimized to improve the reproduction of translational and rotational diffusion of pure water and proteins. The SPC/E(b) model was developed from the original SPC/E model with a slight increase of the O-H bond length of 1%. This tuning has significantly improved the translational and rotational diffusion when compared to the experimental values, whereas only small changes were observed in the other thermodynamic properties examined. The overall tumbling correlation times (τ(p)) from ubiquitin, protein G, bovine pancreatic trypsin inhibitor, and barstar C42/80A were successfully reproduced using the SPC/E(b) model. Calculated site-specific spectral densities of the main chain amide bond rotation in ubiquitin and protein G were in good agreement with those derived from nuclear magnetic resonance reduced spectral density mapping. The SPC/E(bT) model was also developed with temperature-dependent bond-length tuning to facilitate reproduction of the experimental τ(p) around room temperature.
authors.affiliation: Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan.
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Takemura
authors.forename: Akio
authors.initials: A
authors.lastname: Kitao
mesh_terms: D004058:Diffusion; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D011506:Proteins / Q000737:chemistry*; D012399:Rotation; D013696:Temperature; D014867:Water / Q000737:chemistry*
chemical_list: D011506:Proteins; D014867:Water