title: Effect of solvent model when probing protein dynamics with molecular dynamics.
abstract: We probe the dynamics of the Bpti and Galectin-3 proteins using molecular dynamics simulations employing three water models at different levels of resolution, viz. the atomistic TIP4P-Ewald, the coarse-grained Elba and an implicit generalised Born model. The dynamics are quantified indirectly by model-free order parameters, S2of the backbone NH and selected side-chain bond vectors, which also have been determined experimentally through NMR relaxation measurements. For the backbone, the order parameters produced with the three solvent models agree to a large extent with experiments, giving average unsigned deviations between 0.03 and 0.06. For the side-chains, for which the experimental data is incomplete, the deviations are considerably larger with mean deviations between 0.13 and 0.17. However, for both backbone and side-chains, it is difficult to pick a winner, as all models perform equally well overall. For a more complete set of side-chain vectors, we resort to analysing the variation among the estimates from different solvent models. Unfortunately, the variations are found to be sizeable with mean deviations between 0.11 and 0.15. Implications for computational assessment of protein dynamics are discussed.
authors.affiliation: Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-405 30 Göteborg, Sweden. Electronic address: samuel.genheden@gu.se.
authors.forename: Samuel
authors.initials: S
authors.lastname: Genheden
mesh_terms: D007611:Aprotinin / Q000737:chemistry; D037502:Galectin 3 / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D014867:Water / Q000737:chemistry*
chemical_list: D037502:Galectin 3; D012997:Solvents; D014867:Water; D007611:Aprotinin
keywords: Coarse-graining; Implicit solvent; Molecular dynamics; Order parameters; Protein dynamics