title: Do we have to explicitly model the ions in brownian dynamics simulations of proteins?
abstract: Brownian dynamics (BD) is a very efficient coarse-grained simulation technique which is based on Einstein's explanation of the diffusion of colloidal particles. On these length scales well beyond the solvent granularity, a treatment of the electrostatic interactions on a Debye-Hückel (DH) level with its continuous ion densities is consistent with the implicit solvent of BD. On the other hand, since many years BD is being used as a workhorse simulation technique for the much smaller biological proteins. Here, the assumption of a continuous ion density, and therefore the validity of the DH electrostatics, becomes questionable. We therefore investigated for a few simple cases how far the efficient DH electrostatics with point charges can be used and when the ions should be included explicitly in the BD simulation. We find that for large many-protein scenarios or for binary association rates, the conventional continuum methods work well and that the ions should be included explicitly when detailed association trajectories or protein folding are investigated.
authors.affiliation: Zentrum für Bioinformatik, Universität des Saarlandes, D-66041 Saarbrücken, Germany.
authors.forename: Melanie J
authors.initials: MJ
authors.lastname: Zimmer
authors.forename: Tihamér
authors.initials: T
authors.lastname: Geyer
mesh_terms: D004058:Diffusion; D019277:Entropy; D007477:Ions / Q000737:chemistry*; D008566:Membranes / Q000737:chemistry*; D008958:Models, Molecular; D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity
chemical_list: D007477:Ions; D011506:Proteins; D012997:Solvents