title: Molecular dynamics study of the KcsA potassium channel.
abstract: The structural, dynamical, and thermodynamic properties of a model potassium channel are studied using molecular dynamics simulations. We use the recently unveiled protein structure for the KcsA potassium channel from Streptomyces lividans. Total and free energy profiles of potassium and sodium ions reveal a considerable preference for the larger potassium ions. The selectivity of the channel arises from its ability to completely solvate the potassium ions, but not the smaller sodium ions. Self-diffusion of water within the narrow selectivity filter is found to be reduced by an order of magnitude from bulk levels, whereas the wider hydrophobic section of the pore maintains near-bulk self-diffusion. Simulations examining multiple ion configurations suggest a two-ion channel. Ion diffusion is found to be reduced to approximately 1/3 of bulk diffusion within the selectivity filter. The reduced ion mobility does not hinder the passage of ions, as permeation appears to be driven by Coulomb repulsion within this multiple ion channel.
authors.affiliation: Protein Dynamics Unit, Department of Chemistry, Research School of Physical Sciences, Australian National University, Canberra, ACT 0200, Australia. toby.allen@anu.edu.au
authors.forename: T W
authors.initials: TW
authors.lastname: Allen
authors.forename: S
authors.initials: S
authors.lastname: Kuyucak
authors.forename: S H
authors.initials: SH
authors.lastname: Chung
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D004058:Diffusion; D004560:Electricity; D056004:Molecular Dynamics Simulation; D024642:Potassium Channels, Voltage-Gated / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D012399:Rotation; D048170:Streptomyces lividans; D013816:Thermodynamics; D014867:Water / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; C504448:KcsA protein, Streptomyces coelicolor; D024642:Potassium Channels, Voltage-Gated; D014867:Water