title: Modeling permeation energetics in the KcsA potassium channel.
abstract: The thermodynamics of cation permeation through the KcsA K(+) channel selectivity filter is studied from the perspective of a physically transparent semimicroscopic model using Monte Carlo free energy integration. The computational approach chosen permits dissection of the separate contributions to ionic stabilization arising from different parts of the channel (selectivity filter carbonyls, single-file water, cavity water, reaction field of bulk water, inner helices, ionizable residues). All features play important roles; their relative significance varies with the ion's position in the filter. The cavity appears to act as an electrostatic buffer, shielding filter ions from structural changes in the inner pore. The model exhibits K(+) vs. Na(+) selectivity, and roughly isoenergetic profiles for K(+) and Rb(+), and discriminates against Cs(+), all in agreement with experimental data. It also indicates that Ba(2+) and Na(+) compete effectively with permeant ions at a site near the boundary between the filter and the cavity, in the vicinity of the barium blocker site.
authors.affiliation: Department of Chemistry, Brandeis University, Waltham, Massachusetts 02454-9110, USA.
authors.forename: S
authors.initials: S
authors.lastname: Garofoli
authors.forename: P C
authors.initials: PC
authors.lastname: Jordan
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D002462:Cell Membrane / Q000737:chemistry*; D002463:Cell Membrane Permeability; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D004735:Energy Transfer; D015640:Ion Channel Gating; D008954:Models, Biological; D008958:Models, Molecular; D008968:Molecular Conformation; D016062:Porosity; D015221:Potassium Channels / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D015221:Potassium Channels; C107790:prokaryotic potassium channel