title: Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics.
abstract: Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K(+) and Na(+) ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K(+) ions were found to display an average coordination number of 6.6 in the filter, and 6.2 in water. Na(+) ions displayed an average coordination number of 5.2 in the filter, and 5.0 in water. A comparison was made with the average coordination numbers obtained from using classical molecular dynamics (6.7 for K(+) in the filter, 6.6 for K(+) in water, 6.0 for Na(+) in the filter, and 5.2 for Na(+) in water). The observation that different coordination numbers were displayed by the ions in QM/MM simulations and in classical molecular dynamics is relevant to the discussion of selectivity in K-channels.
authors.affiliation: Laboratory of Computational Chemistry and Biochemistry, Swiss Federal Institute of Technology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. bucher.denis@gmail.com
authors.forename: Denis
authors.initials: D
authors.lastname: Bucher
authors.forename: Leonardo
authors.initials: L
authors.lastname: Guidoni
authors.forename: Paolo
authors.initials: P
authors.lastname: Carloni
authors.forename: Ursula
authors.initials: U
authors.lastname: Rothlisberger
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D015640:Ion Channel Gating / Q000502:physiology; D007477:Ions / Q000378:metabolism; D008956:Models, Chemical; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D016062:Porosity; D011188:Potassium / Q000378:metabolism*; D015221:Potassium Channels / Q000378:metabolism*; D012964:Sodium / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D007477:Ions; D015221:Potassium Channels; C107790:prokaryotic potassium channel; D012964:Sodium; D011188:Potassium