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Coordination Numbers of K and Na Ions Inside the Selectivity Filter of the KcsA Potassium Channel: Insights from First Principles Molecular Dynamics |
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| Authors: | Denis Bucher Leonardo Guidoni Paolo Carloni Ursula Rothlisberger |
| Institution: | † Laboratory of Computational Chemistry and Biochemistry, Swiss Federal Institute of Technology, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland ‡ Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California § Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università degli Studi de L'Aquila, Italy ¶ International School for Advanced Studies, Trieste, Italy ‖ German Research School for Simulation Science, Jülich, Germany †† Rheinisch-Westfaelische Technische Hochschule Aachen, Aachen, Germany |
| 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. |
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