Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of Kþ and Naþ ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, Kþ ions were found to display an average coordination number of 6.6 in the filter, and 6.2 in water. Naþ 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 Kþ in the filter, 6.6 for Kþ in water, 6.0 for Naþ in the filter, and 5.2 for Naþ 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.
Coordination numbers of K+ and Na+ ions inside the selectivity filter of the KcsA potassium channel: Insights from first principles molecular dynamics
GUIDONI, Leonardo;
2010-01-01
Abstract
Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of Kþ and Naþ ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, Kþ ions were found to display an average coordination number of 6.6 in the filter, and 6.2 in water. Naþ 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 Kþ in the filter, 6.6 for Kþ in water, 6.0 for Naþ in the filter, and 5.2 for Naþ 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.Pubblicazioni consigliate
I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
