Paper Citing NAMD - Abstract
Shen, Rong; Guo, Wanlin
Mechanism for Variable Selectivity and Conductance in Mutated NaK Channels
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:2887-2891, OCT 4 2012
Na+ conduction has been demonstrated in a few K+ channels and has been widely used to characterize the physiological selectivity and C-type inactivation in channels. By using molecular dynamics simulations and free-energy calculations, we found that K+ and Na+ have distinct preferable binding configurations in the conductive filter of two highly K+ selective channels, which are mutated from the nonselective NaK channel and can conduct Na+ upon removal of K+. Disruption of a conserved hydrogen bond interaction between residues in the filter and the pore helices can significantly decrease the free-energy differences and barriers between the K+ binding configurations, whereas it has little effect on the free-energy landscape for Na+. We propose that the enhancement of the fluctuation of the filter structure decreases the affinity and conducting barrier of K+ and therefore the ability of K+ to block Na+ currents, predominantly responsible for the reduced K+ selectivity.
