Paper Citing NAMD - Abstract
Mahdavi, Somayeh; Kuyucak, Serdar
Mechanism of Ion Permeation in Mammalian Voltage-Gated Sodium Channels
PLOS ONE, 10 Art. No. e0133000, AUG 14 2015
Recent determination of the crystal structures of bacterial voltage-gated sodium (Na-V) channels have raised hopes that modeling of the mammalian counterparts could soon be achieved. However, there are substantial differences between the pore domains of the bacterial and mammalian Na-V channels, which necessitates careful validation of mammalian homology models constructed from the bacterial Na-V structures. Such a validated homology model for the Na(V)1.4 channel was constructed recently using the extensive mutagenesis data available for binding of mu-conotoxins. Here we use this Na(V)1.4 model to study the ion permeation mechanism in mammalian Na-V channels. Linking of the DEKA residues in the selectivity filter with residues in the neighboring domains is found to be important for keeping the permeation pathway open. Molecular dynamics simulations and potential of mean force calculations reveal that there is a binding site for a Na+ ion just inside the DEKA locus, and 1-2 Na+ ions can occupy the vestibule near the EEDD ring. These sites are separated by a low free energy barrier, suggesting that inward conduction occurs when a Na+ ion in the vestibule goes over the free energy barrier and pushes the Na+ ion in the filter to the intracellular cavity, consistent with the classical knock-on mechanism. The Na(V)1.4 model also provides a good description of the observed Na+/K+ selectivity.
