Paper Citing NAMD - Abstract
Qiu, Hu; Shen, Rong; Guo, Wanlin
Ion solvation and structural stability in a sodium channel investigated by molecular dynamics calculations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:2529-2535, NOV 2012
The stability and ion binding properties of the homo-tetrameric pore domain of a prokaryotic, voltage-gated sodium channel are studied by extensive all-atom molecular dynamics simulations, with the channel protein being embedded in a fully hydrated lipid bilayer. It is found that Na+ ion presents in a mostly hydrated state inside the wide pore of the selectivity filter of the sodium channel, in sharp contrast to the nearly fully dehydrated state for K+ ions in potassium channels. Our results also indicate that Na+ ions make contact with only one or two out of the four polypeptide chains forming the selectivity filter, and surprisingly, the selectivity filter exhibits robust stability for various initial ion configurations even in the absence of ions. These findings are quite different from those in potassium channels. Furthermore, an electric field above 0.5 V/nm is suggested to be able to induce Na+ permeation through the selectivity filter. (C) 2012 Elsevier B.V. All rights reserved.
