Fig. 2
From: In silico analysis of sodium ion permeation mechanisms in transient receptor potential vanilloid 1
Sodium ion dynamics in the channel pore during permeation events. (a) The channel pore region is shown as a tan-colored ribbon diagram. Areas of relatively high sodium ion density (green) were observed near the polar residues located at the site of channel pore narrowing. The threshold for plotting the density was set to 0.005 Å−3. Three binding sites (A, B and C) were defined based on the areas of relatively high sodium ion density. The regions corresponding to the SF and Gate are shown as gray ovals. (b) The upper panel shows the positions of the permeated sodium ions along the z-axis of wild-type TRPV1 in run 1 of the MD simulation. The section from 200 to 280 ns (red bar) is enlarged in the lower panel.
