Figure 2.

Activation gate opening and permeation. (A) Activation gate closure (WT; Sim. 2) and opening (G178R; Sim. 3) measured by the C_α–C_α diagonal distance at gate residues I177 and M181. Insets: Intracellular view of the TM pore with I177 residues indicated as spheres and the TM region in grey. (B) Movement of the inner TM helices illustrating the main activation gate conformational change with only two diagonally opposed subunits shown. (C) Pore opening viewed from the intracellular side with the same representations as in B; double-headed arrow indicates S174–I177 positional interchange. (D) Ion permeation events obtained under depolarizing voltages of different magnitude (Sims. 8–12). (E) Density profiles of ion (solid lines) and water (dashed lines) permeating across the SF (Sim. 7, black; Sim. 8, red; both at 310 mV) with a simulation snapshot of the ion-occupied SF (residues 144–148) and the rectification controller D173, located in the pore cavity, with two of the four D173 residues (de)protonated; ions are individually colored, and water molecules appear in red and white. (F) Position of the incoming ion vs. the centroid of the two SF-bound ions located above it (left), and position of the leaving ion vs. the centroid of the two SF-bound ions located below it (right). Color bar in units of log(ρ[x,y]); ρ[x,y] is the two-dimensional histogram of ion positions averaged over the entire simulation time of Sim. 7 and Sim. 8. Blue minima represent the four predominant three-ion and four-ion configurations observed during permeation that occurs by a knock-on mechanism. S0–S6 denote SF ion-binding sites, and the predominant permeation mechanism is summarized in the right panel. Formation of the knock-on intermediate S5[S3,S2],S0 is the rate limiting step of the permeation.