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. 2005 Jun 10;89(3):1744–1759. doi: 10.1529/biophysj.104.058206

FIGURE 7.

FIGURE 7

(a) Simulation snapshots of the key part of GlpF taken from ion transfer simulation where the wire initially was deprotonated in the periplasmic lumen. For clarity only QM water molecules within the single file are displayed. The R206/N68/N203 side chains with their polar Hs, the exposed carbonyl groups of residues 65–66 and 199–201, are shown in licorice and CPK representations, respectively. Nonexposed carbonyl groups of residues L67 and M202, engaged in two hydrogen bonds to N203 and N68, respectively, are displayed along with the hydrogen bonds. The M3 and M7 half-helices are shown as solid cylinders/purple ribbons. (b) OH− trajectory and relative distributions of OH− along the channel axis. Trajectories of the water molecules explicitly involved in the ion transfer appear as gray lines for reference along with the center-of-mass trajectory of the N68/N203 side chains. (c) Schematic representation of a fourfold coordinated hydroxide ion trapped at the channel center between the N68/N203 side chains of the NPA motifs. (d) Corresponding electron density map calculated from the simulations and represented by the electron localizing function at contour level η = 0.9 (66).