Skip to main content
. Author manuscript; available in PMC: 2016 Jul 10.
Published in final edited form as: Biochim Biophys Acta. 2016 Feb 16;1858(7 Pt B):1722–1732. doi: 10.1016/j.bbamem.2016.02.019

Figure 1.

Figure 1

Schematic illustration of the configuration of the 3 ions along the axis of the selectivity filter of the KcsA channel that are included in the Potential of Mean Force (PMF) calculation. The figure shows the topmost and bottommost umbrella sampling window configurations. The central permeating ion, either Na+ or K+ (in yellow), is bracketed by two K+ ions (green). The sampling for the central ion covers a 16.5 Å range, going from −5.75 Å to 10.75 Å relative to the center of mass of the selectivity filter (the backbone of residues 75 to 78). This corresponds to the movement from the site S4 to the site S0. Intermediate windows were places on a 0.75 Å grid, with neighboring ions spaced between 3 Å and 9 Å apart, and the top and bottom ions not more than 15 Å apart.