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. 2009 May;133(5):497–509. doi: 10.1085/jgp.200910211

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© 2009 Boda et al.

This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.jgp.org/misc/terms.shtml). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 3.0 Unported license, as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).

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Figure 1. — Geometry of the model. (A) Axial cross section through the central region of the cylindrical simulation cell containing the pore. The selectivity filter is the central pore region (R = 3.5 Å, L = 10 Å) confining the oxygen ions of the EEEE locus. The dielectric coefficients are ϵ_w = 80 (aqueous regions, light gray) and ϵ_p = 10 (protein and membrane regions, white and dark gray). (B and C) Spatial views of the surface grid used in discretizing the dielectric interface at the pore wall, and a snapshot of the eight structural oxygen anions (red) and two cations dwelling in the pore (green, Ca²⁺; blue, Na⁺). Ions are represented as charged hard spheres with crystal radii (in Å: Ca²⁺ 0.99; Ba²⁺ 1.35; Li⁺ 0.6; Na⁺ 0.95; K⁺ 1.33; Cl⁻ 1.81; O^1/2− 1.4).