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Review
. 2011 May;137(5):415-26.
doi: 10.1085/jgp.201010577.

Ion selectivity in channels and transporters

Benoît Roux  1 , Simon Bernèche, Bernhard Egwolf, Bogdan Lev, Sergei Y Noskov, Christopher N Rowley, Haibo Yu
Affiliations
Review

Ion selectivity in channels and transporters

Benoît Roux et al. J Gen Physiol. 2011 May.
No abstract available

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Figures

Figure 1.
Figure 1.
Reduced model of the S2 site in the selectivity filter of the KcsA channel used by Yu et al. (2010b). (A) The full-length KcsA channel is shown with its four subunits. (B) The selectivity filter is represented with three K+ ions occupying the sites S0, S2, and S4. (C) The reduced model of the site S2 based on four diglycines is shown. This is adapted from Yu et al. (2010b).
Figure 2.
Figure 2.
Summary of the main computational results for the entry of K+ and Na+ in the selectivity filter of the KcsA channel from the extracellular side (Z > 12 Å) in the presence of two other K+ ions in the pore in a K+/K+/K+ or a Na+/K+/K+ configuration. (A) The PMFs for the entry of K+ and Na+ in the selectivity filter (the thin red line is the original PMF for Na+ before it was shifted by 0.7 Å along Z to match the wells and barriers of the PMF for K+). (B) Coordination numbers for the ion entering the selectivity filter. The average numbers of water, carbonyl, and total oxygen atoms closer than 3.2 Å from an entering K+ or 2.8 Å for the entering Na+ are shown. The number of coordinating water molecules decreases as the ion moves from the bulk phase into the narrow selectivity filter for Z < 7 Å. However, the total coordination number displays only small variations: over the entire entry process, the average coordination number of K+ increases slightly from 6 to 7, whereas that of Na+ remains constant around 5.5. This is adapted from Egwolf and Roux (2010).
Figure 3.
Figure 3.
Selectivity in reduced models in which the optimal geometry is adapted to best-fit K+ or Na+ (a binding site is K+ selective when ΔΔGNa,K is positive and Na+ selective when it is negative). The curves with solid lines correspond to realistic models of KcsA and LeuT, and the curves with dashed lines correspond to putative KcsA and LeuT sites stabilizing an optimal geometry adapted by energy minimization to best-fit Na+ or K+, respectively. Except for the site Na2 of LeuT, the onset of selectivity is established only for very large values of the architectural rigidity λg, indicating that a fairly stiff geometry is required to counterbalance the inherent trend that is already observed in the confined microdroplet limit (λg = 0) with loosely restricted ligands. This is adapted from Yu et al. (2010b).
Figure 4.
Figure 4.
Average solvation structure of K+ in liquid water (the radial distribution function g(r) of the ion–oxygen pair) at 298 K. Results are shown for the non-polarizable TIP3P/CHARMM force field and Drude polarizable force field (SWM4-NDP water model; Lamoureux et al., 2006) as well as two ab initio CPMD models. CPMD (version 3.13.3) simulations were performed using a cubic periodic cell with a length of 12.41 Å containing 64 water molecules and one K+ ion. The electronic structure was calculated with the BLYP functional (Becke, 1988; Lee et al., 1988), Troullier and Martins pseudopotentials (Troullier and Martins, 1991), and a plane-wave cutoff of 80 Ry. Also included are CPMD results with the BLYP function with an empirical correction (+D) for van der Waals dispersion (Grimme, 2006). CPMD results were generated by a 20-ps equilibration followed by a 30-ps trajectory for analysis, using a time step of 0.12 fs. Each CPMD simulation was initiated from an equilibrated Drude force field simulation, as described by Whitfield et al. (2007). The multiple gray lines for the neutron scattering correspond to experiments on solutions of different potassium-halide salts (Soper and Weckström, 2006).
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References

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