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. 2015 Jun 22;112(27):E3619–E3628. doi: 10.1073/pnas.1503334112

Fig. 6.

Fig. 6.

Free energies of the Na+ and Cs+ systems. (A, B) Projection of the free energy (kcal/mol) as a function of the distances of the ions from the center of the mass of the heavy atom of the four Gly65 residues using only the z direction for the Na+ (A) and Cs+ (B) systems. (Lower) Representative structures of the minima: the selectivity filter is shown in cyan sticks and Glu66 in green sticks, whereas the ions are shown as yellow (Na+) or green (Cs+) spheres. (C) The transition state between the two free energy minima in the Cs+ system is indicated by a white cross in B. Pro68 is shown in blue sticks. This has been identified by a cluster analysis of structures sampled by the BE simulations with respect to the two CVs on which the free energy is projected, and selecting the structure corresponding to a saddle point. Glu66 residues are shown in green sticks with their oxygens in red. For reference, the structure of Pro68 corresponding to the lower-left free energy minimum is shown as orange spheres centered on each nonhydrogen heavy atom, whose radius is equal to their fluctuation in the minimum.