Figure 3.

Na⁺ binding and selectivity in the Na1 site. (A) PMF profiles for Na⁺ moving from the Na1 site to the extracellular side. The profiles are shown for the occluded state with bound substrate (red), Na⁺-only 2A65-like (blue), and 3F3A-like (magenta) frames. (B) Na⁺/K⁺ and Na⁺/Li⁺ selectivity. The selectivities for the ion in the Na1 site of the occluded state of LeuT with substrate and both ions bound (occluded (Occ.) data are from Caplan et al. (7)) and eight frames (F1–F8) selected from the MD1 trajectory (see text). By definition, positive values of ΔΔG_Na⁺_→X⁺ (where X⁺ represents K⁺ or Li⁺) indicate that the conformation is selective for Na⁺ over X⁺. Thus the blue region is Na⁺ selective, the gray region corresponds to an ambiguous selectivity between Na⁺ and ion X⁺, and the green region corresponds to X⁺ selective sites. The SDs of ion selectivity are plotted as error bars.