Fig. 2: Molecular dynamics simulations indicate that K⁺ passes through the Tyr132 collar in a partially hydrated state.

Wild-type panels are shown in a, c and e, and a disulfide-linked mutant in b, d and f. a The potential of mean force along the axis of the wild-type structure is shown as a function of the distance between a K⁺ cavity ion ‘pulled’ along the conduction pathway (z axis) and the center of mass of the four Thr96 side chains (the global reaction coordinate). SEM are depicted as vertical gray bars and represents n = 200 bootstraps. The Tyr132 side chain position from Cβ (~20 Å) to OH (~25 Å) is indicated by dotted lines. b A comparable plot for disulfide-linked S129C-F135C. c Normalized histograms enumerate the number of oxygen atoms coordinating K⁺ as a function of distance from Thr96. Data are accumulated from umbrella sampling simulations of wild-type KirBac3.1. Each bin represents the number of oxygen atoms within 3.0 Å of K⁺, expressed as a percentage. d Histograms for disulfide-linked S129C-F135C. e Potential of mean force (PMF) for the wild-type channel is depicted as a function of the distance along the molecular axis from Thr96 and the number of coordinating ligands per ion. f PMF for disulfide-linked S129C-F135C. Energy units are kJ mol⁻¹. g Selected structures from simulations revealing K⁺ ions in a partially dehydrated state as they pass Tyr132. Potassium ions are represented as green spheres and water depicted in red and white.