Fig. 2

Structure of the KcsA channel and the MD-simulated ion trajectories observed at [K⁺] = 0.15 M. a The transmembrane pore domain structure of the KcsA channel (cyan ribbon) in a membrane (brown line). Residues 22–117 in two diagonal subunits are shown to illustrate the inside of the pore. K⁺ and Cl⁻ ions are denoted by green and violet spheres, respectively. Water molecules are shown with a space-filling model (the oxygen atoms are colored in dark red) in the SF, as a stick model in the NC, and as a blue line model in the bulk solution. b Trajectories of individual ions (varying colors) permeating through the pore (z axis) as a function of time (t). The black arrowheads denote SF-in events. The red arrowhead denotes spontaneous release. c Ion trajectories aligned to the SF-in event of I₀ (Δt = 0). The positions of the ions after relaxation are indicated by multi symbol. An ion (I₀) undergoing SF-in is shown in red and the preceding ions in blue (I₁) and green (I₂). Water molecules intercalated upon the SF-in of I₀ are shown in sky blue, and the preceding intercalated water molecules are shown light blue. d Snapshots of K⁺ and intercalated water molecules (cyan and white) as I₀ undergoes SF-in. Between zero and two water molecules (marked blue circles) were intercalated