Evolution of the open pore in unrestrained MD simulations. Characteristic frames from all-atom simulations of the relaxed resting (A) and open (B) states in a fully hydrated POPC bilayer in the presence of 0.2 M KCl. The coordinates for the resting state are taken from Anishkin et al. (2008). The protein is represented as solvent-accessible surface with areas designated as apolar (white), aliphatic lining of the gate (yellow), polar (green), negatively charged (red), and positively charged (blue). The Cl⁻ and K⁺ ions are shown as pink and cyan spheres, respectively. The hydrocarbon chains of lipids are shown as yellow wires. Panel C shows computed hydration energy profiles for the open pore lining before (red) and after (blue) 4-ns MD simulation of the open state. D and E show the reorientation of TM3s that led to the surface polarity increase illustrated in C: conserved leucines (L105, L109, L111, and L115) interact more tightly after a 4-ns simulation and brief symmetry annealing (E) as compared with the initial extrapolated model (D). The helices rotate clockwise, looking from the periplasm. Water-accessible surface inside the equilibrated open pore with two completely solvated ions (F).