This is the crystal structure used as the initial conformation in MD simulations.

The cross-subunit distance (shown in parentheses) between the Cα atoms of Thr112 of diagonally opposed monomer was used as an indicator for the opening degree of the inner gate in the initial conformation.

To produce an open-conductive model from the 3F7V structure, which displays a constricted filter, the 2.0-Å resolution x-ray structure 1K4C was used as a template, and the filter was aligned to the channel using the backbone atoms of residues 65–74 and 80–84. The backbone atoms of the filter residues 74–80 have been restrained to maintain the conductive conformation in the initial phase of MD simulations. Video 1 shows the conformational transition in Traj-1 (0–800 ns).

An alternative open-conductive model based on the open-conductive crystal structure 5VK6 for mutant E71A. In the initial conformation of this simulation, residue 71 was mutated back to Glu as the WT. In addition, the original disulfide bonds in the crystal structure were removed by mutating all of the relevant residues back to WT.

These simulations were performed to test the permeability of partially opening inner gate. To collect enough sample within limited time, the ion concentration is higher than other simulations, and these are the only two trajectories with external electric field (300 mV). In addition, the initial conformations of Traj-12 and Traj-13 were snapshots, respectively, from Traj-6 and Traj-1, and the inner gate was restrained as 17.5 Å and 23 Å through the whole trajectory.