Fig. 5: Central cavity gate fluctuation.
a Pore radius profiles along the central axis of cryo-EM structure and during simulations of different constructs using HOLE program version 2.052,53. The deep-colored line represents the average value and the light-colored shading represents the standard deviation of 10,000 snapshots from five independent simulation runs. b Two representative simulation runs illustrating the relationship between the number of water molecules in the gate region, the distance between the two opposing gate residues (F389), and the number of ion permeation events. The distribution of the number of water molecules in the gate region and the distance between the two opposing gate residues (F389) are shown along the y-axis. c The distribution of the minimum distance between opposing F389 across different simulation setups. The relationship between the average number of water molecules in the gate region per 20 ns interval and the average distance between the two opposing gate residues (F389) during the same time interval, in total 225 data points from five independent simulation runs (the first 100 ns segment was considered as equilibration phases and discarded). K+ permeation simulations were performed at d –100 mV and e + 100 mV, respectively. The simulations were performed with the pore domain+VSD.
