Panel A shows a line graph. The x-axis represents the distance along the lateral fenestration in angstroms, and the y-axis represents the fenestration radius in angstroms. The solid lines indicate the mean pore radius, and the transparent areas represent the standard deviation. A horizontal dashed line shows the radius of an unsolvated sodium ion for reference. Panel B presents a line graph of the radius of the residues at two levels of the apical pathway energetic barrier, R65 and K90, over the last 500 nanoseconds of unrestrained simulation. The x-axis represents the simulation time in microseconds, and the y-axis represents the axial opening radius in angstroms. Vertical dashed lines indicate the time points used for the MD refined structures in the computational electrophysiology simulations. Panel C features a bar graph showing the number of conducted sodium ions traversing the lateral (solid bars) or apical (hashed bars) pathways for each applied transmembrane potential from computational electrophysiology simulations of cryo-EM ELIC5. The x-axis represents the applied potential in millivolts, and the y-axis represents the number of sodium ion permeation events. Panel D and E display similar bar graphs for ELIC5 MD refined Structure 1 and Structure 2, respectively. Panel F shows a line graph of the number density of sodium ions along the channel for cryo-EM ELIC5 at different transmembrane potentials. The x-axis represents the distance along the ion conduction pore from L9 to L240 in angstroms, and the y-axis represents the relative sodium ion number density. The solid traces indicate the mean number density, and the shaded areas represent the standard deviation. Panel G provides a close-up of the apical barrier region sodium ion number density. Panel H presents a stacked bar plot showing the number of conducted sodium ions crossing each lateral fenestration for all applied transmembrane potentials for ELIC5 MD refined structure 1 and structure 2. The x-axis represents the intersubunit number, and the y-axis represents the number of sodium ion permeation events.
Na + conduction along the lateral and apical pathways. (A) HOLE radius of the lateral fenestration over the last 500 ns of unrestrained simulation of ELIC5 for all four simulation replicates (mean pore radius-solid line, standard deviation–transparent area), and the initial HOLE radius of ELIC5 cryo-EM (PDB 8TWV). The radius of an unsolvated Na+ ion is shown as a horizontal dashed line for reference. (B) The radius of the residues at the two levels of the apical pathway energetic barrier, R65 (dark blue) and K90 (light blue) over the last 500 ns of unrestrained simulation. The time points used for the MD refined structures in the computational electrophysiology simulations (structure 1 and structure 2) are noted as vertical dashed lines. (C–E) Plots of the number of conducted Na+ ions traversing the lateral (solid bars) or apical (hashed bars) pathways is shown for each applied transmembrane potential from computational electrophysiology simulations of cryo-EM ELIC5 (C), ELIC5 MD refined structure 1 (D), and ELIC5 MD refined structure 2 (E). (F) Plot of the number density of Na+ ions along the channel is shown for cryo-EM ELIC5 at −250 mV (red), 0 mV (light blue), and +250 mV (blue) with the mean number density (n = 3) shown as the solid trace and the standard deviation shown as the shaded area. (G) Number density is shown relative to bulk solution. A close-up of the apical barrier region Na+ number density is shown in G. (H) A stacked bar plot showing the number of conducted Na+ ions that cross each lateral fenestration for all applied transmembrane potentials is shown for ELIC5 MD refined structure 1 (gray) and structure 2 (black).