Panel A shows a molecular surface representation of a protein with three colored subunits and a black membrane region. Black arrows indicate the distance along the ion conduction pore and distance from the center of the ion conduction pore. Panel B features a line graph showing the 2D PMF RMSD over window time in nanoseconds, with an inset displaying the 2D PMF RMSD for the last 5 nanoseconds in the window. Panel C includes a line graph with two traces: one for sampling entropy and another for sampling heterogeneity, both plotted against window time in nanoseconds. Panel D presents a heatmap of the full 2D PMF for cryo-EM ELIC5, with energy relative to bulk solution and a solid black line representing the channel radius. Panel E shows a molecular image of ELIC5 cryo-EM with two subunits highlighted in blue and red, indicating the locations of the apical pathway residues (R65 and K90) and the lateral pathway. Panel F provides molecular images of the acidic residues in the lateral pathway from the extracellular solution and the central vestibule. Panel G includes a line graph showing the minimum energy pathway and energy along the pathway for the apical and lateral pathways, with the distance along the minimum energy pathway normalized to the total length of the path. Panel H features molecular images of the apical pathway, highlighting the location of residues R65 and K90.
PMF for Na + in cryo-EM ELIC5. (A) Molecular image showing the two axes used in calculating the 2D PMF for Na+ translocation across cryo-EM ELIC5. (B and C) Representative plots of the 2D PMF RMSD (B), sampling entropy (C, gold trace), and sampling heterogeneity (C, orange trace) used to monitor convergence in each ABF window shown for one window. The inset in B shows the 2D PMF RMSD for the last 5 ns in the window. (D) The full 2D PMF for cryo-EM ELIC5 shown with the energy relative to bulk solution. The radius of the entire channel as calculated by HOLE is shown as a solid black line. (E) Molecular image of ELIC5 cryo-EM with two subunits highlighted in blue and red. The location of the apical pathway residues (R65 and K90) is shown as a dark purple box, and the lateral pathway as a light purple box. (F) The acidic residues in the lateral pathway are displayed from the extracellular solution (left) and the central vestibule (right). (G) The minimum energy pathway (right) and energy along the pathway (left) is shown for the apical (dark purple) and lateral (light purple) pathways. As the two paths have different absolute lengths, the independent axis displays the distance along the minimum energy pathway normalized to the total length of the path. (H) Molecular images of the apical pathway highlighting the location of residues R65 and K90.