Panel A shows a line graph plotting the root mean square deviation (RMSD) of the transmembrane domain (TMD) and M2 helices over time. The x-axis represents time in microseconds, and the y-axis represents RMSD in angstroms. The blue line represents the TMD, and the red line represents the M2 helices. Panel B displays a molecular image of the protein segments used for the RMSD measurement, highlighting the M1, M2, M3, and M4 helices. Panel C shows a snapshot image of the ELIC5 protein from the simulation, depicting a hydrated pore with water molecules and sodium ions traversing the pore. The M2 helices are shown in gray, and POPC lipids are displayed in the background. Panel D presents a line graph showing the ion conduction pore radius of ELIC5 over the last 500 nanoseconds of the simulation. The x-axis represents the distance along the pore from L9/L240 in angstroms, and the y-axis represents the pore radius in angstroms. The graph includes data from four simulation replicates, with the mean pore radius shown as a solid line and the standard deviation as a transparent area. The positions of the hydrophobic gate residues (L9 and F16) and the selectivity filter (E-1) are marked, along with the ionic radius of an unsolvated sodium ion. Panel E shows a line graph of the cumulative number of sodium ions traversing the ion conduction pore over the entire length of the simulation. The x-axis represents time in microseconds, and the y-axis represents the number of permeation events. Data from four simulation replicates are shown in different colors. Panel F displays a line graph of the total number of water molecules in the ion conduction pore over the entire length of the simulation. The x-axis represents time in microseconds, and the y-axis represents the number of water molecules. Data from four simulation replicates are shown in different colors.
Cryo-EM ELIC5 is stable on the microsecond timescale. (A and B) Plot of the RMSD of the TMD (blue) and M2 (red) helices during unrestrained MD (A) with a molecular image (B) displaying the protein segments used for the measurement. (C) A snapshot image of ELIC5 from the unrestrained simulation showing a hydrated pore (red/white water molecules) and Na+ ions traversing the pore (gold). Only the M2 helices of ELIC5 (gray surface) are shown for clarity. POPC lipids are shown as multicolored models in the background. (D) The ion conduction pore radius of ELIC5 over the last 500 ns of unrestrained simulation as measured with HOLE is shown for all four simulation replicates (mean pore radius-solid line, standard deviation–transparent area) along with the starting ion conduction pore radius (black) measured from the cryo-EM structure (PDB 8TWV). The position of the hydrophobic gate residues (L9′ and F16′) as well as the selectivity filter (E−1′) is marked. The ionic radius of an unsolvated Na+ ion is shown as a dashed black line. (E and F) The cumulative number of Na+ ions traversing the ion conduction pore (E) as well as the total number of waters in the ion conduction pore (F) is shown for the entire length of the unrestrained simulation. No transmembrane potential was applied for these unrestrained simulations.