Panel A shows a schematic comparison of two protein models. The left schematic represents Cryo-EM ELIC5 with occluded lateral fenestrations and an apical opening. The extracellular domain (ECD) and transmembrane domain (TMD) are indicated on the left. An arrow labeled unbiased MD simulation points to the right schematic representing MD refined ELIC5, which shows open lateral fenestrations. A dashed pathway with a red cross on the left and a green check mark on the right illustrates the movement of a sodium ion toward the channel. Panel B shows a molecular surface representation of the protein embedded in a membrane. Different subunits are displayed in distinct colors, and selected residues are labeled R65, K90, D113, E30, and D155. The membrane is shown as a gray and red molecular layer surrounding the transmembrane region.
The lateral fenestration of ELIC. (A) A cartoon depicting ELIC5 with each subunit colored differently. The cryo-EM ELIC5 structure (left) shows tightly packed ECD intersubunit spaces and a positively charged apical opening that do not allow Na+ ions to be conducted from the extracellular solution through the channel. Following unbiased MD simulation of the cryo-EM ELIC5 structure, the ECD intersubunit spaces expand, revealing a lateral fenestration that is now able to conduct Na+ ions from the extracellular solution through the channel. The apical opening is positively charged, preventing conduction along this pathway. (B) A representative molecular image from the computational electrophysiology simulations showing the trajectory of a single Na+ ion (green ball, position recorded every 0.2 ns) traversing from the extracellular solution through the lateral fenestration to reach the ion conduction pore and finally exit the channel to the intracellular solution. Coloring of ELIC subunits is the same as in A with the red and green subunits omitted for clarity. A selection of POPC lipids surrounding the channel is shown as multicolored species. Residues mutated in this study (from Fig. 7, namely E30, R65, K90, D113, and D155) are shown demonstrating their positions in the apical or lateral pathways.