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Figure 3. Free energy profiles from Umbrella Sampling of PDB:2QTS.(A) ASIC PDBs compared with voltage-gated Na+ channel NavAb (PDB:3RVY). Two opposing helices shown, with NavAb inverted for comparison. Selected leucine/isoleucine (black), serine/threonine (blue) and glutamate (red) side chains shown as spheres. (B) Snapshot of E18’ and D21’ creating multiple ion/carboxylate complex (left) and single ion free energy profiles (right) for Na+ and K+ in the lower pore of the presumed closed conformation PDB:2QTS (see Figure 2—figure supplement 1 for convergence). (C) Distribution of single and double ion occupancy in 2QTS. Double ion occupancy dominates, usually involving multiple side chains. In this case, states are defined by the radial distribution function g(r) for ion-ion distance (right), revealing: two ions in a tightly shared complex with multiple carboxylates (2 tight); a two ion complex involving neighboring carboxylates that do not share single ions (2 loose); and the remainder involving ion binding to distant groups on opposing subunits (2 disperse). Snapshots below illustrate each configuration.DOI: http://dx.doi.org/10.7554/eLife.24630.007 Image published in: Lynagh T et al. (2017) © 2017, Lynagh et al. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View

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