The Role of Proton Transport in Gating Current in a Voltage Gated Ion Channel, as Shown by Quantum Calculations

Alisher M Kariev; Michael E Green

While not done for this purpose, this also helped show that the backbone is not inherently immobile in these calculations. (It also suggests that an Rïƒ C mutation, which leaves a volume of the order of 100 Ã… 3 , could be subject to collapse, so that the SCAM results must be evaluated with this in mind.) The 976 atom structure contained all the side chains that could interact with each other. There is no cavity, so no collapse, and we observe no vertical motion of the backbone of S4 either. The central region of the cluster in this case is far enough from the boundary that we can be reasonably confident that the changes calculated on transferring protons in the center are accurate. We have already discussed the fact that what we get is the energy minimum, which corresponds to 0 K. We noted this does have one advantage, in that it allows comparison with Xray structures that are determined at temperatures below the lowest phase transition of water, and are thus presumably not very different from the 0 K structures. Cryo EM structures are of course also determined at low temperature. (An alternative, starting from snapshots of MD simulations (124) , and then finding an energy minimum, seems to combine disadvantages of both methods.) By using a larger structure we minimize boundary issues. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It . https://doi.org/10.1101/371914 doi: bioRxiv preprint