Author: Alisher M Kariev; Michael E Green
Title: The Role of Proton Transport in Gating Current in a Voltage Gated Ion Channel, as Shown by Quantum Calculations Document date: 2018_7_19
ID: cyxdy7hg_39
Snippet: Both MD and QM calculations can allow exchanges of hydrogen bonds, but only QM can allow a proton to switch the atom to which it is covalently bonded, when this provides a lower energy. There are disadvantages as well for QM calculations. To begin with, there are no dynamics. Second, the number of atoms is limited; until recently, only a small section of the channel could be calculated, but as computers become more powerful, the section that can .....
Document: Both MD and QM calculations can allow exchanges of hydrogen bonds, but only QM can allow a proton to switch the atom to which it is covalently bonded, when this provides a lower energy. There are disadvantages as well for QM calculations. To begin with, there are no dynamics. Second, the number of atoms is limited; until recently, only a small section of the channel could be calculated, but as computers become more powerful, the section that can be calculated is, as of 2018, in the neighborhood of 1000 atoms with a high performance cluster, and a fair amount of patience. This is enough that the central The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 section of the calculation will be relatively unaffected by boundary issues, which are important in small sections. QM also produces static local energy minima, corresponding to 0 K structures; one does not get a global minimum. These structures are relevant however; the most common experimental method of getting an ion channel structure has been X-ray diffraction, which is done at temperatures below 220 K, the lowest temperature phase transition for water. The X-ray structures should therefore essentially be the same as those at 0 K. Since the X-ray structures have proven to be essentially correct, the QM structures should be also. One can test for which local minima are correct, as a function of voltage, the relevant parameter in gating, by doing multiple optimizations, starting from different initial configurations, getting multiple local minima, which should include all that are relevant. For example, one may start with different states of ionization of the acids and bases (i.e., proton positions). If there is a local minimum so that the proton does not shift, the energy of that local minimum can be compared with the local minimum found in which a proton does shift. In other words, with other ionization states of the acids and bases. If all the relevant structures are determined, the lowest energy can be found for each of several voltages. Although this is time consuming, it is not so much so as to be impractical, as computers have become sufficiently powerful (134) .
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