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

It usually requires too short a run to show the behavior of an ion channel, and also limits the number of atoms that can be included. Sometimes calculations on relatively small to medium size systems are useful (136) (137) (138) (139) , but in general we need to make the clusters large enough that the part we are most concerned with does not have very significant boundary effects. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder.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 SOME INTERESTING THINGS THAT WATER DOES: Proton transfer often involves water. We will show an example that does not involve water, but there are two unusual cases that may be relevant to our problem. First, it is possible to set up a system of guanidinium (thus, functionally arginine) plus a carboxylic acid, that incorporates two water molecules between the guanidinium and the acid, so as to form a ring. When the ring is complete, the energy drops sharply. On further study of the system, the behavior is most easily understandable as a resonance hybrid structure, as referred to briefly above (117) . The fact that there is a small resonance structure that could stabilize a more complex system suggests care must be taken in trying to understand a structure of protein that contains water. In a sense this is not a surprise; most proteins interact with water in one way or another.