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

, nor is charge transfer. Seemingly symmetric atoms also do not have the charge symmetry that is typically assumed, e.g., the amines (NH1 and NH2 in the pdb notation) that are part of the guanidinium ion; these effects are small on a percentage basis, but, leading to energy differences larger than k B T, would lead to differences in structure that cannot be taken into account in a strictly classical computation. Even including Drude polarizability (39) does not cure this problem. There is no way to compare the classical energy to the QM energy, as the Coulomb and the kinetic energy terms are computed on a different basis. There is further discussion below, in the section on Computational Methods, where the differences between classical and quantum calculations are also discussed.