Quantum Calculations Of A Large Section Of The Voltage Sensing Domain Of The Kv1.2 Channel Show That Proton Transfer, Not S4 Motion, Provides The Gating Current

Abstract

Quantum calculations on much of the voltage sensing domain (VSD) of the Kv1.2 potassium channel (pdb: 3Lut) have been carried out on a 904 atom subset of the VSD, plus 24 water molecules (total, 976 atoms). Those side chains that point away from the center of the VSD were truncated; in all calculations, S1,S2,S3 end atoms were fixed; in some calculations, S4 end atoms were also fixed, while in other calculations they were free. After optimization at Hartree-Fock level, single point calculations of energy were carried out using DFT (B3LYP/6-31G**), allowing accurate energies of different cases to be compared. Open conformations (i.e., zero or positive membrane potentials) are consistent with the known X-ray structure of the open state when the salt bridges in the VSD are not ionized (H+ on the acid), whether S4 end atoms were fixed or free (closer fixed than free). Based on these calculations, the backbone of the S4 segment, free or not, moves no more than 2.5 [A] upon switching from positive to negative membrane potential, and the movement is in the wrong direction for closing the channel. This leaves H+ motion as the principal component of gating current. Groups of 3-5 side chains are important for proton transport, based on the calculations. Our calculations point to a pair of steps in which a proton transfers from a tyrosine, Y266, through arginine (R300), to a glutamate (E183); this would account for approximately 20-25% of the gating charge. The calculated charges on each arginine and glutamate are appreciably less than one. Groupings of five amino acids appear to exchange a proton; the group is bounded by the conserved aromatic F233. Dipole rotations appear to also contribute. Alternate interpretations of experiments usually understood in terms of the standard model are shown to be plausible.