Noncontact Dipole Effects on Channel Permeation. V. Computed Potentials for Fluorinated Gramicidin

Abstract

Experimental and theoretical calculations indicate that the dipole moment of the four Trp side chains in gramicidin A (gA) channels modify channel conductance through long-range electrostatic interactions. Electrostatic ion/side-chain interaction energies along the channel were computed with CHARMM using ab initio atom charges for native and 4-, 5-, or 6-fluorinated Trp side chains. The bulk water reaction to the polar side chains was included using the method of images as implemented by, and channel waters in idealized structures were included. Ion/Trp interaction energies were approximately -0.6 kcal/mol throughout the channel for all four of the native Trp pairs. Channel waters produced a modest reduction in the magnitude of interactions, essentially offsetting images representing the bulk water outside the channel. The effects of side-chain fluorination depended on ring position and, to a lesser extent, residue number. Compared with native Trp, 5-fluorination reduces the translocation barrier with minor effects on the exit barrier. In contrast, 6-fluorination primarily reduces exit barrier. 4-Fluorination produces a more complex double-well energy profile. Effects of measured side-chain movements resulting from fluorination or change in lipid bilayer were negligible whereas thermal side chain librations cause large effects, especially in the region of the ion-binding sites.

Noncontact Dipole Effects on Channel Permeation. VI. 5F- and 6F-Trp Gramicidin Channel Currents

“…Opposite or no effects are generally observed for 6-fluorination at position 9. These results are consistent with electrostatic predictions (Anderson et al, 2001) and the 3B2S fitted parameters, indicating that the relative translocation barrier, the difference in energy between the depth of the binding site well and the peak of the central barrier, is reduced for all 6F analogs except 6F-Trp 9 .…”

“…5F-and 6F-Trp Gramicidin Currents Fig. 10 displays the fluorination-induced perturbations of the parameters from the 3B2S fitting in comparison with the electrostatic predictions computed using CHARMM by Anderson et al (2001). The bars show the fluorinationinduced changes in barrier free energies taken from the coupling constants according to the following equations:…”

“…Based on the ab initio partial charges for the side chains (Cotten et al, 1999), Anderson et al (2001) recently computed the axial electrostatic potential energy of the side chains for native, 4F-, 5F-, and 6F-Trp in a gramicidin channel. The computations included corrections for water in the channel and bulk.…”

“…We then fit the data with the 3B2S rate theory model, constrained using the coupling technique developed by Thompson et al (2001). We focused on the fluorination-induced changes in rate constants, which we compare to the changes in electrostatic energy computed by Anderson et al (2001) under the logic that perturbations in the rate constants should reflect perturbations in the rates of the major steps according to the Boltzmann equation. It will be seen that this approach is successful for five of eight fluorinated analogs tested, but disagrees for three.…”

Numerical framework models of single proton conduction through Gramicidin

“…Very good agreement was obtained with previous calculations of the electrostatic interaction between the tryptophan indoles and cations in the pore (11). The permeation mechanism suggested by Figure 1C describes at most only a single excess proton in the pore.…”