18] Computation of energy profiles in the gramicidin A channel

Abstract

Publisher Summary This chapter summarizes the principles of the method used for the establishment of energy profiles and its application to the Gramicidin A (GA) channel. GA is the best characterized prototype of an ion-transmembrane channel, providing an ideal model for understanding, at the microscopic level, the mechanisms involved in channel transport. The basis of the computations is a refined additive procedure for the fast calculation of intermolecular interaction energies among molecular systems, the size of which excludes the direct utilization of standard quantum mechanical methods apt to yield accurate results for studying interactions involving small ligands. This treatment utilizes an expression of the energy of interaction consisting of a sum of terms representing its various parts. These parts include electrostatic, polarization, repulsion, dispersion, and charge transfer components, the parameters of which are calibrated to reproduce the results of accurate ab initio calculations on small ligands, calculations themselves tested on experimental enthalpy measurements. The method is utilized to calculate the energy profiles for the alkali ions, Na + , K + , and Cs + , in the GA channel.