The Solvent-Excluding Surface as a descriptor of ionic channels: Gramicidin-A

Abstract

We have set out a methodology for checking the performance of the methods used to compute the Solvent-Excluding Surface. The method consists of computing the area of the Solvent-Excluding Surface of a model of channel, with a fixed pore size, for several values of the solvent radius. The graphical representation of the value of the area versus the radius of the solvent sphere shows a sharp change just at the radius of the pore. With this model we may analyze the ability of each method to describe small changes of the surface. We made the study with GEPOL93, older versions of GEPOL and MSDOT. The study is applied to a natural protein channel, as is Gramicidin-A, showing that this type of analysis may be helpful to characterize a channel. We conclude by showing the different behavior of the Solvent-Excluding Surface and the Solvent-Accessible Surface when the solvent radius is changed.