Jl. Pascualahuir et al., THE SOLVENT-EXCLUDING SURFACE AS A DESCRIPTOR OF IONIC CHANNELS - GRAMICIDIN-A, Journal of molecular structure. Theochem, 426, 1998, pp. 331-338
We have set out a methodology for checking the performance of the meth
ods 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 rad
ius. The graphical representation of the value of the area versus the
radius of the solvent sphere shows a sharp change just at the radius o
f 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 GEPOL
93, older versions of GEPOL and MSDOT. The study is applied to a natur
al protein channel, as is Gramicidin-A, showing that this type of anal
ysis may be helpful to characterize a channel. We conclude by showing
the different behavior of the Solvent-Excluding Surface and the Solven
t-Accessible Surface when the solvent radius is changed. (C) 1998 Else
vier Science B.V.