Modelling van der Waals interaction between water molecules and biological channels

Abstract

We examine the van der Waals interactions between water molecules with both water channels, aquaporin-Z and glycerol channel GlpF. Here we model these problems using classical applied mathematics and obtain the potential energy for a water molecule interacting with the channels which we assume in both cases to have a flaired right cylindrical geometry. We propose a continuous model where all the atoms comprising the channels are assumed to be uniformly distributed within their volume. We model a water molecule as comprising two parts: firstly as a single point representing the location of the oxygen atom, and a spherical shell over which we assume a uniform distribution of the two hydrogen atoms. Our results indicate the spontaneous acceptance of water molecules into these channels.