Modelling Water Behaviour in Hydrophobic Gates of Ion Channels

Abstract

Ion channels are a key class of membrane proteins as they enable ions and water to pass into and out of cells. Some of these ion channels possess a hydrophobic gate, which enables the channel to switch between wetted and de-wetted states without sterically occluding the channel. The transition between wetting and de-wetting can be determined as a function of both the radius and hydrophobicity of the channel lining. Molecular dynamics simulations are a powerful tool for exploring this parameter space. However, due to the complexity of modelling bulk water interactions and the translation of these to nano-confined environments, the level of theory chosen for modelling the water is an important consideration. We present a study of how different techniques for modelling water affect simulations of hydrophobic gating in selected ion channels.