The importance of water molecules in ion channel simulations

Crozier et al (2001 Biophys. J. 81 3077) have simulated an electrically neutral but polar model channel under an applied field and found that there was a current of positive Na+ ions but there was no current of negative Cl- ions unless the concentration was high or a very large field was applied. They suggested that this asymmetry in an electrically symmetric model was not due to differences in ion size but was due to the asymmetry of the water molecules, that results in frustrated orientations of the solvation water molecules near the Cl- ions in the confined geometry of the channel. This suggestion is tested by two simulations that are reported here. In the first simulation, we repeat the Crozier et al simulations but with the ion sizes reversed, with the cation having the Cl ion diameter and the anion having the Na ion diameter. As before, it is the cations that pass through the channel. The second simulation is a Langevin dynamics simulation for the Crozier et al channel but without explicit water molecules. In this second simulation, both Na+ and Cl- ions pass through the channel with roughly equal currents. Both simulations confirm the important role of water in channel simulations