Ionic interactions in multiply occupied channels

A significant number of physiologically important ion channels function via multi-ion mechanisms where repulsion between ions at slightly separated locations is believed to be critical for permeation. We apply the semi-microscopic Monte Carlo approach and analyse how multiple occupancy affects permeation energetics and ion-water-peptide correlations. We consider double occupancy in idealized models of two systems: gramicidin A and the KcsA K+ channel. We focus on the excess repulsion energy due to ion-water and ion-peptide correlations (repulsion energy adjusted for direct ion-ion interaction). Gramicidin, where multiple occupancy is marginally important functionally, is ideal for correlating structure and ion interactions. Pair occupancy is stabilized by interaction with bulk solvent, destabilized by interaction with both the channel water and, as binding sites are far apart, the peptide backbone. In the KcsA K+ channel, double occupancy is promoted by the uneven spacing and the large ion-water separations in the selectivity filter. The carbonyls forming the binding cavities are equally important for pair stabilization. Due to the binding pocket's design, net ionic repulsion is approximately 25-30% of what it would be in a gramicidin-like structure with the same interionic spacing.