On the selective ion binding hypothesis for potassium channels

The mechanism by which K+ channels select for K+ over Na+ ions has been debated for the better part of a century. The prevailing view is that K+ channels contain highly conserved sites that selectively bind K+ over Na+ ions through optimal coordination. We demonstrate that a series of alternating sites within the KcsA channel selectivity filter exists, which are thermodynamically selective for either K+ (cage made from two planes of oxygen atoms) or Na+ ions (a single plane of four oxygen atoms). By combining Bennett free energy perturbation calculations with umbrella sampling, we show that when K+ and Na+ are both permitted to move into their preferred positions, the thermodynamic preference for K+ over Na+ is significantly reduced throughout the entire selectivity filter. We offer a rationale for experimental measures of thermodynamic preference for K+ over Na+ from Ba2+ blocking data, by demonstrating that the presence of Ba2+ ions exaggerates K+ over Na+ thermodynamic stability due to the different binding locations of these ions. These studies reveal that K+ channel selectivity may not be associated with the thermodynamics of ions in crystallographic K+ binding sites, but requires consideration of the kinetic barriers associated with the different multi-ion permeation mechanisms.