K+/Na+ selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations

Microscopic molecular dynamics free energy perturbation calculations of the K+/Na+ selectivity in the KcsA potassium channel, based on its experimenta l three-dimensional structure, are reported. The relative binding free ener gies for K+ and Na+ in the most relevant ion occupancy states of the four-s ite selectivity filter are calculated. The previously proposed mechanism fo r ion permeation through the KcsA channel is predicted, in agreement with a vailable experimental data, to have a significant selectivity for K+ over N a+. The calculations also show that the individual 'binding site' selectivi ties are generally not additive and the doubly loaded states of the filter thus display cooperative effects. The only site that is not K+ selective is that which is located at the entrance to the internal water cavity, sugges ting the possibility that internal Na+ could block outward currents. (C) 20 01 Elsevier Science B.V. All rights reserved.