A Universal Molecular Mechanism for C-type Inactivation in Potassium Channels

Abstract

C-type inactivation of K+ channels is an elusive molecular process that is thought to involve a subtle conformational change at the level of the selectivity filter. C-type inactivation is also of great physiological significance, as it affects the firing patterns of neurons in the central nervous system, and the repolarization of cardiac cells in the heart. In the present study, extended molecular dynamics simulation of the hERG channel with an open inner gate converged toward a stable constricted conformation for the selectivity filter. This conformation displays both similarities and differences with the known constricted conformation observed in X-ray structures of the KcsA channel. The constricted hERG filter involves a considerable reorientation of phenylalanine at position 627 along the selectivity filter to dock into the binding pocket occupied by the inactivating water molecules in the constricted KcsA structure. This observation supports the notion that constriction of the filter is the molecular basis of inactivation, but with alternative structural factors stabilizing the conformation. Additional MD simulations and free energy calculations carried out on the KcsA channel show that the filter can remain conductive as long as the intracellular gate is not fully open, but rapidly transitions to a constricted non-conductive conformation on a microsecond timescale once the inner gate is fully open. The short microsecond lifetime of the conductive filter with a fully open gate, cannot explain the relatively long periods of sustained ion conduction observed experimentally, suggesting that the conduction period must predominantly correspond to long-lived states of the channel with a partially open activation gate. In summary, C-type inactivation is linked to a conductive-to-constricted transition of the selectivity filter that is allosterically driven by the slow opening of the intracellular gate.