Inactivation and Voltage-Dependent Rectification Mechanisms in the KcsA Potassium Channel

Abstract

Potassium channels regulate ion permeation by varying their conductance notably through a mechanism known as C-type inactivation, which implies that shortly after activation, their selectivity filter stops conducting ions at rates that depend on various stimuli. This inactivation process plays a critical role in controlling the length and frequency of cardiac action potentials, as well as the firing patterns in neurons.It's been shown that the prokaryotic KcsA channel undergoes C-type inactivation like its eukaryotic counterparts (Gao et al., PNAS 102:17630 (2005)), suggesting KcsA as a prototypic model for structural studies of inactivation gating. The detailed microscopic process underlying C-type inactivation remains unexplained despite the accumulation of experimental evidences showing the key role played by the selectivity filter and some neighboring residues. In particular, the interactions between Asp80, Glu71 and Trp67, as well as the water molecules trapped in the P-loop of the channel, seem to be strongly linked to the stability of the filter and its ability to adopt a stable inactivated state (Cordero-Morales et al., Nat. Struct. & Mol. Biol. 14:1062 (2007)). Models of inactivation gating that were proposed on the basis of x-ray crystallography studies involve transitions between conducting states, containing two ions, and non conducting ones, containing a single ion (Zhou et al., Nature 414:23 (2001); Cuello et al., Nature 466:272 (2010)).Using molecular dynamic simulations and free energy calculations, we investigated the possible transitions between different ion occupancy states involving the conducting and putatively inactivated conformations of KcsA. A comparative study of key mutants showing different inactivation phenotypes allows us to propose a structural model describing the inactivation mechanism of KcsA, as well as the voltage dependent rectification observed in WT and some mutants.