Stability And Conductance Assessment Of A Putative Low-k+ Inactivated State Of The Kcsa Channel

Abstract

Potassium channels constitute a large family of proteins, notably involved in the regulation of the activity of excitable cells. The channels partly exert that function by varying their conductance through a mechanism known as C-type inactivation: Shortly after the activation of K+ channels, their selectivity filter stop conducting ions at a rate that depends 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. The molecular process underlying the C-type inactivation mechanism remains unexplained despite the accumulation of experimental evidences showing the key role played by the channels' selectivity filter and some neighboring residues.It's been recently shown that the prokaryotic KcsA channel undergoes C-type inactivation like its eukaryotic counterparts (Gao et al., PNAS, 102:17630 (2005)), establishing KcsA as a perfect prototypic model to study the structural basis of the inactivation mechanism. An X-ray structure of the KcsA channel obtained in presence of low K+ concentration (Zhou et al., Nature 414:43 (2001), pdb code 1K4D) has since then been postulated to correspond to the C-type inactivated state of the channel. While the structural analysis of this static conformation suggests that pore lining amide hydrogens would prevent the permeation of ions, uncertainties remain about its stability under physiological conditions and its ion occupancy state. These questions are of primary importance to better understand the relevance of this structure to the physiological regulation of ion permeation in K+ channels. Using molecular dynamics simulations and free energy calculations, we investigated on the stability, selectivity, and conductance of the selectivity filter of KcsA in this putative inactivated state.