Unraveling of a Strongly Correlated Dynamical Network of Residues Controlling the Permeation of Potassium in KcsA Ion Channel

Abstract

The complicated patterns of the single-channel currents in potassium ion channel KcsA are governed by the structural variability of the selectivity filter. A comparative analysis of the dynamics of the wild type KcsA channel and several of its mutants showing different conducting patterns was performed. A strongly correlated dynamical network of interacting residues is found to play a key role in regulating the state of the wild type channel. The network is centered on the aspartate D80 which plays the role of a hub by strong interacting via hydrogen bonds with residues E71, R64, R89, and W67. Residue D80 also affects the selectivity filter via its backbones. This network further compromises ions and water molecules located inside the channel that results in the mutual influence: the permeation depends on the configuration of residues in the network, and the dynamics of network’s residues depends on locations of ions and water molecules inside the selectivity filter. Some features of the network provide a further understanding of experimental results describing the KcsA activity. In particular, the necessity of anionic lipids to be present for functioning the channel is explained by the interaction between the lipids and the arginine residues R64 and R89 that prevents destabilizing the structure of the selectivity filter.

Anionic Phospholipids Shift the Conformational Equilibrium of the Selectivity Filter in the KcsA Channel to the Conductive Conformation: Predicted Consequences on Inactivation

“…Nonetheless, similar effects to those of PA on KcsA currents were seen when either one of the "non-annular" arginine residues were mutated to alanine, regardless of the added anionic lipid [20]. Finally, NMR and Molecular Dynamics simulation studies concluded that, indeed, the effects of lipids were a consequence of their binding to the "non-annular" arginines (R64 and R89) in KcsA [20,22,43,54]. According to Molecular Dynamics predictions, such lipid binding prevents interaction between those arginines and the inactivation triad (E71-D80-W67) behind the selectivity filter, which seems critical to stabilize the triad and to allow inactivation.…”

“…Interestingly, the addition of anionic phospholipids to these mutant channels reconstituted in asolectin giant liposomes did not modify their macroscopic current profile in electrophysiological measurements [20,64]. Furthermore, MD simulation studies highlighted the main role of the R64 residue not only in mediating the specific binding of anionic lipids to the "non-annular" binding sites, but also in translating such binding to specific conformational changes in the SF [20,54].…”

“…A reduction in the macroscopic rate of inactivation and an increase in the single-channel mean open time are also observed as the concentration of anionic phospholipids is increased; these effects are attributed to specific lipid interaction with the "non-annular" arginines [20]. Such interaction and its role on inactivation has been documented by functional, structural and molecular dynamics simulation studies [20][21][22]54]. Still, the molecular mechanisms involved in the alteration of the selectivity filter by lipid binding need to be further addressed.…”

Introduction to the Physics of Ionic Conduction in Narrow Biological and Artificial Channels

“…First, S.M. Cosseddu et al [ 6 ] present an extended MD-based analysis of ion motion within the KcsA channel. They reveal complicated patterns of potassium currents that are governed by the structural variability of the selectivity filter.…”