Gating and modulation of an inward-rectifier potassium channel

Inward-rectifier potassium channels (Kirs) are lipid-gated ion channels that differ from other K+ channels in that they allow K+ ions to flow more easily into, rather than out of, the cell. Inward rectification is known to result from endogenous magnesium ions or polyamines (e.g., spermine) binding to Kirs, resulting in a block of outward potassium currents, but questions remain regarding the structural and dynamic basis of the rectification process and lipid-dependent channel activation. Here, we present the results of long-timescale molecular dynamics simulations starting from a crystal structure of phosphatidylinositol 4,5-bisphosphate (PIP2)-bound chicken Kir2.2 with a non-conducting pore. After introducing a mutation (G178R) that is known to increase the open probability of a homologous channel, we were able to observe transitions to a stably open, ion-conducting pore, during which key conformational changes occurred in the main activation gate and the cytoplasmic domain. PIP2 binding appeared to increase stability of the pore in its open and conducting state, as PIP2 removal resulted in pore closure, with a median closure time about half of that with PIP2 present. To investigate structural details of inward rectification, we simulated spermine binding to and unbinding from the open pore conformation at positive and negative voltages, respectively, and identified a spermine-binding site located near a previously hypothesized site between the pore cavity and the selectivity filter. We also studied the effects of long-range electrostatics on conduction and spermine binding by mutating charged residues in the cytoplasmic domain and found that a finely tuned charge density, arising from basic and acidic residues within the cytoplasmic domain, modulated conduction and rectification. Based on the results of long-timescale molecular dynamics simulations, Jogini et al. provide atomic-level mechanistic and structural descriptions of lipid-dependent gating and spermine-induced inward rectification of the inward-rectifier potassium channel Kir2.2.

Automated summary

This article presents the results of long-timescale molecular dynamics simulations to describe the lipid-dependent gating and spermine-induced inward rectification of the inward-rectifier potassium channel Kir2.2. PIP2 binding increases the stability of the channel in its open and conducting state, while spermine binds to a site located between the pore cavity and the selectivity filter. Additionally, charged residues in the cytoplasmic domain modulate conduction and rectification through finely tuned charge density.