Atomistic basis of opening and conduction in mammalian inward rectifier potassium (Kir2.2) channels

Abstract

Potassium ion conduction through open potassium channels is essential to control of membrane potentials in all cells. To elucidate the open conformation and hence the mechanism of K+ ion conduction in the classic inward rectifier Kir2.2, we introduced a negative charge (G178D) at the crossing point of the inner helix bundle, the location of ligand-dependent gating. This “forced open” mutation generated channels that were active even in the complete absence of phosphatidylinositol-4,5-bisphosphate (PIP2), an otherwise essential ligand for Kir channel opening. Crystal structures were obtained at a resolution of 3.6 Å without PIP2 bound, or 2.8 Å in complex with PIP2. The latter revealed a slight widening at the helix bundle crossing (HBC) through backbone movement. MD simulations showed that subsequent spontaneous wetting of the pore through the HBC gate region allowed K+ ion movement across the HBC and conduction through the channel. Further simulations reveal atomistic details of the opening process and highlight the role of pore-lining acidic residues in K+ conduction through Kir2 channels.

Computational Insights Into Voltage Dependence of Polyamine Block in a Strong Inwardly Rectifying K+ Channel

“…Further, the open state structure of the extremely well characterized Kir2.1 channel is still not available. Given the very recent success to crystallize Kir2.2 channels in an open, conductive conformation (Zangerl-Plessl et al, 2020) future studies will need to be performed to address polyamine block in the classic strong rectifier Kir2 family. Comparison of conductance studies on Kir3.2 and Kir2.2 channels reveal very interesting differences, which might affect polyamine block.…”

“…Recent MD simulations on K IR crystal structures have provided unprecedented details concerning the K + conduction mechanism of Kir3.2 and 2.2 channels (Bernsteiner et al, 2019;Zangerl-Plessl et al, 2020) and can serve as excellent starting point to address inward rectification. Here, we perform multimicrosecond-timescale MD simulations with applied field to provide first atomistic insights into the voltage dependent block of putrescine (PUT 2+ ), using the conductive state of the strong inwardly rectifying Kir3.2 channel as a starting point.…”

Simulating PIP2-induced gating transitions in Kir6.2 channels

“…A more detailed analysis suggests a ~ 80% correlation between the R176-PIP2 h-bonds and the helical content of the C-linker, corroborating the importance of this interaction for PIP2-induced conformational changes. Another important conformational change that has been reported in several previous studies concerns the dynamics of the cytoplasmic domain, including a rotation of the whole domain (Bavro et al 2012;Clarke et al 2010;Li et al 2015Li et al , 2017Linder et al 2015;MacKinnon 2011, 2013;Wu et al 2018;Zangerl-Plessl et al 2019). We therefore monitored the rotation of the CTD over simulation time, as shown in supplementary Figure 4.…”

“…Since PIP 2 binding sites are well resolved in Kir2 (Hansen et al 2011; S. J. Lee et al 2016; Zangerl-Plessl et al 2019) and Kir3 channels (Niu et al 2020; Whorton and MacKinnon 2011, 2013), we used this structural information together with functional data to investigate the possible structural basis for K ATP channel regulation by PIP 2 . Specifically, the aim of the present study was to examine PIP 2 -induced gating transitions after unbinding of ATP from the cytoplasmic domain using Molecular Dynamics (MD) simulations.…”

The biophysical basis of protein domain compatibility

“…The class representing interfaces is an intermediate that is structured and dynamic. It contains many Kir2.1 regions (PIP2 binding site, TM/CTD and subunit interfaces) that conformationally change upon PIP2 binding and during closed to open state transitions (21,22). Since gating mechanisms are conserved across the inward rectifier family (23), the interface class may also be enriched for other inward rectifier regulator binding sites, such as Gbg (GIRK), and ATP (Kir6.2).…”