Simulating PIP2-Induced Gating Transitions in Kir6.2 Channels

Abstract

ATP-sensitive potassium (KATP) channels consist of an inwardly rectifying K+ channel (Kir6.2) pore, to which four ATP-sensitive sulfonylurea receptor (SUR) domains are attached, thereby coupling K+ permeation directly to the metabolic state of the cell. Dysfunction is linked to neonatal diabetes and other diseases. K+ flux through these channels is controlled by conformational changes in the helix bundle region, which acts as a physical barrier for K+ permeation. In addition, the G-loop, located in the cytoplasmic domain, and the selectivity filter might contribute to gating, as suggested by different disease-causing mutations. Gating of Kir channels is regulated by different ligands, like Gβγ, H+, Na+, adenosine nucleotides, and the signaling lipid phosphatidyl-inositol 4,5-bisphosphate (PIP2), which is an essential activator for all eukaryotic Kir family members. Although molecular determinants of PIP2 activation of KATP channels have been investigated in functional studies, structural information of the binding site is still lacking as PIP2 could not be resolved in Kir6.2 cryo-EM structures. In this study, we used Molecular Dynamics (MD) simulations to examine the dynamics of residues associated with gating in Kir6.2. By combining this structural information with functional data, we investigated the mechanism underlying Kir6.2 channel regulation by PIP2.

Structural insights into ATP-sensitive potassium channel mechanics: a role of intrinsically disordered regions

“…In our model, of the four available binding sites, in two PIP2 is stably bound to the channel, in one it is occasionally bound, and one site was vacant throughout all simulation (see SI). Our characterization of the PIP2 binding site is in agreements with recent numericall results 28 (see Figure 4 c, d). It mainly consists of residues K39 and K67, and R54 from the neighboring Kir6.2 unit.…”

“…We know that the N-terminal L0-loop residues (199-214) contribute to the binding site of ATP in Kir6.2 (the so-called ABLOS-"ATP Binding Loop on SUR" ) 27 . The ATP binding site partially overlaps with the PIP2 (phosphatidylinositol 4,5-bisphosphate) binding site 28 . PIP2 is a minor phospholipid from the inner leaflet of the membrane, which binding promotes the open structure of Kir6.2 29 .…”

Ligand-mediated Structural Dynamics of a Mammalian Pancreatic KATP Channel

“…In the Kir6.2-CTD-up structure, in addition to Kir6.2 K67, W68, and R176 previously implicated in PIP2 binding (Brundl et al, 2021;Cukras et al, 2002;Shyng and Nichols, 1998), K134 in TMD0 of SUR1 comes into close contact with the density corresponding to lipid headgroups (Fig. 5A).…”

Structural Insights into ATP-Sensitive Potassium Channel Mechanics: A Role of Intrinsically Disordered Regions

“…We know that the N-terminal L0-loop residues (199–214) contribute to the binding site of ATP in Kir6.2 (the so-called ABLOS-“ATP binding loop on SUR”) . The ATP binding site partially overlaps with the PIP2 (phosphatidylinositol 4,5-bisphosphate) binding site . PIP2 is a minor phospholipid from the inner leaflet of the membrane, which binding promotes the open structure of Kir6.2 .…”