Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2

Abstract

The regulation of ion channel activity by specific lipid molecules is widely recognized as an integral component of electrical signaling in cells1,2. In particular, phosphatidylinositol 4,5-bisphosphate (PIP2), a minor yet dynamic phospholipid component of cell membranes, is known to regulate many different ion channels3–7. PIP2 is the primary agonist for classical inward rectifier (Kir2) channels, through which this lipid can regulate a cell’s resting membrane potential2,7–9. However, the molecular mechanism by which PIP2 exerts its action is unknown. Here we present the x-ray crystal structure of a Kir2.2 channel in complex with a short-chain (dioctanoyl) derivative of PIP2. We found that PIP2 binds at an interface between the transmembrane domain (TMD) and the cytoplasmic domain (CTD). The PIP2 binding site consists of a conserved non-specific phospholipid binding region (RWR) in the TMD and a specific phosphatidylinositol binding region in the CTD. Upon PIP2 binding a flexible expansion linker contracts to a compact helical structure, the CTD translates 6 Å and becomes tethered to the TMD, and the inner helix gate begins to open. In contrast, the small anionic lipid dioctanoyl glycerol pyrophosphatidic acid (PPA) also binds to the non-specific TMD region, but not to the specific phosphatidylinositol region, and thus fails to engage the CTD or open the channel. Our results show how PIP2 can control the resting membrane potential through a specific ion channel receptor-ligand interaction that brings about a large conformational change, analogous to neurotransmitter activation of ion channels at synapses.

Amphipathic antenna of an inward rectifier K + channel responds to changes in the inner membrane leaflet

“…These charges are crucial sites for PIP 2 -binding in the Kir channels (16,36,37). In the crystal structure of Kir2.2, the IF helix (residues 61-69) forms an α-helix that corresponds to the C-terminal half of M0 (numbers [11][12][13][14][15][16][17][18], and R65 in the IF helix (corresponding to K14 in M0) interacts with the tether helix in the cytoplasmic domain. On the other hand, the KcsA channel has the least bulky CPD among the K channels, and the open-stabilizing effect of M0 is directed toward the charged lipids on the inner leaflet.…”

“…In voltage-gated channels, the voltage-sensor domain (VSD) primarily senses changes in the membrane electric field, but this sensing is modulated by the lipid composition (9,11,13). For the non-voltage-gated (the twotransmembrane-helix inward-rectifier type) channels, such as the KcsA potassium channel from Streptomyces lividans, the underlying mechanism of the effect exerted by lipids is still undergoing extensive investigation, even though the structural information on the channel proteins cocrystallized with lipid molecules has already been reported (14)(15)(16)). …”

Analysis of the selectivity filter of the voltage-gated sodium channel NavRh

“…The pore of KcsA only permits the passage of dehydrated potassium ions [10,11]. This property is highly conserved in most types of potassium channels [4][5][6][12][13][14][15][16][17]. The ion permeation, however, is different in Na v channels where Na + is…”

Regulation of EGFR nanocluster formation by ionic protein-lipid interaction

“…The SNAP (Soluble NSF (N-ethylmaleimide Sensitive Fusion protein) Attachment Protein) receptor protein syntaxin-1A forms microclusters in the plasma membrane via the ionic interaction between its polybasic JM region and the strong anionic lipid phosphatidylinositol-4,5-bisphosphate (PIP2), which is essential for the vesicle docking and membrane fusion during neuronal exocytosis [15]. As a critical co-factor, PIP2 can also induce big conformational change in inward-rectifier K+ (Kir) 2.2 channel through the ionic interaction with polybasic amino acids at the interface of transmembrane domain and cytoplasmic domain [16]. Previous studies with Ras superfamily members show that PIP2 and PIP3 can target small GTPases to the plasma membrane via ionic interactions [17].…”