Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels

Abstract

Protein–lipid interactions are a key element of the function of many integral membrane proteins. These potential interactions should be considered alongside the complexity and diversity of membrane lipid composition. Inward rectifier potassium channel (Kir) Kir2.2 has multiple interactions with plasma membrane lipids: Phosphatidylinositol (4, 5)-bisphosphate (PIP2) activates the channel; a secondary anionic lipid site has been identified, which augments the activation by PIP2; and cholesterol inhibits the channel. Molecular dynamics simulations are used to characterize in molecular detail the protein–lipid interactions of Kir2.2 in a model of the complex plasma membrane. Kir2.2 has been simulated with multiple, functionally important lipid species. From our simulations we show that PIP2interacts most tightly at the crystallographic interaction sites, outcompeting other lipid species at this site. Phosphatidylserine (PS) interacts at the previously identified secondary anionic lipid interaction site, in a PIP2concentration-dependent manner. There is interplay between these anionic lipids: PS interactions are diminished when PIP2is not present in the membrane, underlining the need to consider multiple lipid species when investigating protein–lipid interactions.

Modulation of A2aR Oligomerisation by Conformational State and PIP2Interactions Revealed by MD Simulations and Markov Models

“…A number of simulation studies using the MARTINI force field have provided valuable insights into the association of membrane proteins 28,32,[49][50][51][52][53] and into protein-lipid interactions [54][55][56] . However, the current MARTINI model may also have some limitations 57,58 .…”

Evaluating Inositol phospholipid interactions with Inward Rectifier Potassium Channels and characterising their role in Disease

“…A previous study demonstrated that crosstalk between different anionic lipids can affect the affinities of each lipid for the Kir2.2 channel 28 . Here, we show that the presence of 10% anionic lipid (POPS) in the lower leaflet of the bilayer does not affect the overall ΔΔG for PIP2 binding to Kir6.2 (Supplementary Figure 7).…”

Structural basis of GIRK2 channel modulation by cholesterol and PIP2

“…Cholesterol binding sites on membrane proteins were initially characterized using a variety of techniques, including electron spin resonance, photoaffinity labeling, molecular modeling and site-directed mutagenesis, which led to the identification of amino acid recognition motifs 15,37,[51][52][53][54] . CRAC (Cholesterol Recognition/interaction Amino acid Consensus) is characterized by the amino acid sequence (L/V)-X 1-5 -(Y)-X 1-5 -(K/R) 55 , while CARC is oriented in the opposite 56 .…”

“…Docking studies and MD simulations identified putative cholesterol binding sites in GIRK channels that involved various amino acid residues 14,28,37 . In particular, two sites are very similar to the positions observed in the cryoEM structure (CHS1 and CHS2).…”

“…Consistent with this, several structures of GPCRs have shown cholesterol bound to a hydrophobic region of the receptor 27,[29][30][31][32][33] . Mutagenesis studies and simulations have implicated several different regions of inwardly rectifying potassium channels in cholesterol modulation, including the cytoplasmic domain, PIP 2 binding site, and the transmembrane domain 14,[34][35][36][37] . However, the exact location of the cholesterol sites remains to be determined.…”