Inositol Phospholipid Interactions with Inward Rectifier Potassium Channels and Their Role in Disease

Abstract

Ion channels are frequently modulated by specific protein-lipid interactions in the phospholipid bilayer. The activation of human inward rectifying potassium (hKir) channels by phosphoinositides (PI) has been well characterised in biophysical studies. Here, we provide an extensive application of a coarse-grained molecular dynamics free-energy perturbation (CG-MD-FEP) methodology to capture the energetics of binding of PI lipids to hKir channels. By using either a single- or multi-step protocol, we establish a consistent value for the binding of PIP2 to hKir channels, relative to the binding of the bulk phosphatidylcholine phospholipid and in the presence of anionic phospholipid such as phosphatidylserine (PS). By perturbing amino acid side chains on hKir6.2, we show that the neonatal diabetes mutation E179K has increased PIP2 affinity, while the congenital hyperinsulinism mutation K67N results in a reduced affinity. This is in good agreement with electrophysiological studies showing the E179K mutant exhibits a reduction in neomycin sensitivity, which implies that PIP2 binds more tightly to E179K mutant channels. We conclude that our application provides a valuable method to compare affinities between lipid species, and for annotating amino acid side chains within lipid-binding pockets.