Investigating the PIP2 Binding Site in Kir Channels Via Multi-Scale Biomolecular Simulations

Abstract

Mammalian inwardly rectifying potassium (Kir) channels are activated by the anionic lipid, Phosphatidylinositol bisphosphate (PIP2). In this study, coarse-grained simulations followed by atomistic molecular dynamics have revealed the interactions made by PIP2 molecules with Kir channels. The three channels investigated are X-ray structures of KirBac1.1 and the Kir3.1-KirBac1.3 chimera, and a homology model of Kir6.2. Coarse-grained simulations of the Kir channels in PIP2-containing POPC lipid bilayers identified the PIP2 binding site on each channel. These models of the PIP2/channel complexes were refined by conversion to an atomistic representation followed by molecular dynamics simulation in a lipid bilayer. All three channels were revealed to contain a conserved binding site at the N-terminal end of the slide (M0) helix, at the interface between adjacent subunits of the channel. This binding site agrees with known functional data and is in close proximity to the site occupied by a detergent molecule in the Kir chimera channel crystal. Polar contacts in the coarse-grained simulations agree well with H-bonding interactions between the channels and PIP2 in the atomistic simulations, enabling identification of key sidechains, which are primarily basic in nature. Notable differences within the KirBac1.1 and Kir6.2 binding sites are apparent; providing hypotheses for why PIP2 activates Kir6.2 channels whilst inhibiting the opening of KirBac1.1 channels.