A Predicted Binding Site for Cholesterol on the GABAA Receptor

Abstract

Modulation of the GABA type A receptor (GABAAR) function by cholesterol and other steroids is documented at the functional level, yet its structural basis is largely unknown. Current data on structurally related modulators suggest that cholesterol binds to subunit interfaces between transmembrane domains of the GABAAR. We construct homology models of a human GABAAR based on the structure of the glutamate-gated chloride channel GluCl of Caenorhabditis elegans. The models show the possibility of previously unreported disulfide bridges linking the M1 and M3 transmembrane helices in the α and γ subunits. We discuss the biological relevance of such disulfide bridges. Using our models, we investigate cholesterol binding to intersubunit cavities of the GABAAR transmembrane domain. We find that very similar binding modes are predicted independently by three approaches: analogy with ivermectin in the GluCl crystal structure, automated docking by AutoDock, and spontaneous rebinding events in unbiased molecular dynamics simulations. Taken together, the models and atomistic simulations suggest a somewhat flexible binding mode, with several possible orientations. Finally, we explore the possibility that cholesterol promotes pore opening through a wedge mechanism.

Nicotinic acetylcholine receptor–lipid interactions: Mechanistic insight and biological function

“…Non-annular cholesterol binding sites between transmembrane α-helices were originally proposed based on fluorescence quenching studies with brominated lipids [64], and are supported by both molecular dynamics simulations and bioinformatics studies [65,66] (see also [67]). Cholesterol binding to non-annular cavities located between α-helices within the TMD α-helical bundles stabilizes the transmembrane domain structure, facilitating interactions with the ECD [65].…”

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

“…Hénin et al (Hénin et al, 2014) built homology models of a GABA A receptor type α 1 β 1 γ 2 based on the crystal structure of GluCl, and investigated the possibility of cholesterol binding through three complementary approaches: alignment of cholesterol with crystallographic coordinates of ivermectin, automated docking with AutoDock, and explicit, atomistic MD simulations. Docking results confirmed the possibility of cholesterol binding to the five intersubunit clefts in a largely symmetric fashion, despite the asymmetric nature of this heteropentameric receptor (Hénin et al, 2014).…”

“…The perspective of the community on the role played by lipids in channel modulation has recently started to shift: whereas earlier work only considered the membrane as an adaptable matrix for protein functioning, recent data suggest that lipid molecules play fundamental structural and functional roles in ion transport. For example, direct interactions of ligand-gated ion channels with cholesterol, which play a functional role, were observed (Hénin et al, 2014). Another challenging area in studying ion channel is how highly charged helical segments can transverse the cell membrane.…”

Multiple Propofol-binding Sites in a γ-Aminobutyric Acid Type A Receptor (GABAAR) Identified Using a Photoreactive Propofol Analog

“…It should be noted that the GABA A R we photolabeled was purified in the absence of cholesterol, although previous reconstitution studies indicate that cholesterol is essential for function (37,38). Furthermore, it is probable that cholesterol actually binds the GABA A R, and candidate sites would certainly include the intersubunit transmembrane cavities identified as anesthetic sites here (39,40). However, bound cholesterol was not localized in the ␤3 GABA A R crystal structure, although the receptor was purified in the presence of 1 M cholesterol (11), and the dimensions of the intersubunit pockets differ only subtly from those in GLIC or GluCl, purified in the absence of cholesterol (13,15).…”