How receptor conformation depends on lipid nanodisc size: Adenosine A2A receptor and implications for class-A GPCR proteins

Nanodiscs have become an exceptionally valuable tool to explore membrane proteins in an environment resembling native membranes. However, it remains unclear how well the lipid nanodisc environment matches the conditions under which membrane proteins function in cells. The goal of this work is to use atomic-level simulations to compare the environments experienced by membrane proteins in nanodiscs and non-strained planar membranes of identical lipid composition. We focus on the adenosine A 2A receptor, a member of the GPCR family, and investigate how nanodisc size affects receptor properties. We specifically study typical nanodiscs, which, together with the surrounding membrane scaffolding protein, are ∼11 nm in diameter. We show that even simple lipid compositions give rise to nanoscale disc structures that modulate receptor conformational states, in contrast to planar, non-strained membrane structures. Deep learning methods reveal that the conformational distribution of the A 2A receptor is skewed towards active-like structures compared to the planar membrane environment. However, the tendency of nanodiscs to modulate the conformation of the receptor turns out to be size-dependent. A reassuring observation is that when the diameter of the nanodiscs reaches ∼19 nm, the receptor conformations settle into a distribution whose key features correspond to those of a non-strained planar bilayer. The results support the view that the membrane environment affects the conformational distribution of GPCRs within them, and when it comes to the use of lipid nanodiscs, potential unwanted effects can be minimized by favoring the largest nanodiscs.