Lipid Spatial Organization Within Nanodiscs Controls GPCR Activation States

A new preprint on bioRxiv reports that the spatial arrangement of anionic lipids within lipid nanodiscs—widely used tools for studying membrane proteins—significantly affects the conformational equilibria of the human A2A adenosine receptor, a class A G protein-coupled receptor. Using a combination of biophysical and biochemical experiments alongside molecular dynamics simulations, the researchers demonstrated that both POPS and POPG anionic lipids form clusters within nanodiscs, which reduces how many lipid molecules are freely accessible to interact with the receptor. This clustering effect is stronger for POPS than for POPG and becomes more pronounced as nanodisc size increases, consistent with experimental observations that a higher threshold concentration of POPS is needed to fully populate active receptor states. Simulations further identified positively charged residues in the membrane scaffold protein (MSP) that coordinate anionic lipid headgroups, effectively sequestering them. Targeted engineering of these MSP residues lowered the anionic lipid threshold required for receptor activation, demonstrating a practical strategy to tune lipid accessibility in nanodisc systems. Because MSPs are derived from apolipoprotein AI, the authors suggest that analogous lipid-protein interactions may also govern lipid organization in high-density lipoprotein (HDL) particles in vivo.