Structure-based comparisons of GPCR interactions with nanobodies and G proteins

G protein coupled receptors (GPCRs) are the targets for roughly one third of all drugs on the market. They modulate numerous physiological processes by activating the molecular switches heterotrimeric G proteins and downstream signaling cascades. Numerous structures of GPCR-Gα complexes have been solved to better understand G protein activation and coupling, but objective comparisons of these structures at the level of individual amino acids are challenging. Different perspectives are offered by structures of GPCRs bound to specific nanobodies that interact with the cytosolic face of GPCRs. Such nanobodies have been assumed to mimic G proteins, based on similar biochemical effects on GPCRs. Nevertheless, a precise and quantitative comparison of these interactions with GPCRs is needed to confirm or refute this hypothesis, but these interfaces are hard to compare because nanobodies and G proteins have dramatically different structures.

We used structure-based energy calculations to quantify the per-residue contributions across GPCRs interfaces with heterotrimeric G proteins and G protein-mimicking nanobodies. We identified contributions that are shared across dissimilar structures, which can pinpoint interactions that are essential for function. However, we also identified variable contributions that can underly interaction specificity. These highlight key differences in GPCR interactions with nanobodies and the G proteins they have been presumed to mimic. Our results can contribute to a better understanding of these physiologically-relevant interactions and enable to design nanobodies with diverging functions or specificities towards particular GPCRs.

Key Words: GPCR, G protein-mimicking nanobodies, structure-based energy calculations, protein-protein interactions.