Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures

Abstract

G protein‐coupled receptors (GPCRs) are important drug targets characterized by a canonical seven transmembrane (TM) helix architecture. Recent advances in X‐ray crystallography and cryo‐EM have resulted in a wealth of GPCR structures that have been used in drug design and formed the basis for mechanistic activation hypotheses. Here, ensemble refinement (ER) of crystallographic structures is applied to explore the impact of binding of agonists and antagonist/inverse agonists to selected structures of cannabinoid receptor 1 (CB1R), β2 adrenergic receptor (β2AR), and A2A adenosine receptor (A2AAR). To assess the conformational flexibility and its role in GPCR activation, hydrogen bond (H‐bond) networks are analyzed by calculating and comparing H‐bond propensities. Mapping pairwise propensity differences between agonist‐ and inverse agonist/antagonist‐bound structures for CB1R and β2AR shows that agonist binding destabilizes H‐bonds in the intracellular parts of TM 5–7, forming the G protein binding cavity, while H‐bonds of the extracellular segment of TMs surrounding the orthosteric site are conversely stabilized. Certain class A GPCRs, for example, A2AAR, bind an allosteric sodium ion that negatively modulates agonist binding. The impact of sodium‐excluding mutants (D522.50N, S913.39A) of A2AAR on agonist binding is examined by applying ER analysis to structures of wildtype and the two mutants in complex with a full agonist. While S913.39A exhibits normal activity, D522.50N quenches the downstream signaling. The mainchain H‐bond pattern of the latter is stabilized in the intracellular part of TM 7 containing the NPxxY motif, indicating that an induced rigidity of the mutation prevents conformational selection of G proteins resulting in receptor inactivation.

Biophysical Dissection of Isolated GPCRs: The Adenosine A2A Receptor under the Bistouries

“…On the other hand, PAMs increase the activation of the receptor. Furthermore, ions are also considered as allosteric modulators for multiple GPCRs, such as Na + for the adenosine A 2A receptor [89,291] or Zn 2+ for the β 2adrenergic receptor [292] for which they have been shown to bind at allosteric sites which differ from the orthosteric site as reviewed by van der Westhuizen et al [290]. While they offer new ways to modulate and fine-tune GPCR activity, they are quite difficult to screen for, as they might be dependent on the nature of the agonist they work in conjunction with.…”