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

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), beta(2) adrenergic receptor (beta(2)AR), and A(2A) adenosine receptor (A(2A)AR). 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 beta(2)AR 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, A(2A)AR, bind an allosteric sodium ion that negatively modulates agonist binding. The impact of sodium-excluding mutants (D52(2.50)N, S91(3.39)A) of A(2A)AR on agonist binding is examined by applying ER analysis to structures of wildtype and the two mutants in complex with a full agonist. While S91(3.39)A exhibits normal activity, D52(2.50)N 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.