Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures
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Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures. / Madsen, Jesper J.; Ye, Libin; Frimurer, Thomas M.; Olsen, Ole H.
In: Protein Science, Vol. 31, No. 11, e4456, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Mechanistic basis of GPCR activation explored by ensemble refinement of crystallographic structures
AU - Madsen, Jesper J.
AU - Ye, Libin
AU - Frimurer, Thomas M.
AU - Olsen, Ole H.
N1 - Publisher Copyright: © 2022 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.
PY - 2022
Y1 - 2022
N2 - 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 (β2 AR), and A2A adenosine receptor (A2A 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 β2 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, A2A AR, bind an allosteric sodium ion that negatively modulates agonist binding. The impact of sodium-excluding mutants (D522.50 N, S913.39 A) of A2A 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 S913.39 A exhibits normal activity, D522.50 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.
AB - 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 (β2 AR), and A2A adenosine receptor (A2A 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 β2 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, A2A AR, bind an allosteric sodium ion that negatively modulates agonist binding. The impact of sodium-excluding mutants (D522.50 N, S913.39 A) of A2A 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 S913.39 A exhibits normal activity, D522.50 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.
KW - allosteric regulation
KW - ensemble refinement
KW - G protein-coupled receptor (GPCR)
KW - hydrogen bond
KW - molecular dynamics
KW - protein conformation
U2 - 10.1002/pro.4456
DO - 10.1002/pro.4456
M3 - Journal article
C2 - 36134696
AN - SCOPUS:85141003862
VL - 31
JO - Protein Science
JF - Protein Science
SN - 0961-8368
IS - 11
M1 - e4456
ER -
ID: 325023959