Allosteric coupling from G protein to the agonist-binding pocket in GPCRs

Abstract

G-protein-coupled receptors (GPCRs) remain the primary conduit by which cells detect environmental stimuli and communicate with each other1. Upon activation by extracellular agonists, these seven-transmembrane-domain-containing receptors interact with heterotrimeric G proteins to regulate downstream second messenger and/or protein kinase cascades1. Crystallographic evidence from a prototypic GPCR, the β2-adrenergic receptor (β2AR), in complex with its cognate G protein, Gs, has provided a model for how agonist binding promotes conformational changes that propagate through the GPCR and into the nucleotide-binding pocket of the G protein α-subunit to catalyse GDP release, the key step required for GTP binding and activation of G proteins2. The structure also offers hints about how G-protein binding may, in turn, allosterically influence ligand binding. Here we provide functional evidence that G-protein coupling to the β2AR stabilizes a ‘closed’ receptor conformation characterized by restricted access to and egress from the hormone-binding site. Surprisingly, the effects of G protein on the hormone-binding site can be observed in the absence of a bound agonist, where G-protein coupling driven by basal receptor activity impedes the association of agonists, partial agonists, antagonists and inverse agonists. The ability of bound ligands to dissociate from the receptor is also hindered, providing a structural explanation for the G-protein-mediated enhancement of agonist affinity, which has been observed for many GPCR–G-protein pairs. Our data also indicate that, in contrast to agonist binding alone, coupling of a G protein in the absence of an agonist stabilizes large structural changes in a GPCR. The effects of nucleotide-free G protein on ligand-binding kinetics are shared by other members of the superfamily of GPCRs, suggesting that a common mechanism may underlie G-protein-mediated enhancement of agonist affinity.

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Figure 1: Guanine nucleotides influence antagonist binding to β2AR•Gs complexes.
Figure 2: Trapping active-state β2AR with Nb80 slows both antagonist and agonist association.
Figure 3: Activation of the β2AR closes the hormone-binding site.
Figure 4: Allosteric communication between the β2AR G-protein- and hormone-binding sites.
Figure 5: Basis for G-protein-dependent high-affinity agonist binding.

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Acknowledgements

We thank T. S. Kobilka for preparation of affinity chromatography reagents and F. S. Thian for help with cell culture. We thank J. Traynor and J. Tesmer for their support and use of their laboratory space for J.P.M. This work was supported by the Lundbeck Foundation (Junior Group Leader Fellowship to S.G.F.R.); Fund for Scientific Research of Flanders (FWO-Vlaanderen) and the Institute for the encouragement of Scientific Research and Innovation of Brussels (ISRIB) (E.P. and J.S.); National Institute of Neural Disorders and Stroke grant RO1-NS28471 (B.K.K.); the Mather Charitable Foundation (B.K.K.); National Institute of General Medical Sciences grants RO1-GM083118 and U19-GM106990 (B.K.K. and R.K.S.) and RO1-GM068603 (R.K.S.); National Institutes of Drug Abuse R21-031418 (B.K.K. and R.K.S.); Michigan Diabetes Research and Training Center Grant, National Institute of Diabetes and Digestive and Kidney Diseases, P60DK-20572 (R.K.S.); University of Michigan Biological Sciences Scholars Program (R.K.S.) and the Rackham School of Graduate Studies (B.T.D.); Molecular Biophysics Training Grant T32GM008270 (B.T.D.); Cell and Molecular Biology Training Grant T32GM007315 (G.A.V.-R.) and Pharmacological Sciences Training Program T32GM007767 (J.P.M.); and AHA Midwest Affiliate Predoctoral Fellowship 13PRE17110027 (J.P.M.).

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Contributions

B.T.D., J.P.M., G.A.V.-R., B.K.K. and R.K.S. designed the experiments. B.T.D., J.P.M., G.A.V.-R. and A.J.K. performed research; S.G.F.R., E.E., J.-J.F., A.M., M.M., Y.D., R.A.M., E.P. and J.S. contributed valuable reagents/analytic tools; B.T.D., J.P.M., G.A.V.-R., B.K.K. and R.K.S. analysed data; and B.T.D., J.P.M., B.K.K. and R.K.S. wrote the paper.

Corresponding author

Correspondence to Roger K. Sunahara.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Confirmation of nucleotide removal from β2AR•Gs by apyrase.

Gs and Flag-tagged β2AR were reconstituted in rHDL and treated with the non-specific nucleotide lyase, apyrase. Samples were applied to an anti-Flag affinity resin to remove products of the GDP degradation (GMP and Pi). Samples were incubated with 100 nM [35S]GTPγS at room temperature. At various times, samples were subjected to rapid filtration through glass fibre filters (GF/B) followed by 10 volumes of ice-cold buffer washes containing 10 μM GDP. Filters were dried and subjected to liquid scintillation counting (Top-Count, Perkin-Elmer). To a first approximation, the rapid binding event suggests that the complex is empty of nucleotide, based on the limited temporal resolution of this mixing and filtration technique. [3H]DHAP and [35S]GTPγS binding to the reconstituted complex yields a final R:G ratio of 1:0.95, suggesting that up to 95% of the β2AR–rHDL particles contain a single functional G protein. This suggests that only those G proteins associated with the β2AR will bind [35S]GTPγS within this time frame in the absence of receptor agonists. Data are shown as mean ± s.e.m. from n = 3 independent experiments performed in duplicate.

Extended Data Figure 2 GDP accelerates [3H]DHAP binding to β2AR•Gs.

a, Time course monitoring [3H]DHAP association to apyrase-treated β2AR•Gs complexes in the presence of varying GDP concentrations. GDP increases both the observed association rate constant and the maximum binding of [3H]DHAP. b, Concentration–response curve showing enhancement of the observed [3H]DHAP association rate constant by GDP (half-maximum effective concentration (EC50) = 181 ± 66 nM). All data are shown as mean ± s.e.m. from n = 3 independent experiments performed in duplicate.

Extended Data Figure 3 Effect of guanine nucleotides on [3H]DHAP binding to β2AR•Gs.

a, In saturation binding assays, addition of GTPγS to apyrase-treated β2AR•Gs complexes increased the observed maximal binding, Bmax, for [3H]DHAP without significantly altering Kd (control: Bmax = 5.5 ± 0.52 fmol, Kd = 0.88 nM; +GTPγS: Bmax = 16.6 ± 1.9 fmol, Kd = 0.56 nM). b, Both GDP and GTPγS could enhance maximal [3H]DHAP binding in a concentration-dependent manner (GDP log(EC50) = −6.42 ± 0.12, or EC50 ≈ 386 nM; GTPγS log(EC50) = −7.45 ± −0.16, or EC50 ≈ 35 nM). All data are shown as mean ± s.e.m. from n = 3 independent experiments performed in duplicate.

Extended Data Figure 4 Effect of Nb80 on antagonist binding to the β2AR.

a, Association of [3H]DHAP is progressively slowed after pre-incubation of the β2AR with increasing concentrations of Nb80. b, If [3H]DHAP is allowed to first equilibrate with the β2AR, Nb80 slows [3H]DHAP dissociation from β2AR in a concentration-dependent manner. c, Owing to the dramatic slowing of [3H]DHAP binding kinetics, Nb80 (but not a control nanobody, Nb30, which has no effect on agonist affinity for β2AR) seems competitive with [3H]DHAP if insufficient time is given to reach equilibrium. Data shown are from assays incubated for 90 min at room temperature. All data are shown as mean ± s.e.m. from n = 3 independent experiments performed in duplicate.

Extended Data Figure 5 Y308A mutation abolishes the rate-slowing effects of Nb80.

a, b, Time course of [3H]DHAP binding to wild-type (WT) β2AR (a) or β2AR(Y308A) (b) after pre-incubation of receptor with Nb80. Nb80 significantly slowed [3H]DHAP association to wild-type β2AR (−Nb80 observed rate constant, kobs = 0.45 ± 0.05 min−1 or association half-time, t½ = 1.5 ± 0.2 min, +Nb80 kobs = 0.20 ± 0.03 min−1 or t½ = 3.5 ± 0.5 min; P = 0.011 by an unpaired two-tailed t-test), but less effectively slowed [3H]DHAP association to β2AR(Y308A) (−Nb80 kobs = 0.50 ± 0.06 min−1 or t½ = 1.4 ± 0.2 min; +Nb80 kobs = 0.32 ± 0.01 min−1 or t½ = 2.2 ± 0.1 min; P = 0.05 by an unpaired two-tailed t-test. All data are shown as mean ± s.e.m. from n = 4 (−Nb80) or n = 3 (+Nb80) independent experiments performed in duplicate. c, d, Time course of [3H]formoterol binding to wild-type β2AR (c) or β2AR(Y308A) (d) after pre-incubation of receptor with Nb80. Nb80 slowed [3H]formoterol association to wild-type β2AR (0.1 μM Nb80 kobs = 0.68 ± 0.13 min−1 or t½ = 1.0 ± 0.2 min, 10 μM Nb80 kobs = 0.27 ± 0.05 min−1 or t½ = 2.6 ± 0.5 min; P = 0.031 by an unpaired two-tailed t-test). However, with β2AR(Y308A), Nb80 had little effect on the observed association rate constant but enhanced the amount of [3H]formoterol bound (0.1 μM Nb80 kobs = 0.37 ± 0.11 min−1 or t½ = 1.9 ± 0.6 min with a plateau of 10.1 ± 0.8 fmol, 10 μM Nb80 kobs = 0.53 ± 0.13 min−1 or t½ = 1.3 ± 0.4 min with a plateau of 21.3 ± 1.2 fmol; unpaired two-tailed t-test of the kobs values showed P = 0.4). All data are shown as mean ± s.e.m. from n = 4 independent experiments performed in duplicate.

Extended Data Figure 6 The closed conformation stabilized by agonist and G protein (or mimic).

Illustrated are the crystal structures of agonist-versus inverse-agonist-bound β2AR (cyan) and β1AR (yellow), where only β2AR is bound to G protein. Similarly, the MOPr (orange) adopts a closed conformation upon binding the G-protein surrogate, Nb39. β2AR, PDB accession 2RH1; β2AR•Gs, PDB accession 3SN6; β1AR, PDB accession 2YCW; β1AR-iso, PDB accession 2Y03; MOPr, PDB accession 4DKL; MOPr–Nb39, PDB accession 5C1M; M2R, PDB accession 3UON; M2R–Nb9-8, PDB accession 4MQS.

Extended Data Figure 7 Effect of guanine nucleotides on [3H]antagonist binding are also seen in competition binding assays.

a, Agonist (isoproterenol) competition binding using apyrase-treated β2AR•Gs complexes shows the characteristic G-protein-dependent shift in agonist affinity, along with a dramatic increase in total [3H]DHAP binding, upon the addition of 10 μM GTPγS. b, Normalization of the data from a yields a plot representative of what is commonly reported in the literature. c, Similar to the β2AR, agonist (morphine) competition binding using MOPr•Go complexes shows the characteristic G-protein-dependent shift in agonist affinity, along with a dramatic increase in total [3H]DPN binding, upon the addition of 10 μM GTPγS. d, Normalization of the data from c. All data are shown as mean ± s.e.m. from n = 3 independent experiments performed in duplicate.

Extended Data Figure 8 The MOPr and M2R behave similarly to the β2AR when bound to nucleotide-free G protein or an active-state-stabilizing nanobody.

a, After apyrase treatment of M2R•Go complexes, addition of 10 μM GTPγS enhances association of [3H]N-methylscopolamine ([3H]NMS) to M2R (vehicle kobs = 0.32 ± 0.02 min−1 or t½ = 2.2 ± 0.1 min, +GTPγS kobs = 0.54 ± 0.02 min−1 or t½ = 1.3 ± 0.1 min; P = 0.002 by an unpaired two-tailed t-test). Data are shown as mean ± s.e.m. from n = 3 independent experiments performed in duplicate. Addition of GDP was also able to increase the rate of [3H]NMS binding (inset; log (EC50) = 6.91 ± 0.18 or EC50 ≈ 123 nM; mean ± s.e.m. from n = 2 independent experiments performed in duplicate). b, Pre-treatment of M2R with either 10 μM (black circles) or 100 μM (red squares) Nb9-8 (ref. 27) impairs association of [3H]iperoxo to M2R (10 μM Nb9-8 kobs = 0.68 ± 0.09 min−1 or t½ = 1.0 ± 0.2 min, 100 μM Nb9-8 kobs = 0.25 ± 0.04 min−1 or t½ = 2.8 ± 0.5 min; P = 0.04 by an unpaired two-tailed t-test). Data are shown as mean ± s.e.m. from n = 3 (10 μM Nb9-8) or n = 2 (100 μM Nb9-8) independent experiments performed in duplicate. c, Addition of 10 μM GTPγS to apyrase-treated MOPr•Go complexes hastened association of the antagonist [3H]diprenorphine ([3H]DPN) to MOPr (apyrase kobs = 0.06 ± 0.02 min−1 or t½ = 9.8 ± 1.3 min, +GTPγS kobs = 0.12 ± 0.01 min−1 or t½ = 5.6 ± 0.6 min; P = 0.1 by an unpaired two-tailed t-test). The effect of nucleotide-free G protein was recapitulated by pre-incubating MOPr with Nb39 (ref. 28) (inset; control kobs = 0.13 ± 0.01 min−1, +100 μM Nb39 kobs = 0.07 ± 0.02 min−1). Data are shown as mean ± s.e.m. from n = 2 (MOPr•Go) or n = 3 (MOPr + Nb39) independent experiments performed in duplicate.

Extended Data Figure 9 The extracellular regions in the active conformations of peptide hormone/agonist receptors MOPr and NTS-R1.

Illustrated are the crystal structures of the inactive and active (or partially active neurotensin receptor 1, NTS-R1) conformations of the MOPr and NTS-R1 from the top or extracellular view of the receptor. The surface rendering highlights residues or structure on the extracellular face that change upon receptor activation (circled). The MOPr in its inactive conformation (purple) is compared to the Nb39-bound (G-protein mimic) form in blue. Similarly, the inactive NTS-R1 (ref. 33) (green) is compared with a mutant NTS-R1 (ref. 34) that adopts a partially active conformation (orange). MOPr, PDB accession 4DKL; MOPr-Nb39, PDB accession 5C1M; NTS-R1, PDB accession 4GRV; active-like NTS-R1, PDB accession 4XEE.

Extended Data Figure 10 Model of G-protein-dependent high-affinity agonist binding.

a, b, As in Fig. 5, nucleotide-free G-protein-stabilized family A GPCRs experience alterations in the extracellular face of the receptor, thus affecting the orthosteric-binding site. In a monoamine receptor such as the β2AR, G-protein binding and GDP loss accompanies the stabilization of a closed, active conformation of the receptor, as in a. b, For family members such as MOPr or NTS-R1, where the peptide hormones/agonists are considerably larger, the influence of the G-protein-mediated changes in the extracellular domain structure result in similar effects on orthosteric ligand dissociation. Rather than closing over the orthosteric site as with monoamine receptors as in a, the extracellular face may contain structures and residues that ‘pinch’ the larger ligands.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, a Supplementary Discussion and additional references. (PDF 297 kb)

Activation of the β2AR

Morph of the β2AR in its inactive conformation bound to inverse agonist carazolol (PDB: 2RH1) and the β2AR in its active conformation bound to agonist BI-167607 and nanobody Nb80 (PDB: 3P0G). For reference, epinephrine is modeled in the orthosteric binding site. Morphs were generated using Chimera (Pettersen, E,F., et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 25, 1605-12) and rendered with Pymol (The PyMOL Molecular Graphics System, Schrödinger, LLC). Highlighted are Phe193ECL2 and Tyr3087.35. (MOV 8205 kb)

Comparison of β1AR and β2AR

The closed, active conformation is stabilized by the G protein. Morph of the β2AR in its inactive conformation bound to inverse agonist carazolol (cyan, PDB: 2RH1) and the β2AR in its active conformation bound to agonist BI-167607 and nanobody Nb80 (PDB: 3P0G). Superimposed on top is a similar morph transitioning between the carazolol-boundββ1-adrenergic receptor (β1AR, lime green, PDB: 2YCW) and isoproterenol-bound (but not G protein- or Nb-bound, PDB: 2Y03). While the β2AR adopts a closed conformation stabilized by agonist and G protein, the β1AR bound only to isoproterenol does not. For reference, epinephrine is modeled in the orthosteric binding site. Note that nanobody Nb80 has been omitted from the animation for simplicity. Highlighted are Phe193ECL2 and Tyr3087.35 on β2AR and the conserved residues Phe201ECL2 and Phe3527.35 on β1AR. Morphs were generated using Chimera (Pettersen, E,F., et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 25, 1605-12) and rendered with Pymol (The PyMOL Molecular Graphics System, Schrödinger, LLC). (MOV 3417 kb)

Activation of the μ-opioid receptor, MOPr

The ribbon structure of the μ-opioid receptor (MOPr) in its inactive conformation bound to β-funaltrexamine (cyan, PDB: 4DKL) and the MOPr in its active conformation bound to agonist BU72 and Nb39 (orange, PDB: 5C1M). For reference only BU72 is displayed as spheres. Note that Nb39 is not illustrated for simplicity. Morph between the inactive and active conformations was generated using Chimera (Pettersen, E,F., et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 25, 1605-12) and rendered with Pymol (The PyMOL Molecular Graphics System, Schrödinger, LLC). (MOV 5952 kb)

Activation of the M2 muscarinic receptor, M2R

Top view of the ribbon structure of the M2 muscarinic receptor (M2R) in its inactive conformation bound to antagonist 3-quinuclidinyl benzilate, (QNB, PDB: 3UON) and the M2R in its active conformation bound to agonist iperoxo and nanobody Nb9-8 (PDB: 4MQS). Illustrated are sidechain residues Y1043.33, Y4036.38 and Y4267.39 to highlight the ‘lid-like’ structure over the orthosteric site. Acetylcholine is modeled into the iperoxo binding site and illustrated in stick figure for reference purposes. Note that Nb9-8 is not depicted for simplicity. Morphs were generated between the inactive and active conformations using Chimera (Pettersen, E,F., et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 25, 1605-12) and rendered with Pymol (The PyMOL Molecular Graphics System, Schrödinger, LLC). (MOV 2726 kb)

Activation of the M2R side view

Side view of the ribbon structure of the M2R (above) to highlight the ‘lid-like’ structure over the orthosteric site. Illustrated are side chain residues Y4036.38 and Y4267.39 moving toward Y1043.33 during the formation of the active conformation. Note that TM5 was removed from the rendering so that the tyrosine residues may be easily viewed. Morphs were generated between the inactive and active conformations using Chimera (Pettersen, E,F., et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 25, 1605-12) and rendered with Pymol (The PyMOL Molecular Graphics System, Schrödinger, LLC). (MOV 2616 kb)

Stabilization of the active state of rhodopsin by G protein

Top view of the ribbon structure of bovine rhodopsin in its inactive conformation (PDB:1F88) (Palczewski, K. et al. Crystal structure of rhodopsin: A G protein-coupled receptor Science 289: 739-745 (2000)) and the photoactivated meta-stable form of rhodopsin bound to the C-terminal fragment of the G protein alpha subunit, transducin (transducin not shown) (PDB:3PAR) (Choe H. W. et al. Crystal structure of metarhodopsin II. Nature 471, 651–655 (2011)). Note the pre-existing ‘lid-like’ structure over the orthosteric site formed by the ECL2 and N-terminus. Photoisomerization of 11-cis retinal is illustrated in magenta. Morphs were generated between the inactive and active conformations using Chimera (Pettersen, E,F., et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 25, 1605-12) and rendered with Pymol (The PyMOL Molecular Graphics System, Schrödinger, LLC). (MOV 6005 kb)

Stabilization of the active state of rhodopsin by arrestin

Top view of the ribbon structure of bovine rhodopsin in its inactive conformation (PDB:1F88) (Palczewski, K. et al. Crystal structure of rhodopsin: A G protein-coupled receptor Science 289: 739-745 (2000)) and an active mutant of opsin bound to activated arrestin (arrestin not shown) (PDB:4ZWJ) (Kang, Y. et al. Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature 523, 561-567 (2015)). Note the similarities in conformational changes as with metarhodopsin bound to the C-terminal helix of transducin. Photoisomerization of 11-cis retinal, based on the metarhodopsin structures (Extended data: Movie SM6) has been modeled into the opsin-arrestin structure and is illustrated in magenta. Morphs were generated between inactive and arrestin-bound conformations of rhodopsin using Chimera (Pettersen, E,F., et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004 25, 1605-12.) and rendered with Pymol (The PyMOL Molecular Graphics System, Schrödinger, LLC). (MOV 5598 kb)

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DeVree, B., Mahoney, J., Vélez-Ruiz, G. et al. Allosteric coupling from G protein to the agonist-binding pocket in GPCRs. Nature 535, 182–186 (2016). https://doi.org/10.1038/nature18324

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