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

DeVree, Brian T.; Mahoney, Jacob P.; Velez-Ruiz, Gisselle; Rasmussen, Søren G. F.; Kuszak, Adam; Edwald, Elin; Fung, Juan José; Manglik, Aashish; Masureel, Matthieu; Du, Yang; Matt, Rachel A.; Pardon, Els; Steyaert, Jan; Kobilka, Brian K.; Sunahara, Roger K.

doi:10.1038/nature18324

Cited by 260 publications

(269 citation statements)

References 32 publications

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“…We have captured both dissociation and binding of an orthosteric ligand in a single all-atom GPCR simulation in the case of ARC binding to the M 2 receptor. These results are consistent with the recent experimental finding that the G-protein mimetic nanobody stabilizes a closed receptor conformation and dramatically affects the association and dissociation of GPCR ligands (17). Notably, Dror et al (23) successfully observed both binding and dissociation of allosteric modulators at the M 2 receptor through long-timescale conventional MD (cMD) simulations.…”

Section: Discussionsupporting

confidence: 80%

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Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor

Miao

McCammon

2016

Proc. Natl. Acad. Sci. U.S.A.

149

170

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G-protein-coupled receptors (GPCRs) recognize ligands of widely different efficacies, from inverse to partial and full agonists, which transduce cellular signals at differentiated levels. However, the mechanism of such graded activation remains unclear. Using the Gaussian accelerated molecular dynamics (GaMD) method that enables both unconstrained enhanced sampling and free energy calculation, we have performed extensive GaMD simulations (∼19 μs in total) to investigate structural dynamics of the M 2 muscarinic GPCR that is bound by the full agonist iperoxo (IXO), the partial agonist arecoline (ARC), and the inverse agonist 3-quinuclidinyl-benzilate (QNB), in the presence or absence of the G-protein mimetic nanobody. In the receptornanobody complex, IXO binding leads to higher fluctuations in the protein-coupling interface than ARC, especially in the receptor transmembrane helix 5 (TM5), TM6, and TM7 intracellular domains that are essential elements for GPCR activation, but less flexibility in the receptor extracellular region due to stronger binding compared with ARC. Two different binding poses are revealed for ARC in the orthosteric pocket. Removal of the nanobody leads to GPCR deactivation that is characterized by inward movement of the TM6 intracellular end. Distinct low-energy intermediate conformational states are identified for the IXO-and ARC-bound M 2 receptor. Both dissociation and binding of an orthosteric ligand are observed in a single all-atom GPCR simulation in the case of partial agonist ARC binding to the M 2 receptor. This study demonstrates the applicability of GaMD for exploring free energy landscapes of large biomolecules and the simulations provide important insights into the GPCR functional mechanism. cellular signaling | ligand recognition | protein-protein interactions | allostery | drug discovery G -protein-coupled receptors (GPCRs) are primary targets of about one-third of currently marketed drugs. They recognize ligands of widely different efficacies, from inverse to partial and full agonists, which transduce cellular signals at differentiated levels. Increasing experimental and computational evidence suggests that GPCRs exist in an ensemble of different conformations that interconvert dynamically during activation and ligand recognition (1-3). The structure, dynamics, and function of GPCRs result from underlying free energy landscapes (4). However, quantitative characterization of the GPCR activation and ligand-dependent free energy profiles has proved challenging (4-12).The M 2 muscarinic GPCR is widely distributed in mammalian tissues. It plays a key role in regulating the human heart rate and heart contraction forces. The M 2 receptor has been crystallized in both an inactive state bound by the inverse agonist 3-quinuclidinylbenzilate (QNB) (13) and an active state bound by the full agonist iperoxo (IXO) and a G-protein mimetic nanobody (14). The receptor activation is characterized by rearrangements of the transmembrane (TM) helices 5, 6, and 7, particularly closing of the ligan...

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Section: Discussionsupporting

confidence: 80%

“…Coupling of the receptor with the G protein or mimetic nanobody typically increases agonist binding affinities (17). However, structural information of partial agonist binding is scarce, except for few other GPCRs (18).…”

mentioning

confidence: 99%

Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor

Miao

McCammon

2016

Proc. Natl. Acad. Sci. U.S.A.

149

170

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“…Conformational selectionbased ligand-binding mechanisms as well as multiple receptor signaling states are well documented for other GPCRs, including the B2AR and CB1 receptor (7,20,(35)(36)(37)(38). Hence, the delayed reversion to the inactive receptor conformation we observe for rhodopsin might play a heretofore unappreciated role here and in other GPCR signaling systems.…”

Section: After Rhodopsin Photoactivation An Equilibrium Of Atr Releamentioning

confidence: 91%

Decay of an active GPCR: Conformational dynamics govern agonist rebinding and persistence of an active, yet empty, receptor state

Schafer

Fay

Janz

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Here, we describe two insights into the role of receptor conformational dynamics during agonist release (all-trans retinal, ATR) from the visual G protein-coupled receptor (GPCR) rhodopsin. First, we show that, after light activation, ATR can continually release and rebind to any receptor remaining in an active-like conformation. As with other GPCRs, we observe that this equilibrium can be shifted by either promoting the active-like population or increasing the agonist concentration. Second, we find that during decay of the signaling state an active-like, yet empty, receptor conformation can transiently persist after retinal release, before the receptor ultimately collapses into an inactive conformation. The latter conclusion is based on timeresolved, site-directed fluorescence labeling experiments that show a small, but reproducible, lag between the retinal leaving the protein and return of transmembrane helix 6 (TM6) to the inactive conformation, as determined from tryptophan-induced quenching studies. Accelerating Schiff base hydrolysis and subsequent ATR dissociation, either by addition of hydroxylamine or introduction of mutations, further increased the time lag between ATR release and TM6 movement. These observations show that rhodopsin can bind its agonist in equilibrium like a traditional GPCR, provide evidence that an active GPCR conformation can persist even after agonist release, and raise the possibility of targeting this key photoreceptor protein by traditional pharmaceutical-based treatments.T he superfamily of G protein-coupled receptors (GPCRs) is one of the largest targets of pharmaceutical drugs in the human genome. Classically, GPCR signaling occurs when a diffusible ligand (such as a drug) binds to the receptor and stabilizes conformations that can couple with and activate intracellular proteins. Our understanding of this process has built on the classical "ternary complex" model of receptor-ligand-G protein interaction (1), a model that, with revisions, has continued to guide our knowledge of how this critical event occurs.However, this paradigm has faced problems when applied to rhodopsin, the dim-light visual receptor. Rhodopsin is kept in an "off" state by a covalently bound inverse agonist, 11-cis retinal (11CR). Light converts the 11CR to an agonist, all-trans retinal (ATR), which enables the receptor to activate its G protein, transducin (G t ) (2, 3). The active receptor, metarhodopsin II (MII), continues signaling until the Schiff base linking ATR to the receptor is hydrolyzed, resulting in the release of ATR and the decay of MII into an inactive apoprotein, opsin (4, 5). Binding of a new 11CR to opsin reforms the dark state (DS), enabling another round of photon detection (6).Due to this unusual light-activated, covalently bound ligand, rhodopsin has usually been considered "different" from the larger superfamily of diffusible ligand-binding GPCRs. However, we recently discovered that rhodopsin behaves more like a traditional ligand-binding GPCR than previously thought (7). Our expe...

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“…For example, addition of an extracellular agonist to β 2 AR results in conformational changes at the intracellular ends of receptor TM helices (45, 71, 107), and enhances the stability of receptor:G protein complexes (144) (“upside-down”). On the other hand, addition of either G protein or a G protein-mimicking nanobody Nb80 (124), both of which bind intracellularly, affects affinity and binding kinetics of extracellular agonists (30, 107) (“downside-up”). The bi-directional communication works not only in the context of receptor activation, but also in inactivation: inactive-state-specific intracellularly-binding nanobodies and antibodies reduce receptor affinity for extracellular agonists and increase affinity for inverse agonists (52, 123).…”

Section: On Allostery Of Chemokine Receptorsmentioning

confidence: 99%

What Do Structures Tell Us About Chemokine Receptor Function and Antagonism?

Kufareva

Gustavsson

Zheng

et al. 2017

Annu. Rev. Biophys.

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Chemokines and their cell surface G protein-coupled receptors are critical for cell migration not only in many fundamental biological processes but also in inflammatory diseases and cancer. Recent X-ray structures of two chemokines complexed with full-length receptors provide unprecedented insight into the atomic details of chemokine recognition and receptor activation, and computational modeling informed by new experiments leverages these insights to gain understanding of many more receptor:chemokine pairs. In parallel, chemokine receptor structures with small molecules reveal complicated and diverse structural foundations of small molecule antagonism and allostery, highlight inherent physicochemical challenges of receptor:chemokine interfaces, and suggest novel epitopes that can be exploited to overcome these challenges. The structures and models promote unique understanding of chemokine receptor biology, including the interpretation of two decades of experimental studies, and will undoubtedly assist future drug discovery endeavors.

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

Cited by 260 publications

References 32 publications

Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor

Graded activation and free energy landscapes of a muscarinic G-protein–coupled receptor

Decay of an active GPCR: Conformational dynamics govern agonist rebinding and persistence of an active, yet empty, receptor state

What Do Structures Tell Us About Chemokine Receptor Function and Antagonism?

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