1
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Kermani AA. Applications of fluorescent protein tagging in structural studies of membrane proteins. FEBS J 2024; 291:2719-2732. [PMID: 37470714 DOI: 10.1111/febs.16910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/16/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Generating active, pure, and monodisperse protein remains a major bottleneck for structural studies using X-ray crystallography and cryo-electron microscopy (cryo-EM). The current methodology heavily relies on overexpressing the recombinant protein fused with a histidine tag in conventional expression systems and evaluating the quality and stability of purified protein using size exclusion chromatography (SEC). This requires a large amount of protein and can be highly laborious and time consuming. Therefore, this approach is not suitable for high-throughput screening and low-expressing macromolecules, particularly eukaryotic membrane proteins. Using fluorescent proteins fused to the target protein (applicable to both soluble and membrane proteins) enables rapid and efficient screening of expression level and monodispersity of tens of unpurified constructs using fluorescence-based size exclusion chromatography (FSEC). Moreover, FSEC proves valuable for screening multiple detergents to identify the most stabilizing agent in the case of membrane proteins. Additionally, FSEC can facilitate nanodisc reconstitution by determining the optimal ratio of membrane scaffold protein (MSP), lipids, and target protein. The distinct advantages offered by FSEC indicate that fluorescent proteins can serve as a viable alternative to commonly used affinity tags for both characterization and purification purposes. In this review, I will summarize the advantages of this technique using examples from my own work. It should be noted that this article is not intended to provide an exhaustive review of all available literature, but rather to offer representative examples of FSEC applications.
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Affiliation(s)
- Ali A Kermani
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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2
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Claff T, Mahardhika AB, Vaaßen VJ, Schlegel J, Vielmuth C, Weiße RH, Sträter N, Müller CE. Structural Insights into Partial Activation of the Prototypic G Protein-Coupled Adenosine A 2A Receptor. ACS Pharmacol Transl Sci 2024; 7:1415-1425. [PMID: 38751633 PMCID: PMC11091970 DOI: 10.1021/acsptsci.4c00051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 05/18/2024]
Abstract
The adenosine A2A receptor (A2AAR) belongs to the rhodopsin-like G protein-coupled receptor (GPCR) family, which constitutes the largest class of GPCRs. Partial agonists show reduced efficacy as compared to physiological agonists and can even act as antagonists in the presence of a full agonist. Here, we determined an X-ray crystal structure of the partial A2AAR agonist 2-amino-6-[(1H-imidazol-2-ylmethyl)sulfanyl]-4-p-hydroxyphenyl-3,5-pyridinedicarbonitrile (LUF5834) in complex with the A2AAR construct A2A-PSB2-bRIL, stabilized in its inactive conformation and being devoid of any mutations in the ligand binding pocket. The determined high-resolution structure (2.43 Å) resolved water networks and crucial binding pocket interactions. A direct hydrogen bond of the p-hydroxy group of LUF5834 with T883.36 was observed, an amino acid that was mutated to alanine in the most frequently used A2AAR crystallization constructs thus preventing the discovery of its interactions in most of the previous A2AAR co-crystal structures. G protein dissociation studies confirmed partial agonistic activity of LUF5834 as compared to that of the full agonist N-ethylcarboxamidoadenosine (NECA). In contrast to NECA, the partial agonist was still able to bind to the receptor construct locked in its inactive conformation by an S913.39K mutation, although with an affinity lower than that at the native receptor. This could explain the compound's partial agonistic activity: while full A2AAR agonists bind exclusively to the active conformation, likely following conformational selection, partial agonists bind to active as well as inactive conformations, showing higher affinity for the active conformation. This might be a general mechanism of partial agonism also applicable to other GPCRs.
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Affiliation(s)
- Tobias Claff
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
| | - Andhika B. Mahardhika
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
- Research
Training Group 2873, University of Bonn, Bonn 53121, Germany
| | - Victoria J. Vaaßen
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
| | - Jonathan
G. Schlegel
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
| | - Christin Vielmuth
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
| | - Renato H. Weiße
- Institute
of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig 04103, Germany
| | - Norbert Sträter
- Institute
of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig 04103, Germany
| | - Christa E. Müller
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
- Research
Training Group 2873, University of Bonn, Bonn 53121, Germany
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3
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Thakur N, Ray AP, Jin B, Afsharian NP, Lyman E, Gao ZG, Jacobson KA, Eddy MT. Membrane mimetic-dependence of GPCR energy landscapes. Structure 2024; 32:523-535.e5. [PMID: 38401537 PMCID: PMC11069452 DOI: 10.1016/j.str.2024.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/03/2024] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
We leveraged variable-temperature 19F-NMR spectroscopy to compare the conformational equilibria of the human A2A adenosine receptor (A2AAR), a class A G protein-coupled receptor (GPCR), across a range of temperatures ranging from lower temperatures typically employed in 19F-NMR experiments to physiological temperature. A2AAR complexes with partial agonists and full agonists showed large increases in the population of a fully active conformation with increasing temperature. NMR data measured at physiological temperature were more in line with functional data. This was pronounced for complexes with partial agonists, where the population of active A2AAR was nearly undetectable at lower temperature but became evident at physiological temperature. Temperature-dependent behavior of complexes with either full or partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. Cellular signaling experiments correlated with the temperature-dependent conformational equilibria of A2AAR in lipid nanodiscs but not in some detergents, underscoring the importance of the membrane environment in studies of GPCR function.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Beining Jin
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | | | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, DE, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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4
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Jones AJY, Harman TH, Harris M, Lewis OE, Ladds G, Nietlispach D. Binding kinetics drive G protein subtype selectivity at the β 1-adrenergic receptor. Nat Commun 2024; 15:1334. [PMID: 38351103 PMCID: PMC10864275 DOI: 10.1038/s41467-024-45680-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
G protein-coupled receptors (GPCRs) bind to different G protein α-subtypes with varying degrees of selectivity. The mechanism by which GPCRs achieve this selectivity is still unclear. Using 13C methyl methionine and 19F NMR, we investigate the agonist-bound active state of β1AR and its ternary complexes with different G proteins in solution. We find the receptor in the ternary complexes adopts very similar conformations. In contrast, the full agonist-bound receptor active state assumes a conformation differing from previously characterised activation intermediates or from β1AR in ternary complexes. Assessing the kinetics of binding for the agonist-bound receptor with different G proteins, we find the increased affinity of β1AR for Gs results from its much faster association with the receptor. Consequently, we suggest a kinetic-driven selectivity gate between canonical and secondary coupling which arises from differential favourability of G protein binding to the agonist-bound receptor active state.
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Affiliation(s)
- Andrew J Y Jones
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Thomas H Harman
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Matthew Harris
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Oliver E Lewis
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Daniel Nietlispach
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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5
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Wei S, Pour NG, Tiruvadi-Krishnan S, Ray AP, Thakur N, Eddy MT, Lamichhane R. Single-molecule visualization of human A 2A adenosine receptor activation by a G protein and constitutively activating mutations. Commun Biol 2023; 6:1218. [PMID: 38036689 PMCID: PMC10689853 DOI: 10.1038/s42003-023-05603-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
Mutations that constitutively activate G protein-coupled receptors (GPCRs), known as constitutively activating mutations (CAMs), modify cell signaling and interfere with drugs, resulting in diseases with limited treatment options. We utilize fluorescence imaging at the single-molecule level to visualize the dynamic process of CAM-mediated activation of the human A2A adenosine receptor (A2AAR) in real time. We observe an active-state population for all CAMs without agonist stimulation. Importantly, activating mutations significantly increase the population of an intermediate state crucial for receptor activation, notably distinct from the addition of a partner G protein. Activation kinetics show that while CAMs increase the frequency of transitions to the intermediate state, mutations altering sodium sensitivity increase transitions away from it. These findings indicate changes in GPCR function caused by mutations may be predicted based on whether they favor or disfavor formation of an intermediate state, providing a framework for designing receptors with altered functions or therapies that target intermediate states.
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Affiliation(s)
- Shushu Wei
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Sriram Tiruvadi-Krishnan
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
| | - Arka Prabha Ray
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Naveen Thakur
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA.
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA.
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6
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Calderón JC, Ibrahim P, Gobbo D, Gervasio FL, Clark T. Activation/Deactivation Free-Energy Profiles for the β 2-Adrenergic Receptor: Ligand Modes of Action. J Chem Inf Model 2023; 63:6332-6343. [PMID: 37824365 DOI: 10.1021/acs.jcim.3c00805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
We use enhanced-sampling simulations with an effective collective variable to study the activation of the β2-adrenergic receptor in the presence of ligands with different efficacy. The free-energy profiles are computed for the ligand-free (apo) receptor and binary (apo-receptor + G-protein α-subunit and receptor + ligand) and ternary complexes. The results are not only compatible with available experiments but also allow unprecedented structural insight into the nature of GPCR conformations along the activation pathway and their role in the activation mechanism. In particular, the simulations reveal an unexpected mode of action of partial agonists such as salmeterol and salbutamol that arises already in the binary complex without the G-protein. Specific differences in the polar interactions with residues in TM5, which are required to stabilize an optimal TM6 conformation that facilitates G-protein binding and receptor activation, play a major role in differentiating them from full agonists.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstraße 25, 91052 Erlangen, Germany
| | - Passainte Ibrahim
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, 04109 Leipzig, Germany
| | - Dorothea Gobbo
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
- Chemistry Department, University College London, WC1H 0AJ London, United Kingdom
- Swiss Bioinformatics Institute, CH1206 Geneva, Switzerland
| | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstraße 25, 91052 Erlangen, Germany
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7
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Thakur N, Ray AP, Lyman E, Gao ZG, Jacobson KA, Eddy MT. Membrane Mimetic-Dependence of GPCR Energy Landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562552. [PMID: 37905159 PMCID: PMC10614885 DOI: 10.1101/2023.10.16.562552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Protein function strongly depends on temperature, which is related to temperature-dependent changes in the equilibria of protein conformational states. We leveraged variable-temperature 19F-NMR spectroscopy to interrogate the temperature dependence of the conformational landscape of the human A2A adenosine receptor (A2AAR), a class A GPCR. Temperature-induced changes in the conformational equilibria of A2AAR in lipid nanodiscs were markedly dependent on the efficacy of bound drugs. While antagonist complexes displayed only modest changes as the temperature rose, both full and partial agonist complexes exhibited substantial increases in the active state population. Importantly, the temperature-dependent response of complexes with both full and partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. In striking contrast to observations within lipid nanodiscs, in detergent micelles the active state population exhibited different behavior for A2AAR complexes with both full and partial agonists. This underscores the importance of the protein environment in understanding the thermodynamics of GPCR activation.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
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8
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Jin B, Thakur N, Wijesekara AV, Eddy MT. Illuminating GPCR signaling mechanisms by NMR spectroscopy with stable-isotope labeled receptors. Curr Opin Pharmacol 2023; 72:102364. [PMID: 37612173 PMCID: PMC11221349 DOI: 10.1016/j.coph.2023.102364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 08/25/2023]
Abstract
G protein-coupled receptors (GPCRs) exhibit remarkable structural plasticity, which underlies their capacity to recognize a wide range of extracellular molecules and interact with intracellular partner proteins. Nuclear magnetic resonance (NMR) spectroscopy is uniquely well-suited to investigate GPCR structural plasticity, enabled by stable-isotope "probes" incorporated into receptors that inform on structure and dynamics. Progress with stable-isotope labeling methods in Eukaryotic expression systems has enabled production of native or nearly-native human receptors with varied and complementary distributions of NMR probes. These advances have opened up new avenues for investigating the roles of conformational dynamics in signaling processes, including by mapping allosteric communication networks, understanding the specificity of GPCR interactions with partner proteins and exploring the impact of membrane environments on GPCR function.
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Affiliation(s)
- Beining Jin
- Department of Chemistry; University of Florida; Gainesville, FL, 32611, USA
| | - Naveen Thakur
- Department of Chemistry; University of Florida; Gainesville, FL, 32611, USA
| | | | - Matthew T Eddy
- Department of Chemistry; University of Florida; Gainesville, FL, 32611, USA.
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9
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Guo C, Yang L, Liu Z, Liu D, Wüthrich K. Two-Dimensional NMR Spectroscopy of the G Protein-Coupled Receptor A 2AAR in Lipid Nanodiscs. Molecules 2023; 28:5419. [PMID: 37513291 PMCID: PMC10383251 DOI: 10.3390/molecules28145419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Eight hundred and twenty-six human G protein-coupled receptors (GPCRs) mediate the actions of two-thirds of the human hormones and neurotransmitters and over one-third of clinically used drugs. Studying the structure and dynamics of human GPCRs in lipid bilayer environments resembling the native cell membrane milieu is of great interest as a basis for understanding structure-function relationships and thus benefits continued drug development. Here, we incorporate the human A2A adenosine receptor (A2AAR) into lipid nanodiscs, which represent a detergent-free environment for structural studies using nuclear magnetic resonance (NMR) in solution. The [15N,1H]-TROSY correlation spectra confirmed that the complex of [u-15N, ~70% 2H]-A2AAR with an inverse agonist adopts its global fold in lipid nanodiscs in solution at physiological temperature. The global assessment led to two observations of practical interest. First, A2AAR in nanodiscs can be stored for at least one month at 4 °C in an aqueous solvent. Second, LMNG/CHS micelles are a very close mimic of the environment of A2AAR in nanodiscs. The NMR signal of five individually assigned tryptophan indole 15N-1H moieties located in different regions of the receptor structure further enabled a detailed assessment of the impact of nanodiscs and LMNG/CHS micelles on the local structure and dynamics of A2AAR. As expected, the largest effects were observed near the lipid-water interface along the intra- and extracellular surfaces, indicating possible roles of tryptophan side chains in stabilizing GPCRs in lipid bilayer membranes.
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Affiliation(s)
- Canyong Guo
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lingyun Yang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Zhijun Liu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Dongsheng Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Kurt Wüthrich
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
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10
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Ray AP, Thakur N, Pour NG, Eddy MT. Dual mechanisms of cholesterol-GPCR interactions that depend on membrane phospholipid composition. Structure 2023; 31:836-847.e6. [PMID: 37236187 PMCID: PMC10330489 DOI: 10.1016/j.str.2023.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/25/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023]
Abstract
Cholesterol is a critical component of mammalian cell membranes and an allosteric modulator of G protein-coupled receptors (GPCRs), but divergent views exist on the mechanisms by which cholesterol influences receptor functions. Leveraging the benefits of lipid nanodiscs, i.e., quantitative control of lipid composition, we observe distinct impacts of cholesterol in the presence and absence of anionic phospholipids on the function-related conformational dynamics of the human A2A adenosine receptor (A2AAR). Direct receptor-cholesterol interactions drive activation of agonist-bound A2AAR in membranes containing zwitterionic phospholipids. Intriguingly, the presence of anionic lipids attenuates cholesterol's impact through direct interactions with the receptor, highlighting a more complex role for cholesterol that depends on membrane phospholipid composition. Targeted amino acid replacements at two frequently predicted cholesterol interaction sites showed distinct impacts of cholesterol at different receptor locations, demonstrating the ability to delineate different roles of cholesterol in modulating receptor signaling and maintaining receptor structural integrity.
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Affiliation(s)
- Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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11
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van Aalst EJ, McDonald CJ, Wylie BJ. Cholesterol Biases the Conformational Landscape of the Chemokine Receptor CCR3: A MAS SSNMR-Filtered Molecular Dynamics Study. J Chem Inf Model 2023; 63:3068-3085. [PMID: 37127541 PMCID: PMC10208230 DOI: 10.1021/acs.jcim.2c01546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Indexed: 05/03/2023]
Abstract
Cholesterol directs the pathway of ligand-induced G protein-coupled receptor (GPCR) signal transduction. The GPCR C-C motif chemokine receptor 3 (CCR3) is the principal chemotactic receptor for eosinophils, with roles in cancer metastasis and autoinflammatory conditions. Recently, we discovered a direct correlation between bilayer cholesterol and increased agonist-triggered CCR3 signal transduction. However, the allosteric molecular mechanism escalating ligand affinity and G protein coupling is unknown. To study cholesterol-guided CCR3 conformational selection, we implement comparative, objective measurement of protein architectures by scoring shifts (COMPASS) to grade model structures from molecular dynamics simulations. In this workflow, we scored predicted chemical shifts against 2-dimensional solid-state NMR 13C-13C correlation spectra of U-15N,13C-CCR3 samples prepared with and without cholesterol. Our analysis of trajectory model structures uncovers that cholesterol induces site-specific conformational restraint of extracellular loop (ECL) 2 and conserved motion in transmembrane helices and ECL3 not observed in simulations of bilayers with only phosphatidylcholine lipids. PyLipID analysis implicates direct cholesterol agency in CCR3 conformational selection and dynamics. Residue-residue contact scoring shows that cholesterol biases the conformational selection of the orthosteric pocket involving Y411.39, Y1133.32, and E2877.39. Lastly, we observe contact remodeling in activation pathway residues centered on the initial transmission switch, Na+ pocket, and R3.50 in the DRY motif. Our observations have unique implications for understanding of CCR3 ligand recognition and specificity and provide mechanistic insight into how cholesterol functions as an allosteric regulator of CCR3 signal transduction.
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Affiliation(s)
- Evan J. van Aalst
- Department of Chemistry and
Biochemistry, Texas Tech University, Lubbock, Texas 79415, United States
| | - Corey J. McDonald
- Department of Chemistry and
Biochemistry, Texas Tech University, Lubbock, Texas 79415, United States
| | - Benjamin J. Wylie
- Department of Chemistry and
Biochemistry, Texas Tech University, Lubbock, Texas 79415, United States
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12
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Calderón JC, Ibrahim P, Gobbo D, Gervasio FL, Clark T. General Metadynamics Protocol To Simulate Activation/Deactivation of Class A GPCRs: Proof of Principle for the Serotonin Receptor. J Chem Inf Model 2023; 63:3105-3117. [PMID: 37161278 DOI: 10.1021/acs.jcim.3c00208] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We present a generally applicable metadynamics protocol for characterizing the activation free-energy profiles of class A G-protein coupled receptors and a proof-of-principle study for the 5HT1A-receptor. The almost universal A100 activation index, which depends on five inter-helix distances, is used as the single collective variable in well-tempered multiple-walker metadynamics simulations. Here, we show free-energy profiles for the serotonin receptor as binary (apo-receptor + G-protein-α-subunit and receptor + ligand) and ternary complexes with two prototypical orthosteric ligands: the full agonist serotonin and the partial agonist aripiprazole. Our results are not only compatible with previously reported experimental and computational data, but they also allow differences between active and inactive conformations to be determined in unprecedented atomic detail, and with respect to the so-called microswitches that have been suggested as determinants of activation, giving insight into their role in the activation mechanism.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany
| | - Passainte Ibrahim
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, Leipzig 04107, Germany
| | - Dorothea Gobbo
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
- Chemistry Department, University College London, WC1H 0AJ London, U.K
| | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany
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13
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Maslov I, Volkov O, Khorn P, Orekhov P, Gusach A, Kuzmichev P, Gerasimov A, Luginina A, Coucke Q, Bogorodskiy A, Gordeliy V, Wanninger S, Barth A, Mishin A, Hofkens J, Cherezov V, Gensch T, Hendrix J, Borshchevskiy V. Sub-millisecond conformational dynamics of the A 2A adenosine receptor revealed by single-molecule FRET. Commun Biol 2023; 6:362. [PMID: 37012383 PMCID: PMC10070357 DOI: 10.1038/s42003-023-04727-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
The complex pharmacology of G-protein-coupled receptors (GPCRs) is defined by their multi-state conformational dynamics. Single-molecule Förster Resonance Energy Transfer (smFRET) is well suited to quantify dynamics for individual protein molecules; however, its application to GPCRs is challenging. Therefore, smFRET has been limited to studies of inter-receptor interactions in cellular membranes and receptors in detergent environments. Here, we performed smFRET experiments on functionally active human A2A adenosine receptor (A2AAR) molecules embedded in freely diffusing lipid nanodiscs to study their intramolecular conformational dynamics. We propose a dynamic model of A2AAR activation that involves a slow (>2 ms) exchange between the active-like and inactive-like conformations in both apo and antagonist-bound A2AAR, explaining the receptor's constitutive activity. For the agonist-bound A2AAR, we detected faster (390 ± 80 µs) ligand efficacy-dependent dynamics. Our work establishes a general smFRET platform for GPCR investigations that can potentially be used for drug screening and/or mechanism-of-action studies.
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Affiliation(s)
- Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | | | - Polina Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Philipp Orekhov
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Anastasiia Gusach
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Pavel Kuzmichev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Andrey Gerasimov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Vyatka State University, Kirov, Russia
| | - Aleksandra Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Quinten Coucke
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Valentin Gordeliy
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
| | - Simon Wanninger
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Anders Barth
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, HZ, Delft, The Netherlands
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Plank Institute for Polymer Research, Mainz, Germany
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium.
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium.
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
- Joint Institute for Nuclear Research, Dubna, Russian Federation.
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14
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Thakur N, Ray AP, Sharp L, Jin B, Duong A, Pour NG, Obeng S, Wijesekara AV, Gao ZG, McCurdy CR, Jacobson KA, Lyman E, Eddy MT. Anionic phospholipids control mechanisms of GPCR-G protein recognition. Nat Commun 2023; 14:794. [PMID: 36781870 PMCID: PMC9925817 DOI: 10.1038/s41467-023-36425-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipids that strongly influence drug-stimulated signaling. Anionic lipids are particularly important for GPCR signaling complex formation, but a mechanism for this role is not understood. Using NMR spectroscopy, we explore the impact of anionic lipids on the function-related conformational equilibria of the human A2A adenosine receptor (A2AAR) in bilayers containing defined mixtures of zwitterionic and anionic phospholipids. Anionic lipids prime the receptor to form complexes with G proteins through a conformational selection process. Without anionic lipids, signaling complex formation proceeds through a less favorable induced fit mechanism. In computational models, anionic lipids mimic interactions between a G protein and positively charged residues in A2AAR at the receptor intracellular surface, stabilizing a pre-activated receptor conformation. Replacing these residues strikingly alters the receptor response to anionic lipids in experiments. High sequence conservation of the same residues among all GPCRs supports a general role for lipid-receptor charge complementarity in signaling.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Arka P Ray
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Liam Sharp
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
| | - Beining Jin
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Alexander Duong
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Samuel Obeng
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Anuradha V Wijesekara
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
- Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, Florida, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA.
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15
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Thakur N, Ray AP, Sharp L, Jin B, Duong A, Pour NG, Obeng S, Wijesekara AV, Gao ZG, McCurdy CR, Jacobson KA, Lyman E, Eddy MT. Anionic Phospholipids Control Mechanisms of GPCR-G Protein Recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523010. [PMID: 36711594 PMCID: PMC9882065 DOI: 10.1101/2023.01.11.523010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipids that strongly influence drug-stimulated signaling. Anionic lipids are particularly important for GPCR signaling complex formation, but a mechanism for this role is not understood. Using NMR spectroscopy, we visualized the impact of anionic lipids on the function-related conformational equilibria of the human A 2A adenosine receptor (A 2A AR) in bilayers containing defined mixtures of zwitterionic and anionic phospholipids. Anionic lipids primed the receptor to form complexes with G proteins through a conformational selection process. Without anionic lipids, signaling complex formation proceeded through a less favorable induced fit mechanism. In computational models, anionic lipids mimicked interactions between a G protein and positively charged residues in A 2A AR at the receptor intracellular surface, stabilizing a pre-activated receptor conformation. Replacing these residues strikingly altered the receptor response to anionic lipids in experiments. High sequence conservation of the same residues among all GPCRs supports a general role for lipid-receptor charge complementarity in signaling.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka P Ray
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Liam Sharp
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware
| | - Beining Jin
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Alexander Duong
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Samuel Obeng
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Anuradha V Wijesekara
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
- Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
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16
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Ferré G, Anazia K, Silva LO, Thakur N, Ray AP, Eddy MT. Global insights into the fine tuning of human A 2AAR conformational dynamics in a ternary complex with an engineered G protein viewed by NMR. Cell Rep 2022; 41:111844. [PMID: 36543140 PMCID: PMC9832913 DOI: 10.1016/j.celrep.2022.111844] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/03/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022] Open
Abstract
G protein-coupled receptor (GPCR) conformational plasticity enables formation of ternary signaling complexes with intracellular proteins in response to binding extracellular ligands. We investigate the dynamic process of GPCR complex formation in solution with the human A2A adenosine receptor (A2AAR) and an engineered Gs protein, mini-Gs. 2D nuclear magnetic resonance (NMR) data with uniform stable isotope-labeled A2AAR enabled a global comparison of A2AAR conformations between complexes with an agonist and mini-Gs and with an agonist alone. The two conformations are similar and show subtle differences at the receptor intracellular surface, supporting a model whereby agonist binding alone is sufficient to populate a conformation resembling the active state. However, an A2AAR "hot spot" connecting the extracellular ligand-binding pocket to the intracellular surface is observed to be highly dynamic in the ternary complex, suggesting a mechanism for allosteric connection between the bound G protein and the drug-binding pocket involving structural plasticity of the "toggle switch" tryptophan.
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Affiliation(s)
- Guillaume Ferré
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA,Present address: Institut de Pharmacologie et Biologie Structurale; Université de Toulouse, CNRS, Université Paul Sabatier; Toulouse 31000, France
| | - Kara Anazia
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Larissa O. Silva
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Naveen Thakur
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Arka P. Ray
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Matthew T. Eddy
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA,Lead contact,Correspondence:
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17
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G Protein-coupled Receptor (GPCR) Reconstitution and Labeling for Solution Nuclear Magnetic Resonance (NMR) Studies of the Structural Basis of Transmembrane Signaling. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092658. [PMID: 35566006 PMCID: PMC9101874 DOI: 10.3390/molecules27092658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 11/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are a large membrane protein family found in higher organisms, including the human body. GPCRs mediate cellular responses to diverse extracellular stimuli and thus control key physiological functions, which makes them important targets for drug design. Signaling by GPCRs is related to the structure and dynamics of these proteins, which are modulated by extrinsic ligands as well as by intracellular binding partners such as G proteins and arrestins. Here, we review some basics of using nuclear magnetic resonance (NMR) spectroscopy in solution for the characterization of GPCR conformations and intermolecular interactions that relate to transmembrane signaling.
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18
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IJzerman AP, Jacobson KA, Müller CE, Cronstein BN, Cunha RA. International Union of Basic and Clinical Pharmacology. CXII: Adenosine Receptors: A Further Update. Pharmacol Rev 2022; 74:340-372. [PMID: 35302044 PMCID: PMC8973513 DOI: 10.1124/pharmrev.121.000445] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Our previous International Union of Basic and Clinical Pharmacology report on the nomenclature and classification of adenosine receptors (2011) contained a number of emerging developments with respect to this G protein-coupled receptor subfamily, including protein structure, protein oligomerization, protein diversity, and allosteric modulation by small molecules. Since then, a wealth of new data and results has been added, allowing us to explore novel concepts such as target binding kinetics and biased signaling of adenosine receptors, to examine a multitude of receptor structures and novel ligands, to gauge new pharmacology, and to evaluate clinical trials with adenosine receptor ligands. This review should therefore be considered a further update of our previous reports from 2001 and 2011. SIGNIFICANCE STATEMENT: Adenosine receptors (ARs) are of continuing interest for future treatment of chronic and acute disease conditions, including inflammatory diseases, neurodegenerative afflictions, and cancer. The design of AR agonists ("biased" or not) and antagonists is largely structure based now, thanks to the tremendous progress in AR structural biology. The A2A- and A2BAR appear to modulate the immune response in tumor biology. Many clinical trials for this indication are ongoing, whereas an A2AAR antagonist (istradefylline) has been approved as an anti-Parkinson agent.
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Affiliation(s)
- Adriaan P IJzerman
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Kenneth A Jacobson
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Christa E Müller
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Bruce N Cronstein
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
| | - Rodrigo A Cunha
- Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.P.IJ.); National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Molecular Recognition Section, Bethesda, Maryland (K.A.J.); Universität Bonn, Bonn, Germany (C.E.M.); New York University School of Medicine, New York, New York (B.N.C.); and Center for Neurosciences and Cell Biology and Faculty of Medicine, University of Coimbra, Coimbra, Portugal (R.A.C.)
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19
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Wei S, Thakur N, Ray AP, Jin B, Obeng S, McCurdy CR, McMahon LR, Gutiérrez-de-Terán H, Eddy MT, Lamichhane R. Slow conformational dynamics of the human A 2A adenosine receptor are temporally ordered. Structure 2022; 30:329-337.e5. [PMID: 34895472 PMCID: PMC8897252 DOI: 10.1016/j.str.2021.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/26/2021] [Accepted: 11/17/2021] [Indexed: 01/12/2023]
Abstract
A more complete depiction of protein energy landscapes includes the identification of different function-related conformational states and the determination of the pathways connecting them. We used total internal reflection fluorescence (TIRF) imaging to investigate the conformational dynamics of the human A2A adenosine receptor (A2AAR), a class A G protein-coupled receptor (GPCR), at the single-molecule level. Slow, reversible conformational exchange was observed among three different fluorescence emission states populated for agonist-bound A2AAR. Transitions among these states predominantly occurred in a specific order, and exchange between inactive and active-like conformations proceeded through an intermediate state. Models derived from molecular dynamics simulations with available A2AAR structures rationalized the relative fluorescence emission intensities for the highest and lowest emission states but not the transition state. This suggests that the functionally critical intermediate state required to achieve activation is not currently visualized among available A2AAR structures.
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Affiliation(s)
- Shushu Wei
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37932, USA
| | - Naveen Thakur
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka P Ray
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Beining Jin
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Samuel Obeng
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, FL 32610, USA
| | - Lance R McMahon
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Uppsala University, B.M.C., Box 596, Uppsala 751 24, Sweden
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, 1311 Cumberland Avenue, Knoxville, TN 37932, USA.
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20
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Huang SK, Prosser RS. Dynamics and Mechanistic Underpinnings to Pharmacology of Class A GPCRs - An NMR Perspective. Am J Physiol Cell Physiol 2022; 322:C739-C753. [PMID: 35235425 DOI: 10.1152/ajpcell.00044.2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
One-third of current pharmaceuticals target G protein-coupled receptors (GPCRs), the largest receptor superfamily in humans and mediators of diverse physiological processes. This review summarizes the recent progress in GPCR structural dynamics, focusing on class A receptors and insights derived from nuclear magnetic resonance (NMR) and other spectroscopic techniques. We describe the structural aspects of GPCR activation and the various pharmacological models that capture aspects of receptor signaling behaviour. Spectroscopic studies revealed that receptors and their signaling complexes are dynamic allosteric systems that sample multiple functional states under basal conditions. The distribution of states within the conformational ensemble and the kinetics of transitions between states are regulated through the binding of ligands, allosteric modulators, and the membrane environment. This ensemble view of GPCRs provides a mechanistic framework for understanding many of the pharmacological phenomena associated with receptor signaling, such as basal activity, efficacy, and functional bias.
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Affiliation(s)
- Shuya Kate Huang
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - R Scott Prosser
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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21
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Mechanistic Origin of Partial Agonism of Tetrahydrocannabinol for Cannabinoid Receptors. J Biol Chem 2022; 298:101764. [PMID: 35227761 PMCID: PMC8965160 DOI: 10.1016/j.jbc.2022.101764] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 01/14/2023] Open
Abstract
Cannabinoid receptor 1 (CB1) is a therapeutically relevant drug target for controlling pain, obesity, and other central nervous system disorders. However, full agonists and antagonists of CB1 have been reported to cause serious side effects in patients. Therefore, partial agonists have emerged as a viable alternative as they can mitigate overstimulation and side effects. One of the key bottlenecks in the design of partial agonists, however, is the lack of understanding of the molecular mechanism of partial agonism itself. In this study, we examine two mechanistic hypotheses for the origin of partial agonism in cannabinoid receptors and predict the mechanistic basis of partial agonism exhibited by Δ9-Tetrahydrocannabinol (THC) against CB1. In particular, we inspect whether partial agonism emerges from the ability of THC to bind in both agonist and antagonist-binding poses or from its ability to only partially activate the receptor. We used extensive molecular dynamics simulations and Markov state modeling to capture the THC binding in both antagonist and agonist-binding poses in the CB1 receptor. Furthermore, we predict that binding of THC in the agonist-binding pose leads to rotation of toggle switch residues and causes partial outward movement of intracellular transmembrane helix 6 (TM6). Our simulations also suggest that the alkyl side chain of THC plays a crucial role in determining partial agonism by stabilizing the ligand in the agonist and antagonist-like poses within the pocket. Taken together, this study provides important insights into the mechanistic origin of the partial agonism of THC.
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22
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Jespers W, Heitman LH, IJzerman AP, Sotelo E, van Westen GJP, Åqvist J, Gutiérrez-de-Terán H. Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations. PLoS Comput Biol 2021; 17:e1009152. [PMID: 34818333 PMCID: PMC8654218 DOI: 10.1371/journal.pcbi.1009152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 12/08/2021] [Accepted: 11/11/2021] [Indexed: 12/25/2022] Open
Abstract
Transmembranal G Protein-Coupled Receptors (GPCRs) transduce extracellular chemical signals to the cell, via conformational change from a resting (inactive) to an active (canonically bound to a G-protein) conformation. Receptor activation is normally modulated by extracellular ligand binding, but mutations in the receptor can also shift this equilibrium by stabilizing different conformational states. In this work, we built structure-energetic relationships of receptor activation based on original thermodynamic cycles that represent the conformational equilibrium of the prototypical A2A adenosine receptor (AR). These cycles were solved with efficient free energy perturbation (FEP) protocols, allowing to distinguish the pharmacological profile of different series of A2AAR agonists with different efficacies. The modulatory effects of point mutations on the basal activity of the receptor or on ligand efficacies could also be detected. This methodology can guide GPCR ligand design with tailored pharmacological properties, or allow the identification of mutations that modulate receptor activation with potential clinical implications. The design of new ligands as chemical modulators of G protein-coupled receptors (GPCRs) has benefited considerably during the last years of advances in both the structural and computational biology disciplines. Within the last area, the use of free energy calculation methods has arisen as a computational tool to predict ligand affinities to explain structure-affinity relationships and guide lead optimization campaigns. However, our comprehension of the structural determinants of ligands with different pharmacological profile is scarce, and knowledge of the chemical modifications associated with an agonistic or antagonistic profile would be extremely valuable. We herein report an original implementation of the thermodynamic cycles associated with free energy perturbation (FEP) simulations, to mimic the conformational equilibrium between active and inactive GPCRs, and establish a framework to describe pharmacological profiles as a function of the ligands selectivity for a given receptor conformation. The advantage of this method resides into its simplicity of use, and the only consideration of active and inactive conformations of the receptor, with no simulation of the transitions between them. This model can accurately predict the pharmacological profile of series of full and partial agonists as opposed to antagonists of the A2A adenosine receptor, and moreover, how certain mutations associated with modulation of basal activity can influence this pharmacological profiles, which enables our understanding of such clinically relevant mutations.
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Affiliation(s)
- Willem Jespers
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC), Uppsala, Sweden
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
- * E-mail: (WJ); (HGT)
| | - Laura H. Heitman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
- Oncode Institute, Leiden, Leiden
| | - Adriaan P. IJzerman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Eddy Sotelo
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Santiago de Compostela, Spain
- Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Gerard J. P. van Westen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC), Uppsala, Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC), Uppsala, Sweden
- Science for Life Laboratories, BMC, Uppsala, Sweden
- * E-mail: (WJ); (HGT)
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23
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Mulry E, Ray AP, Eddy MT. Production of a Human Histamine Receptor for NMR Spectroscopy in Aqueous Solutions. Biomolecules 2021; 11:632. [PMID: 33923140 PMCID: PMC8146376 DOI: 10.3390/biom11050632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 12/26/2022] Open
Abstract
G protein-coupled receptors (GPCRs) bind a broad array of extracellular molecules and transmit intracellular signals that initiate physiological responses. The signal transduction functions of GPCRs are inherently related to their structural plasticity, which can be experimentally observed by spectroscopic techniques. Nuclear magnetic resonance (NMR) spectroscopy in particular is an especially advantageous method to study the dynamic behavior of GPCRs. The success of NMR studies critically relies on the production of functional GPCRs containing stable-isotope labeled probes, which remains a challenging endeavor for most human GPCRs. We report a protocol for the production of the human histamine H1 receptor (H1R) in the methylotrophic yeast Pichia pastoris for NMR experiments. Systematic evaluation of multiple expression parameters resulted in a ten-fold increase in the yield of expressed H1R over initial efforts in defined media. The expressed receptor could be purified to homogeneity and was found to respond to the addition of known H1R ligands. Two-dimensional transverse relaxation-optimized spectroscopy (TROSY) NMR spectra of stable-isotope labeled H1R show well-dispersed and resolved signals consistent with a properly folded protein, and 19F-NMR data register a response of the protein to differences in efficacies of bound ligands.
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MESH Headings
- Gene Expression
- Humans
- Ligands
- Magnetic Resonance Spectroscopy/methods
- Nuclear Magnetic Resonance, Biomolecular/methods
- Protein Binding
- Protein Conformation
- Protein Engineering/methods
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/isolation & purification
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Histamine/chemistry
- Receptors, Histamine/isolation & purification
- Receptors, Histamine/metabolism
- Receptors, Histamine H1/chemistry
- Receptors, Histamine H1/isolation & purification
- Receptors, Histamine H1/metabolism
- Saccharomycetales/metabolism
- Signal Transduction
- Structure-Activity Relationship
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Affiliation(s)
| | | | - Matthew T. Eddy
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA; (E.M.); (A.P.R.)
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24
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Hilger D. The role of structural dynamics in GPCR‐mediated signaling. FEBS J 2021; 288:2461-2489. [DOI: 10.1111/febs.15841] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel Hilger
- Department of Pharmaceutical Chemistry Philipps‐University Marburg Germany
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25
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Stahl EL, Bohn LM. Decaf or regular? Energizing the caffeine receptor. Cell 2021; 184:1659-1660. [PMID: 33798438 DOI: 10.1016/j.cell.2021.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Partial agonism describes the relative efficacy of a drug compared to one that produces a greater response in a particular system; the designation is dependent upon the comparator and the system. In this issue of Cell, Huang et al. describe biophysical approaches to define the signature of GPCR partial agonists, providing direct measures of varying intrinsic efficacy.
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Affiliation(s)
- Edward L Stahl
- The Scripps Research Institute, Department of Molecular Medicine, Jupiter, FL 33458, USA.
| | - Laura M Bohn
- The Scripps Research Institute, Department of Molecular Medicine, Jupiter, FL 33458, USA.
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