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Li M, Lan X, Shi X, Zhu C, Lu X, Pu J, Lu S, Zhang J. Delineating the stepwise millisecond allosteric activation mechanism of the class C GPCR dimer mGlu5. Nat Commun 2024; 15:7519. [PMID: 39209876 PMCID: PMC11362167 DOI: 10.1038/s41467-024-51999-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
Two-thirds of signaling hormones and one-third of approved drugs exert their effects by binding and modulating the G protein-coupled receptors (GPCRs) activation. While the activation mechanism for monomeric GPCRs has been well-established, little is known about GPCRs in dimeric form. Here, by combining transition pathway generation, extensive atomistic simulation-based Markov state models, and experimental signaling assays, we reveal an asymmetric, stepwise millisecond allosteric activation mechanism for the metabotropic glutamate receptor subtype 5 receptor (mGlu5), an obligate dimeric class C GPCR. The dynamic picture is presented that agonist binding induces dimeric ectodomains compaction, amplified by the precise association of the cysteine-rich domains, ultimately loosely bringing the intracellular 7-transmembrane (7TM) domains into proximity and establishing an asymmetric TM6-TM6 interface. The active inter-domain interface enhances their intra-domain flexibility, triggering the activation of micro-switches crucial for downstream signal transduction. Furthermore, we show that the positive allosteric modulator stabilizes both the active inter-domain 7TM interface and an open, extended intra-domain ICL2 conformation. This stabilization leads to the formation of a pseudo-cavity composed of the ICL2, ICL3, TM3, and C-terminus, which facilitates G protein coordination. Our strategy may be generalizable for characterizing millisecond events in other allosteric systems.
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Affiliation(s)
- Mingyu Li
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Medicinal Chemistry and Bioinformatics Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Xiaobing Lan
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Xinchao Shi
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Medicinal Chemistry and Bioinformatics Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chunhao Zhu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Xun Lu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Medicinal Chemistry and Bioinformatics Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jun Pu
- Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200120, China
| | - Shaoyong Lu
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Medicinal Chemistry and Bioinformatics Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China.
| | - Jian Zhang
- State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Medicinal Chemistry and Bioinformatics Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China.
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Panarello S, González-Díez A, Berizzi AE, Malhaire F, Borràs-Tudurí R, Rovira X, Serra C, Prézeau L, Pin JP, Goudet C, Llebaria A, Gómez-Santacana X. Photoswitchable positive allosteric modulators of metabotropic glutamate receptor 4 to improve selectivity. iScience 2024; 27:110123. [PMID: 38966572 PMCID: PMC11223089 DOI: 10.1016/j.isci.2024.110123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/15/2024] [Accepted: 05/24/2024] [Indexed: 07/06/2024] Open
Abstract
Metabotropic glutamate receptors (mGlu) regulate multiple functions in the nervous systems and are involved in several neurological disorders. However, selectively targeting individual mGlu subtypes with spatiotemporal precision is still an unmet need. Photopharmacology can address this concern through the utilization of photoswitchable compounds such as optogluram, which is a positive allosteric modulator (PAM) of mGlu4 that enables the precise control of physiological responses using light but does not have an optimal selectivity profile. Optogluram analogs were developed to obtain photoswitchable PAMs of mGlu4 receptor with an improved selectivity. Among them, optogluram-2 emerged as a photoswitchable ligand for mGlu4 receptor with activity as both PAM and allosteric agonists. It presents a higher selectivity and offers improved photoswitching of mGlu4 activity. These improved properties make optogluram-2 an excellent candidate to study the role of mGlu4 with a high spatiotemporal precision in systems where mGlu4 can be co-expressed with other mGlu receptors.
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Affiliation(s)
- Silvia Panarello
- MCS, Institute for Advanced Chemistry of Catalonia – CSIC, Barcelona, Spain
- PhD Program in Organic Chemistry of the University of Barcelona, Barcelona, Spain
| | - Aleix González-Díez
- MCS, Institute for Advanced Chemistry of Catalonia – CSIC, Barcelona, Spain
- PhD Program in Organic Chemistry of the University of Barcelona, Barcelona, Spain
| | - Alice E. Berizzi
- Institut de Génomique Fonctionnelle, Université de Montpellier, UMR 5203 CNRS and U 1191 INSERM, Montpellier, France
| | - Fanny Malhaire
- Institut de Génomique Fonctionnelle, Université de Montpellier, UMR 5203 CNRS and U 1191 INSERM, Montpellier, France
| | | | - Xavier Rovira
- MCS, Institute for Advanced Chemistry of Catalonia – CSIC, Barcelona, Spain
| | - Carme Serra
- MCS, Institute for Advanced Chemistry of Catalonia – CSIC, Barcelona, Spain
| | - Laurent Prézeau
- Institut de Génomique Fonctionnelle, Université de Montpellier, UMR 5203 CNRS and U 1191 INSERM, Montpellier, France
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, Université de Montpellier, UMR 5203 CNRS and U 1191 INSERM, Montpellier, France
| | - Cyril Goudet
- Institut de Génomique Fonctionnelle, Université de Montpellier, UMR 5203 CNRS and U 1191 INSERM, Montpellier, France
| | - Amadeu Llebaria
- MCS, Institute for Advanced Chemistry of Catalonia – CSIC, Barcelona, Spain
| | - Xavier Gómez-Santacana
- MCS, Institute for Advanced Chemistry of Catalonia – CSIC, Barcelona, Spain
- Institut de Génomique Fonctionnelle, Université de Montpellier, UMR 5203 CNRS and U 1191 INSERM, Montpellier, France
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Eshak F, Pion L, Scholler P, Nevoltris D, Chames P, Rondard P, Pin JP, Acher FC, Goupil-Lamy A. Epitope Identification of an mGlu5 Receptor Nanobody Using Physics-Based Molecular Modeling and Deep Learning Techniques. J Chem Inf Model 2024; 64:4436-4461. [PMID: 38423996 DOI: 10.1021/acs.jcim.3c01620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The world has witnessed a revolution in therapeutics with the development of biological medicines such as antibodies and antibody fragments, notably nanobodies. These nanobodies possess unique characteristics including high specificity and modulatory activity, making them promising candidates for therapeutic applications. Identifying their binding mode is essential for their development. Experimental structural techniques are effective to get such information, but they are expensive and time-consuming. Here, we propose a computational approach, aiming to identify the epitope of a nanobody that acts as an agonist and a positive allosteric modulator at the rat metabotropic glutamate receptor 5. We employed multiple structure modeling tools, including various artificial intelligence algorithms for epitope mapping. The computationally identified epitope was experimentally validated, confirming the success of our approach. Additional dynamics studies provided further insights on the modulatory activity of the nanobody. The employed methodologies and approaches initiate a discussion on the efficacy of diverse techniques for epitope mapping and later nanobody engineering.
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Affiliation(s)
- Floriane Eshak
- SPPIN CNRS UMR 8003, Université Paris Cité, 75006 Paris, France
| | - Léo Pion
- Institut de Génomique Fonctionnelle, Université Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Pauline Scholler
- Institut de Génomique Fonctionnelle, Université Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Damien Nevoltris
- Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 13009 Marseille, France
| | - Patrick Chames
- Aix Marseille University, CNRS, Inserm, Institut Paoli-Calmettes, CRCM, 13009 Marseille, France
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle, Université Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, Université Montpellier, CNRS, Inserm, 34094 Montpellier, France
| | | | - Anne Goupil-Lamy
- BIOVIA Science Council, Dassault Systèmes, 78140 Vélizy-Villacoublay, France
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Cramer JF, Miller ET, Ko MC, Liang Q, Cockburn G, Nakagita T, Cardinale M, Fusani L, Toda Y, Baldwin MW. A single residue confers selective loss of sugar sensing in wrynecks. Curr Biol 2022; 32:4270-4278.e5. [PMID: 35985327 DOI: 10.1016/j.cub.2022.07.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 07/21/2022] [Indexed: 12/14/2022]
Abstract
Sensory receptors evolve, and changes to their response profiles can directly impact sensory perception and affect diverse behaviors, from mate choice to foraging decisions.1-3 Although receptor sensitivities can be highly contingent on changes occurring early in a lineage's evolutionary history,4 subsequent shifts in a species' behavior and ecology may exert selective pressure to modify and even reverse sensory receptor capabilities.5-7 Neither the extent to which sensory reversion occurs nor the mechanisms underlying such shifts is well understood. Using receptor profiling and behavioral tests, we uncover both an early gain and an unexpected subsequent loss of sugar sensing in woodpeckers, a primarily insectivorous family of landbirds.8,9 Our analyses show that, similar to hummingbirds10 and songbirds,4 the ancestors of woodpeckers repurposed their T1R1-T1R3 savory receptor to detect sugars. Importantly, whereas woodpeckers seem to have broadly retained this ability, our experiments demonstrate that wrynecks (an enigmatic ant-eating group sister to all other woodpeckers) selectively lost sugar sensing through a novel mechanism involving a single amino acid change in the T1R3 transmembrane domain. The identification of this molecular microswitch responsible for a sensory shift in taste receptors provides an example of the molecular basis of a sensory reversion in vertebrates and offers novel insights into structure-function relationships during sensory receptor evolution.
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Affiliation(s)
- Julia F Cramer
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Eliot T Miller
- Macaulay Library, Cornell Lab of Ornithology, Ithaca, NY 14850, USA
| | - Meng-Ching Ko
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Qiaoyi Liang
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Glenn Cockburn
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Tomoya Nakagita
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan; Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Massimiliano Cardinale
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, 453 30 Lysekil, Sweden
| | - Leonida Fusani
- Austrian Ornithological Centre, Konrad-Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, 1160 Wien, Austria; Department of Behavioural and Cognitive Biology, University of Vienna, 1160 Wien, Austria
| | - Yasuka Toda
- Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Maude W Baldwin
- Evolution of Sensory Systems Research Group, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany.
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Ellaithy A, Gonzalez-Maeso J, Logothetis DA, Levitz J. Structural and Biophysical Mechanisms of Class C G Protein-Coupled Receptor Function. Trends Biochem Sci 2020; 45:1049-1064. [PMID: 32861513 PMCID: PMC7642020 DOI: 10.1016/j.tibs.2020.07.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/22/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Groundbreaking structural and spectroscopic studies of class A G protein-coupled receptors (GPCRs), such as rhodopsin and the β2 adrenergic receptor, have provided a picture of how structural rearrangements between transmembrane helices control ligand binding, receptor activation, and effector coupling. However, the activation mechanism of other GPCR classes remains more elusive, in large part due to complexity in their domain assembly and quaternary structure. In this review, we focus on the class C GPCRs, which include metabotropic glutamate receptors (mGluRs) and gamma-aminobutyric acid B (GABAB) receptors (GABABRs) most prominently. We discuss the unique biophysical questions raised by the presence of large extracellular ligand-binding domains (LBDs) and constitutive homo/heterodimerization. Furthermore, we discuss how recent studies have begun to unravel how these fundamental class C GPCR features impact the processes of ligand binding, receptor activation, signal transduction, regulation by accessory proteins, and crosstalk with other GPCRs.
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Affiliation(s)
- Amr Ellaithy
- Department of Neurology, University of Iowa, Iowa City, IA 52242, USA; Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Javier Gonzalez-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Diomedes A Logothetis
- Department of Pharmaceutical Sciences, School of Pharmacy, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA; Department of Chemistry and Chemical Biology, College of Science and Center for Drug Discovery, Northeastern University, Boston, MA 02115, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065, USA.
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