1
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Kim J, Choi C. Orphan GPCRs in Neurodegenerative Disorders: Integrating Structural Biology and Drug Discovery Approaches. Curr Issues Mol Biol 2024; 46:11646-11664. [PMID: 39451571 PMCID: PMC11505999 DOI: 10.3390/cimb46100691] [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: 09/30/2024] [Revised: 10/11/2024] [Accepted: 10/17/2024] [Indexed: 10/26/2024] Open
Abstract
Neurodegenerative disorders, particularly Alzheimer's and Parkinson's diseases, continue to challenge modern medicine despite therapeutic advances. Orphan G-protein-coupled receptors (GPCRs) have emerged as promising targets in the central nervous system, offering new avenues for drug development. This review focuses on the structural biology of orphan GPCRs implicated in these disorders, providing a comprehensive analysis of their molecular architecture and functional mechanisms. We examine recent breakthroughs in structural determination techniques, such as cryo-electron microscopy and X-ray crystallography, which have elucidated the intricate conformations of these receptors. The review highlights how structural insights inform our understanding of orphan GPCR activation, ligand binding and signaling pathways. By integrating structural data with molecular pharmacology, we explore the potential of structure-guided approaches in developing targeted therapeutics toward orphan GPCRs. This structural-biology-centered perspective aims to deepen our comprehension of orphan GPCRs and guide future drug discovery efforts in neurodegenerative disorders.
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Affiliation(s)
- Jinuk Kim
- Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea;
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2
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Fan L, Zhuang Y, Wu H, Li H, Xu Y, Wang Y, He L, Wang S, Chen Z, Cheng J, Xu HE, Wang S. Structural basis of psychedelic LSD recognition at dopamine D 1 receptor. Neuron 2024; 112:3295-3310.e8. [PMID: 39094559 DOI: 10.1016/j.neuron.2024.07.003] [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: 04/03/2024] [Revised: 06/11/2024] [Accepted: 07/05/2024] [Indexed: 08/04/2024]
Abstract
Understanding the kinetics of LSD in receptors and subsequent induced signaling is crucial for comprehending both the psychoactive and therapeutic effects of LSD. Despite extensive research on LSD's interactions with serotonin 2A and 2B receptors, its behavior on other targets, including dopamine receptors, has remained elusive. Here, we present cryo-EM structures of LSD/PF6142-bound dopamine D1 receptor (DRD1)-legobody complexes, accompanied by a β-arrestin-mimicking nanobody, NBA3, shedding light on the determinants of G protein coupling versus β-arrestin coupling. Structural analysis unveils a distinctive binding mode of LSD in DRD1, particularly with the ergoline moiety oriented toward TM4. Kinetic investigations uncover an exceptionally rapid dissociation rate of LSD in DRD1, attributed to the flexibility of extracellular loop 2 (ECL2). Moreover, G protein can stabilize ECL2 conformation, leading to a significant slowdown in ligand's dissociation rate. These findings establish a solid foundation for further exploration of G protein-coupled receptor (GPCR) dynamics and their relevance to signal transduction.
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Affiliation(s)
- Luyu Fan
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Youwen Zhuang
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongyu Wu
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Huiqiong Li
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Youwei Xu
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yue Wang
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Licong He
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Shishan Wang
- Laboratory of Anesthesia and Critical Care Medicine in Colleges and Universities of Shandong Province, School of Anesthesiology, Shandong Second Medical University, Weifang 261021, China
| | - Zhangcheng Chen
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - H Eric Xu
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; Lingang Laboratory, Shanghai 200031, China.
| | - Sheng Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China.
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3
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Isu U, Polasa A, Moradi M. Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1. J Phys Chem B 2024; 128:8437-8447. [PMID: 39169808 PMCID: PMC11382280 DOI: 10.1021/acs.jpcb.4c02828] [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: 04/30/2024] [Revised: 08/05/2024] [Accepted: 08/15/2024] [Indexed: 08/23/2024]
Abstract
Cannabinoid receptor 1 (CB1) is a G protein-coupled receptor that regulates critical physiological processes including pain, appetite, and cognition. Understanding the conformational dynamics of CB1 associated with transitions between inactive and active signaling states is imperative for developing targeted modulators. Using microsecond-level all-atom molecular dynamics simulations, we identified marked differences in the conformational ensembles of inactive and active CB1 in apo. The inactive state exhibited substantially increased structural heterogeneity and plasticity compared to the more rigidified active state in the absence of stabilizing ligands. Transmembrane helices TM3 and TM7 were identified as distinguishing factors modulating the state-dependent dynamics. TM7 displayed amplified fluctuations selectively in the inactive state simulations attributed to disruption of conserved electrostatic contacts anchoring it to surrounding helices in the active state. Additionally, we identified significant reorganizations in key salt bridge and hydrogen bond networks contributing to the CB1 activation/inactivation. For instance, D213-Y224 hydrogen bond and D184-K192 salt bridge showed marked rearrangements between the states. Collectively, these findings reveal the specialized role of TM7 in directing state-dependent CB1 dynamics through electrostatic switch mechanisms. By elucidating the intrinsic enhanced flexibility of inactive CB1, this study provides valuable insights into the conformational landscape enabling functional transitions. Our perspective advances understanding of CB1 activation mechanisms and offers opportunities for structure-based drug discovery targeting the state-specific conformational dynamics of this receptor.
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Affiliation(s)
- Ugochi
H. Isu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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4
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Liu H, Yan P, Zhang Z, Han H, Zhou Q, Zheng J, Zhang J, Xu F, Shui W. Structural Mass Spectrometry Captures Residue-Resolved Comprehensive Conformational Rearrangements of a G Protein-Coupled Receptor. J Am Chem Soc 2024; 146:20045-20058. [PMID: 39001877 DOI: 10.1021/jacs.4c03922] [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: 07/15/2024]
Abstract
G protein-coupled receptor (GPCR) structural studies with in-solution spectroscopic approaches have offered distinctive insights into GPCR activation and signaling that highly complement those yielded from structural snapshots by crystallography or cryo-EM. While most current spectroscopic approaches allow for probing structural changes at selected residues or loop regions, they are not suitable for capturing a holistic view of GPCR conformational rearrangements across multiple domains. Herein, we develop an approach based on limited proteolysis mass spectrometry (LiP-MS) to simultaneously monitor conformational alterations of a large number of residues spanning both flexible loops and structured transmembrane domains for a given GPCR. To benchmark LiP-MS for GPCR conformational profiling, we studied the adenosine 2A receptor (A2AR) in response to different ligand binding (agonist/antagonist/allosteric modulators) and G protein coupling. Systematic and residue-resolved profiling of A2AR conformational rearrangements by LiP-MS precisely captures structural mechanisms in multiple domains underlying ligand engagement, receptor activation, and allostery, and may also reflect local conformational flexibility. Furthermore, these residue-resolution structural fingerprints of the A2AR protein allow us to readily classify ligands of different pharmacology and distinguish the G protein-coupled state. Thus, our study provides a new structural MS approach that would be generalizable to characterizing conformational transition and plasticity for challenging integral membrane proteins.
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Affiliation(s)
- Hongyue Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengfei Yan
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoyu Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongbo Han
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jie Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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5
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Otun O, Aljamous C, Del Nero E, Arimont-Segura M, Bosma R, Zarzycka B, Girbau T, Leyrat C, de Graaf C, Leurs R, Durroux T, Granier S, Cong X, Bechara C. Conformational dynamics underlying atypical chemokine receptor 3 activation. Proc Natl Acad Sci U S A 2024; 121:e2404000121. [PMID: 39008676 PMCID: PMC11287255 DOI: 10.1073/pnas.2404000121] [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: 02/26/2024] [Accepted: 05/28/2024] [Indexed: 07/17/2024] Open
Abstract
Atypical Chemokine Receptor 3 (ACKR3) belongs to the G protein-coupled receptor family but it does not signal through G proteins. The structural properties that govern the functional selectivity and the conformational dynamics of ACKR3 activation are poorly understood. Here, we combined hydrogen/deuterium exchange mass spectrometry, site-directed mutagenesis, and molecular dynamics simulations to examine the binding mode and mechanism of action of ACKR3 ligands of different efficacies. Our results show that activation or inhibition of ACKR3 is governed by intracellular conformational changes of helix 6, intracellular loop 2, and helix 7, while the DRY motif becomes protected during both processes. Moreover, we identified the binding sites and the allosteric modulation of ACKR3 upon β-arrestin 1 binding. In summary, this study highlights the structure-function relationship of small ligands, the binding mode of β-arrestin 1, the activation dynamics, and the atypical dynamic features in ACKR3 that may contribute to its inability to activate G proteins.
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Affiliation(s)
- Omolade Otun
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Christelle Aljamous
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Elise Del Nero
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Marta Arimont-Segura
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Reggie Bosma
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Barbara Zarzycka
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Tristan Girbau
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Cédric Leyrat
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Chris de Graaf
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Rob Leurs
- Department of Medicinal Chemistry, Amsterdam Institute for Molecular Life Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Thierry Durroux
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Sébastien Granier
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Xiaojing Cong
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
| | - Cherine Bechara
- Institut de Génomique Fonctionnelle, University of Montpellier, CNRS, INSERM, Montpellier Cedex 534094, France
- Institut Universitaire de France, Paris75005, France
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6
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Isu UH, Polasa A, Moradi M. Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589939. [PMID: 38659869 PMCID: PMC11042334 DOI: 10.1101/2024.04.17.589939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The cannabinoid receptor CB1 is a G protein-coupled receptor that regulates critical physiological processes including pain, appetite, and cognition. Understanding the conformational dynamics of CB1 associated with transitions between inactive and active signaling states is imperative for developing targeted modulators. Using microsecond-level all-atom molecular dynamics simulations, we identified marked differences in the conformational ensembles of inactive and active CB1 states in apo conditions. The inactive state exhibited substantially increased structural heterogeneity and plasticity compared to the more rigidified active state in the absence of stabilizing ligands. Transmembrane helices TM3 and TM7 were identified as distinguishing factors modulating the state-dependent dynamics. TM7 displayed amplified fluctuations selectively in the inactive state simulations attributed to disruption of conserved electrostatic contacts anchoring it to surrounding helices in the active state. Additionally, we identified significant reorganization of key salt bridge and hydrogen bond networks known to control CB1 activation between states. For instance, a conserved D213-Y224 hydrogen bond and D184-K192 salt bridge interactions showed marked rearrangements between the states. Collectively, these findings reveal the specialized role of TM7 in directing state-dependent CB1 dynamics through electrostatic switch mechanisms. By elucidating the intrinsic enhanced flexibility of inactive CB1, this study provides valuable insights into the conformational landscape enabling functional transitions. Our perspective advances understanding of CB1 activation mechanisms and offers opportunities for structure-based drug discovery targeting the state-specific conformational dynamics of this receptor.
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7
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Sink A, Gerwe H, Hübner H, Boivin-Jahns V, Fender J, Lorenz K, Gmeiner P, Decker M. "Photo-Adrenalines": Photoswitchable β 2 -Adrenergic Receptor Agonists as Molecular Probes for the Study of Spatiotemporal Adrenergic Signaling. Chemistry 2024; 30:e202303506. [PMID: 38212242 DOI: 10.1002/chem.202303506] [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: 10/24/2023] [Indexed: 01/13/2024]
Abstract
β2 -adrenergic receptor (β2 -AR) agonists are used for the treatment of asthma and chronic obstructive pulmonary disease, but also play a role in other complex disorders including cancer, diabetes and heart diseases. As the cellular and molecular mechanisms in various cells and tissues of the β2 -AR remain vastly elusive, we developed tools for this investigation with high temporal and spatial resolution. Several photoswitchable β2 -AR agonists with nanomolar activity were synthesized. The most potent agonist for β2 -AR with reasonable switching is a one-digit nanomolar active, trans-on arylazopyrazole-based adrenaline derivative and comprises valuable photopharmacological properties for further biological studies with high structural accordance to the native ligand adrenaline.
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Affiliation(s)
- Alexandra Sink
- Pharmaceutical and Medicinal Chemistry Institute for Pharmacy and Food Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Hubert Gerwe
- Pharmaceutical and Medicinal Chemistry Institute for Pharmacy and Food Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Harald Hübner
- Medicinal Chemistry Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Valerie Boivin-Jahns
- Institute for Pharmacology and Toxicology, Julius-Maximilians-Universität Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
| | - Julia Fender
- Institute for Pharmacology and Toxicology, Julius-Maximilians-Universität Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
| | - Kristina Lorenz
- Institute for Pharmacology and Toxicology, Julius-Maximilians-Universität Würzburg, Versbacher Straße 9, 97078, Würzburg, Germany
- Leibniz-Institut für Analytische Wissenschaften - ISAS-e.V., Bunsen-Kirchhoff-Str. 11, 44139, Dortmund, Germany
| | - Peter Gmeiner
- Medicinal Chemistry Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Michael Decker
- Pharmaceutical and Medicinal Chemistry Institute for Pharmacy and Food Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
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8
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Choi C, Bae J, Kim S, Lee S, Kang H, Kim J, Bang I, Kim K, Huh WK, Seok C, Park H, Im W, Choi HJ. Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family. Nat Commun 2023; 14:8105. [PMID: 38062020 PMCID: PMC10703812 DOI: 10.1038/s41467-023-43983-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of OR51E2 bound to propionate provided molecular insight into odorant recognition, but the lack of an inactive OR structure limited understanding of the activation mechanism of ORs upon odorant binding. Here, we determined the cryo-electron microscopy structures of consensus OR52 (OR52cs), a representative of the OR52 family, in the ligand-free (apo) and octanoate-bound states. The apo structure of OR52cs reveals a large opening between transmembrane helices (TMs) 5 and 6. A comparison between the apo and active structures of OR52cs demonstrates the inward and outward movements of the extracellular and intracellular segments of TM6, respectively. These results, combined with molecular dynamics simulations and signaling assays, shed light on the molecular mechanisms of odorant binding and activation of the OR52 family.
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Affiliation(s)
- Chulwon Choi
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jungnam Bae
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seonghan Kim
- Department of Bioengineering, Lehigh University, Bethlehem, PA, 18015, USA
| | - Seho Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyunook Kang
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinuk Kim
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Injin Bang
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Kiheon Kim
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Won-Ki Huh
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hahnbeom Park
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Wonpil Im
- Department of Bioengineering, Lehigh University, Bethlehem, PA, 18015, USA
- Departments of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, Bethlehem, PA, 18015, USA
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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9
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Luginina A, Maslov I, Khorn P, Volkov O, Khnykin A, Kuzmichev P, Shevtsov M, Belousov A, Kapranov I, Dashevskii D, Kornilov D, Bestsennaia E, Hofkens J, Hendrix J, Gensch T, Cherezov V, Ivanovich V, Mishin A, Borshchevskiy V. Functional GPCR Expression in Eukaryotic LEXSY System. J Mol Biol 2023; 435:168310. [PMID: 37806553 DOI: 10.1016/j.jmb.2023.168310] [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: 06/29/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
G protein-coupled receptors (GPCRs) form the largest superfamily of membrane proteins in the human genome, and represent one of the most important classes of drug targets. Their structural studies facilitate rational drug discovery. However, atomic structures of only about 20% of human GPCRs have been solved to date. Recombinant production of GPCRs for structural studies at a large scale is challenging due to their low expression levels and stability. Therefore, in this study, we explored the efficacy of the eukaryotic system LEXSY (Leishmania tarentolae) for GPCR production. We selected the human A2A adenosine receptor (A2AAR), as a model protein, expressed it in LEXSY, purified it, and compared with the same receptor produced in insect cells, which is the most popular expression system for structural studies of GPCRs. The A2AAR purified from both expression systems showed similar purity, stability, ligand-induced conformational changes and structural dynamics, with a remarkably higher protein yield in the case of LEXSY expression. Overall, our results suggest that LEXSY is a promising platform for large-scale production of GPCRs for structural studies.
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Affiliation(s)
- Aleksandra Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - 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
| | | | - Andrey Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Pavel Kuzmichev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Mikhail Shevtsov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Anatoliy Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ivan Kapranov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Dmitrii Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Daniil Kornilov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Ekaterina Bestsennaia
- 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 Planck Institute for Polymer Research, Mainz, Germany
| | - 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
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Valentin Ivanovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - 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, Russia.
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10
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Luginina A, Gusach A, Lyapina E, Khorn P, Safronova N, Shevtsov M, Dmitirieva D, Dashevskii D, Kotova T, Smirnova E, Borshchevskiy V, Cherezov V, Mishin A. Structural diversity of leukotriene G-protein coupled receptors. J Biol Chem 2023; 299:105247. [PMID: 37703990 PMCID: PMC10570957 DOI: 10.1016/j.jbc.2023.105247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/01/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023] Open
Abstract
Dihydroxy acid leukotriene (LTB4) and cysteinyl leukotrienes (LTC4, LTD4, and LTE4) are inflammatory mediators derived from arachidonic acid via the 5-lipoxygenase pathway. While structurally similar, these two types of leukotrienes (LTs) exert their functions through interactions with two distinct G protein-coupled receptor (GPCR) families, BLT and CysLT receptors, which share low sequence similarity and belong to phylogenetically divergent GPCR groups. Selective antagonism of LT receptors has been proposed as a promising strategy for the treatment of many inflammation-related diseases including asthma and chronic obstructive pulmonary disease, rheumatoid arthritis, cystic fibrosis, diabetes, and several types of cancer. Selective CysLT1R antagonists are currently used as antiasthmatic drugs, however, there are no approved drugs targeting CysLT2 and BLT receptors. In this review, we highlight recently published structures of BLT1R and CysLTRs revealing unique structural features of the two receptor families. X-ray and cryo-EM data shed light on their overall conformations, differences in functional motifs involved in receptor activation, and details of the ligand-binding pockets. An unexpected binding mode of the selective antagonist BIIL260 in the BLT1R structure makes it the first example of a compound targeting the sodium-binding site of GPCRs and suggests a novel strategy for the receptor activity modulation. Taken together, these recent structural data reveal dramatic differences in the molecular architecture of the two LT receptor families and pave the way to new therapeutic strategies of selective targeting individual receptors with novel tool compounds obtained by the structure-based drug design approach.
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Affiliation(s)
- Aleksandra Luginina
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anastasiia Gusach
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Elizaveta Lyapina
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Polina Khorn
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nadezda Safronova
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mikhail Shevtsov
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Daria Dmitirieva
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmitrii Dashevskii
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Tatiana Kotova
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ekaterina Smirnova
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Joint Institute for Nuclear Research, Dubna, Russia
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, California, USA.
| | - Alexey Mishin
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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11
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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: 2] [Impact Index Per Article: 2.0] [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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12
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Watanabe A, Nakajima A, Shiroishi M. Recovery of the histamine H 3 receptor activity lost in yeast cells through error-prone PCR and in vivo selection. Sci Rep 2023; 13:16127. [PMID: 37752220 PMCID: PMC10522717 DOI: 10.1038/s41598-023-43389-z] [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: 07/22/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest protein family in humans and are important drug targets. Yeast, especially Saccharomyces cerevisiae, is a useful host for modifying the function and stability of GPCRs through protein engineering, which is advantageous for mammalian cells. When GPCRs are expressed in yeast, their function is often impaired. In this study, we performed random mutagenesis using error-prone PCR and then an in vivo screening to obtain mutants that recovered the activity of the human histamine H3 receptor (H3R), which loses its signaling function when expressed in yeast. Four mutations with recovered activity were identified after screening. Three of the mutations were identified near the DRY and NPxxY motifs of H3R, which are important for activation and are commonly found in class A GPCRs. The mutants responded exclusively to the yeast YB1 strain harboring Gi-chimera proteins, showing retention of G protein specificity. Analysis of one of the mutants with recovered activity, C415R, revealed that it maintained its ligand-binding characteristics. The strategy used in this study may enable the recovery of the activity of other GPCRs that do not function in S. cerevisiae and may be useful in creating GPCRs mutants stabilized in their active conformations.
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Affiliation(s)
- Ayami Watanabe
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Ami Nakajima
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Mitsunori Shiroishi
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan.
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13
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Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens RC, Sali A, Sun L, Shui W. Conformational Dynamics of the Activated GLP-1 Receptor-G s Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling. ACS CENTRAL SCIENCE 2023; 9:992-1007. [PMID: 37252352 PMCID: PMC10214531 DOI: 10.1021/acscentsci.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Indexed: 05/31/2023]
Abstract
Despite advances in characterizing the structures and functions of G protein-coupled receptors (GPCRs), our understanding of GPCR activation and signaling is still limited by the lack of information on conformational dynamics. It is particularly challenging to study the dynamics of GPCR complexes with their signaling partners because of their transient nature and low stability. Here, by combining cross-linking mass spectrometry (CLMS) with integrative structure modeling, we map the conformational ensemble of an activated GPCR-G protein complex at near-atomic resolution. The integrative structures describe heterogeneous conformations for a high number of potential alternative active states of the GLP-1 receptor-Gs complex. These structures show marked differences from the previously determined cryo-EM structure, especially at the receptor-Gs interface and in the interior of the Gs heterotrimer. Alanine-scanning mutagenesis coupled with pharmacological assays validates the functional significance of 24 interface residue contacts only observed in the integrative structures, yet absent in the cryo-EM structure. Through the integration of spatial connectivity data from CLMS with structure modeling, our study provides a new approach that is generalizable to characterizing the conformational dynamics of GPCR signaling complexes.
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Affiliation(s)
- Shijia Yuan
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Lisha Xia
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxi Wang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Wu
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Bingjie Zhang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Chen Pan
- National
Facility for Protein Science in Shanghai, Shanghai Advanced Research
Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Zhiran Fan
- Biocreater
(WuHan) Biotechnology Co., Ltd, Wuhan 430075, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory of
Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Department of
Chemical Biology, College of Chemistry and Molecular Engineering,
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Raymond C. Stevens
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Andrej Sali
- Quantitative
Biosciences Institute, University of California,
San Francisco, San Francisco, California 94143, United States
- Department
of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, United States
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, San
Francisco, California 94143, United States
| | - Liping Sun
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Wenqing Shui
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
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14
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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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15
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Hillman T. A Predictive Model for Identifying the Most Effective Anti-CCR5 Monoclonal Antibody. ARCHIVES OF PHARMACY PRACTICE 2023. [DOI: 10.51847/d9m2zufqr4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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16
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Kaczor AA, Wróbel TM, Bartuzi D. Allosteric Modulators of Dopamine D 2 Receptors for Fine-Tuning of Dopaminergic Neurotransmission in CNS Diseases: Overview, Pharmacology, Structural Aspects and Synthesis. Molecules 2022; 28:molecules28010178. [PMID: 36615372 PMCID: PMC9822192 DOI: 10.3390/molecules28010178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Allosteric modulation of G protein-coupled receptors (GPCRs) is nowadays a hot topic in medicinal chemistry. Allosteric modulators, i.e., compounds which bind in a receptor site topologically distinct from orthosteric sites, exhibit a number of advantages. They are more selective, safer and display a ceiling effect which prevents overdosing. Allosteric modulators of dopamine D2 receptor are potential drugs against a number of psychiatric and neurological diseases, such as schizophrenia and Parkinson's disease. In this review, an insightful summary of current research on D2 receptor modulators is presented, ranging from their pharmacology and structural aspects of ligand-receptor interactions to their synthesis.
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Affiliation(s)
- Agnieszka A. Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., PL-20093 Lublin, Poland
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, FI-70211 Kuopio, Finland
- Correspondence: ; Tel.: +48-81-448-72-73
| | - Tomasz M. Wróbel
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., PL-20093 Lublin, Poland
| | - Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, 4A Chodźki St., PL-20093 Lublin, Poland
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-75124 Uppsala, Sweden
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17
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An K, Zhu X, Bai C. The Nature of Functional Features of Different Classes of G-Protein-Coupled Receptors. BIOLOGY 2022; 11:1839. [PMID: 36552350 PMCID: PMC9775959 DOI: 10.3390/biology11121839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
G-protein-coupled receptors (GPCRs) are a critical family in the human proteome and are involved in various physiological processes. They are also the most important drug target, with approximately 30% of approved drugs acting on such receptors. The members of the family are divided into six classes based on their structural and functional characteristics. Understanding their structural-functional relationships will benefit us in future drug development. In this article, we investigate the features of protein function, structure, and energy that describe the dynamics of the GPCR activation process between different families. GPCRs straddle the cell membrane and transduce signals from outside the membrane into the cell. During the process, the conformational change in GPCRs that is activated by the binding of signal molecules is essential. During the binding process, different types of signal molecules result in different signal transfer efficiencies. Therefore, the GPCR classes show a variety of structures and activation processes. Based on the experimental crystal structures, we modeled the activation process of the β2 adrenergic receptor (β2AR), glucagon receptor (GCGR), and metabotropic glutamate receptor 2 (mGluR2), which represent class A, B, and C GPCRs, respectively. We calculated their activation free-energy landscapes and analyzed the structure-energy-function relationship. The results show a consistent picture of the activation mechanisms between different types of GPCRs. This could also provide us a way to understand other signal transduction proteins.
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Affiliation(s)
- Ke An
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Xiaohong Zhu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China
- Chenzhu (MoMeD) Biotechnology Co., Ltd., Hangzhou 310005, China
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18
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Sonker M, Doppler D, Egatz-Gomez A, Zaare S, Rabbani MT, Manna A, Cruz Villarreal J, Nelson G, Ketawala GK, Karpos K, Alvarez RC, Nazari R, Thifault D, Jernigan R, Oberthür D, Han H, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Poitevin F, Lisova S, Mariani V, Tolstikova A, Boutet S, Messerschmidt M, Meza-Aguilar JD, Fromme R, Martin-Garcia JM, Botha S, Fromme P, Grant TD, Kirian RA, Ros A. Electrically stimulated droplet injector for reduced sample consumption in serial crystallography. BIOPHYSICAL REPORTS 2022; 2:100081. [PMID: 36425668 PMCID: PMC9680787 DOI: 10.1016/j.bpr.2022.100081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
With advances in X-ray free-electron lasers (XFELs), serial femtosecond crystallography (SFX) has enabled the static and dynamic structure determination for challenging proteins such as membrane protein complexes. In SFX with XFELs, the crystals are typically destroyed after interacting with a single XFEL pulse. Therefore, thousands of new crystals must be sequentially introduced into the X-ray beam to collect full data sets. Because of the serial nature of any SFX experiment, up to 99% of the sample delivered to the X-ray beam during its "off-time" between X-ray pulses is wasted due to the intrinsic pulsed nature of all current XFELs. To solve this major problem of large and often limiting sample consumption, we report on improvements of a revolutionary sample-saving method that is compatible with all current XFELs. We previously reported 3D-printed injection devices coupled with gas dynamic virtual nozzles (GDVNs) capable of generating samples containing droplets segmented by an immiscible oil phase for jetting crystal-laden droplets into the path of an XFEL. Here, we have further improved the device design by including metal electrodes inducing electrowetting effects for improved control over droplet generation frequency to stimulate the droplet release to matching the XFEL repetition rate by employing an electrical feedback mechanism. We report the improvements in this electrically triggered segmented flow approach for sample conservation in comparison with a continuous GDVN injection using the microcrystals of lysozyme and 3-deoxy-D-manno-octulosonate 8-phosphate synthase and report the segmented flow approach for sample injection applied at the Macromolecular Femtosecond Crystallography instrument at the Linear Coherent Light Source for the first time.
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Affiliation(s)
- Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Sahba Zaare
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Abhik Manna
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Reza Nazari
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Darren Thifault
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Rebecca Jernigan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | | | - Raymond Sierra
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Mark S. Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Alexander Batyuk
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Christopher J. Kupitz
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Robert E. Sublett
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Frederic Poitevin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Stella Lisova
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Valerio Mariani
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Alexandra Tolstikova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | - Sebastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, Menlo Park, California
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - J. Domingo Meza-Aguilar
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Jose M. Martin-Garcia
- Institute Physical-Chemistry Rocasolano, Spanish National Research Council, Madrid, Spain
| | - Sabine Botha
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Thomas D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Richard A. Kirian
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
- Department of Physics, Arizona State University, Tempe, Arizona
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona
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19
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A Statistical Journey through the Topological Determinants of the β2 Adrenergic Receptor Dynamics. ENTROPY 2022; 24:e24070998. [PMID: 35885221 PMCID: PMC9318934 DOI: 10.3390/e24070998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 02/06/2023]
Abstract
Activation of G-protein-coupled receptors (GPCRs) is mediated by molecular switches throughout the transmembrane region of the receptor. In this work, we continued along the path of a previous computational study wherein energy transport in the β2 Adrenergic Receptor (β2-AR) was examined and allosteric switches were identified in the molecular structure through the reorganization of energy transport networks during activation. In this work, we further investigated the allosteric properties of β2-AR, using Protein Contact Networks (PCNs). In this paper, we report an extensive statistical analysis of the topological and structural properties of β2-AR along its molecular dynamics trajectory to identify the activation pattern of this molecular system. The results show a distinct character to the activation that both helps to understand the allosteric switching previously identified and confirms the relevance of the network formalism to uncover relevant functional features of protein molecules.
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20
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Leysen H, Walter D, Clauwaert L, Hellemans L, van Gastel J, Vasudevan L, Martin B, Maudsley S. The Relaxin-3 Receptor, RXFP3, Is a Modulator of Aging-Related Disease. Int J Mol Sci 2022; 23:4387. [PMID: 35457203 PMCID: PMC9027355 DOI: 10.3390/ijms23084387] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
During the aging process our body becomes less well equipped to deal with cellular stress, resulting in an increase in unrepaired damage. This causes varying degrees of impaired functionality and an increased risk of mortality. One of the most effective anti-aging strategies involves interventions that combine simultaneous glucometabolic support with augmented DNA damage protection/repair. Thus, it seems prudent to develop therapeutic strategies that target this combinatorial approach. Studies have shown that the ADP-ribosylation factor (ARF) GTPase activating protein GIT2 (GIT2) acts as a keystone protein in the aging process. GIT2 can control both DNA repair and glucose metabolism. Through in vivo co-regulation analyses it was found that GIT2 forms a close coexpression-based relationship with the relaxin-3 receptor (RXFP3). Cellular RXFP3 expression is directly affected by DNA damage and oxidative stress. Overexpression or stimulation of this receptor, by its endogenous ligand relaxin 3 (RLN3), can regulate the DNA damage response and repair processes. Interestingly, RLN3 is an insulin-like peptide and has been shown to control multiple disease processes linked to aging mechanisms, e.g., anxiety, depression, memory dysfunction, appetite, and anti-apoptotic mechanisms. Here we discuss the molecular mechanisms underlying the various roles of RXFP3/RLN3 signaling in aging and age-related disorders.
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Affiliation(s)
- Hanne Leysen
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Deborah Walter
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Lore Clauwaert
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Lieselot Hellemans
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
| | - Jaana van Gastel
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
- SGS Belgium, Intercity Business Park, Generaal De Wittelaan 19-A5, 2800 Mechelen, Belgium
| | | | - Bronwen Martin
- Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, 2610 Wilrijk, Belgium;
| | - Stuart Maudsley
- Receptor Biology Laboratory, University of Antwerp, 2610 Wilrijk, Belgium; (H.L.); (D.W.); (L.C.); (L.H.); (J.v.G.)
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21
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Seyedabadi M, Gharghabi M, Gurevich EV, Gurevich VV. Structural basis of GPCR coupling to distinct signal transducers: implications for biased signaling. Trends Biochem Sci 2022; 47:570-581. [PMID: 35396120 DOI: 10.1016/j.tibs.2022.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/10/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
Three classes of G-protein-coupled receptor (GPCR) partners - G proteins, GPCR kinases, and arrestins - preferentially bind active GPCRs. Our analysis suggests that the structures of GPCRs bound to these interaction partners available today do not reveal a clear conformational basis for signaling bias, which would have enabled the rational design of biased GRCR ligands. In view of this, three possibilities are conceivable: (i) there are no generalizable GPCR conformations conducive to binding a particular type of partner; (ii) subtle differences in the orientation of individual residues and/or their interactions not easily detectable in the receptor-transducer structures determine partner preference; or (iii) the dynamics of GPCR binding to different types of partners rather than the structures of the final complexes might underlie transducer bias.
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Affiliation(s)
- Mohammad Seyedabadi
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran; Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mehdi Gharghabi
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
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22
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del Alamo D, Sala D, Mchaourab HS, Meiler J. Sampling alternative conformational states of transporters and receptors with AlphaFold2. eLife 2022; 11:75751. [PMID: 35238773 PMCID: PMC9023059 DOI: 10.7554/elife.75751] [Citation(s) in RCA: 161] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/02/2022] [Indexed: 11/13/2022] Open
Abstract
Equilibrium fluctuations and triggered conformational changes often underlie the functional cycles of membrane proteins. For example, transporters mediate the passage of molecules across cell membranes by alternating between inward- and outward-facing states, while receptors undergo intracellular structural rearrangements that initiate signaling cascades. Although the conformational plasticity of these proteins has historically posed a challenge for traditional de novo protein structure prediction pipelines, the recent success of AlphaFold2 (AF2) in CASP14 culminated in the modeling of a transporter in multiple conformations to high accuracy. Given that AF2 was designed to predict static structures of proteins, it remains unclear if this result represents an underexplored capability to accurately predict multiple conformations and/or structural heterogeneity. Here, we present an approach to drive AF2 to sample alternative conformations of topologically diverse transporters and G-protein-coupled receptors that are absent from the AF2 training set. Whereas models of most proteins generated using the default AF2 pipeline are conformationally homogeneous and nearly identical to one another, reducing the depth of the input multiple sequence alignments by stochastic subsampling led to the generation of accurate models in multiple conformations. In our benchmark, these conformations spanned the range between two experimental structures of interest, with models at the extremes of these conformational distributions observed to be among the most accurate (average template modeling score of 0.94). These results suggest a straightforward approach to identifying native-like alternative states, while also highlighting the need for the next generation of deep learning algorithms to be designed to predict ensembles of biophysically relevant states.
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Affiliation(s)
- Diego del Alamo
- Department of Molecular Physiology and Biophysics, Vanderbilt UniversityNashvilleUnited States
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
| | - Davide Sala
- Institute for Drug Discovery, Leipzig UniversityLeipzigGermany
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt UniversityNashvilleUnited States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt UniversityNashvilleUnited States
- Institute for Drug Discovery, Leipzig UniversityLeipzigGermany
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23
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Doppler D, Rabbani MT, Letrun R, Cruz Villarreal J, Kim DH, Gandhi S, Egatz-Gomez A, Sonker M, Chen J, Koua FHM, Yang J, Youssef M, Mazalova V, Bajt S, Shelby ML, Coleman MA, Wiedorn MO, Knoska J, Schön S, Sato T, Hunter MS, Hosseinizadeh A, Kuptiz C, Nazari R, Alvarez RC, Karpos K, Zaare S, Dobson Z, Discianno E, Zhang S, Zook JD, Bielecki J, de Wijn R, Round AR, Vagovic P, Kloos M, Vakili M, Ketawala GK, Stander NE, Olson TL, Morin K, Mondal J, Nguyen J, Meza-Aguilar JD, Kodis G, Vaiana S, Martin-Garcia JM, Mariani V, Schwander P, Schmidt M, Messerschmidt M, Ourmazd A, Zatsepin N, Weierstall U, Bruce BD, Mancuso AP, Grant T, Barty A, Chapman HN, Frank M, Fromme R, Spence JCH, Botha S, Fromme P, Kirian RA, Ros A. Co-flow injection for serial crystallography at X-ray free-electron lasers. J Appl Crystallogr 2022; 55:1-13. [PMID: 35153640 PMCID: PMC8805165 DOI: 10.1107/s1600576721011079] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/22/2021] [Indexed: 02/03/2023] Open
Abstract
Serial femtosecond crystallography (SFX) is a powerful technique that exploits X-ray free-electron lasers to determine the structure of macro-molecules at room temperature. Despite the impressive exposition of structural details with this novel crystallographic approach, the methods currently available to introduce crystals into the path of the X-ray beam sometimes exhibit serious drawbacks. Samples requiring liquid injection of crystal slurries consume large quantities of crystals (at times up to a gram of protein per data set), may not be compatible with vacuum configurations on beamlines or provide a high background due to additional sheathing liquids present during the injection. Proposed and characterized here is the use of an immiscible inert oil phase to supplement the flow of sample in a hybrid microfluidic 3D-printed co-flow device. Co-flow generation is reported with sample and oil phases flowing in parallel, resulting in stable injection conditions for two different resin materials experimentally. A numerical model is presented that adequately predicts these flow-rate conditions. The co-flow generating devices reduce crystal clogging effects, have the potential to conserve protein crystal samples up to 95% and will allow degradation-free light-induced time-resolved SFX.
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Affiliation(s)
- Diandra Doppler
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohammad T. Rabbani
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | - Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Dai Hyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Sahir Gandhi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Joe Chen
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Faisal H. M. Koua
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Jayhow Yang
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Mohamed Youssef
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Victoria Mazalova
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Saša Bajt
- Hamburg Center for Ultrafast Imaging, Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Megan L. Shelby
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Matt A. Coleman
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Max O. Wiedorn
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- Hamburg Center for Ultrafast Imaging, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Juraj Knoska
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Silvan Schön
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | - Mark S. Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Christopher Kuptiz
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Reza Nazari
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Roberto C. Alvarez
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Konstantinos Karpos
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sahba Zaare
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Zachary Dobson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Erin Discianno
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Shangji Zhang
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - James D. Zook
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | | | | | - Adam R. Round
- European XFEL, Schenefeld, Germany
- School of Chemical and Physical Sciences, Keele University, Staffordshire, UK
| | - Patrik Vagovic
- European XFEL, Schenefeld, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | | | | | - Gihan K. Ketawala
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Natasha E. Stander
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Tien L. Olson
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Katherine Morin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Jyotirmory Mondal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jonathan Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - José Domingo Meza-Aguilar
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- European XFEL, Schenefeld, Germany
| | - Gerdenis Kodis
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sara Vaiana
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Jose M. Martin-Garcia
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry ‘Rocasolano’, CSIC, Madrid, Spain
| | - Valerio Mariani
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marc Messerschmidt
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Nadia Zatsepin
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Uwe Weierstall
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Barry D. Bruce
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Adrian P. Mancuso
- European XFEL, Schenefeld, Germany
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia
| | - Thomas Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- Center for Data and Computing in Natural Science CDCS, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron (DESY), Hamburg, Germany
- Hamburg Center for Ultrafast Imaging, Hamburg, Germany
- Department of Physics, Universität Hamburg, Hamburg, Germany
| | - Matthias Frank
- Lawrence Livermore National Laboratory (LLNL), Livermore, California, USA
| | - Raimund Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - John C. H. Spence
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Sabine Botha
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Richard A. Kirian
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- Department of Physics, Arizona State University, Tempe, Arizona, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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24
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Visualizing G protein-coupled receptor homomers using photoactivatable dye localization microscopy. Methods Cell Biol 2022; 169:27-41. [DOI: 10.1016/bs.mcb.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Abrol R, Serrano E, Santiago LJ. Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:325-359. [PMID: 35034722 PMCID: PMC11476118 DOI: 10.1016/bs.apcsb.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
G protein-coupled receptors (GPCRs) make up the largest superfamily of integral membrane proteins and play critical signal transduction roles in many physiological processes. Developments in molecular biology, biophysical, biochemical, pharmacological, and computational techniques aimed at these important therapeutic targets are beginning to provide unprecedented details on the structural as well as functional basis of their pleiotropic signaling mediated by G proteins, β arrestins, and other transducers. This pleiotropy presents a pharmacological challenge as the same ligand-receptor interaction can cause a therapeutic effect as well as an undesirable on-target side-effect through different downstream pathways. GPCRs don't function as simple binary on-off switches but as finely tuned shape-shifting machines described by conformational ensembles, where unique subsets of conformations may be responsible for specific signaling cascades. X-ray crystallography and more recently cryo-electron microscopy are providing snapshots of some of these functionally-important receptor conformations bound to ligands and/or transducers, which are being utilized by computational methods to describe the dynamic conformational energy landscape of GPCRs. In this chapter, we review the progress in computational conformational sampling methods based on molecular dynamics and discrete sampling approaches that have been successful in complementing biophysical and biochemical studies on these receptors in terms of their activation mechanisms, allosteric effects, actions of biased ligands, and effects of pathological mutations. Some of the sampled simulation time scales are beginning to approach receptor activation time scales. The list of conformational sampling methods and example uses discussed is not exhaustive but includes representative examples that have pushed the limits of classical molecular dynamics and discrete sampling methods to describe the activation energy landscape of GPCRs.
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Affiliation(s)
- Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States.
| | - Erik Serrano
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States
| | - Luis Jaimes Santiago
- Department of Chemistry and Biochemistry, California State University, Northridge, CA, United States
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Le HTT, Murugesan A, Ramesh T, Yli-Harja O, Konda Mani S, Kandhavelu M. Molecular interaction of HIC, an agonist of P2Y1 receptor, and its role in prostate cancer apoptosis. Int J Biol Macromol 2021; 189:142-150. [PMID: 34425116 DOI: 10.1016/j.ijbiomac.2021.08.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Prostate cancer is a heterogeneous, slow growing asymptomatic cancer that predominantly affects man. A purinergic G-protein coupled receptor, P2Y1R, is targeted for its therapeutic value since it plays a crucial role in many key molecular events of cancer progression and invasion. Our previous study demonstrated that indoline derivative, 1 ((1-(2-Hydroxy-5-nitrophenyl) (4-hydroxyphenyl) methyl)indoline-4‑carbonitrile; HIC), stimulates prostate cancer cell (PCa) growth inhibition via P2Y1R. However, the mode of interaction of P2Y1R with HIC involved in this process remains unclear. Here, we have reported the molecular interactions of HIC with P2Y1R. Molecular dynamics simulation was performed that revealed the stable specific binding of the protein-ligand complex. In vitro analysis has shown increased apoptosis of PCa-cells, PC3, and DU145, upon specific interaction of P2Y1R-HIC. This was further validated using siRNA analysis that showed a higher percentage of apoptotic cells in PCa-cells transfected with P2Y-siRNA-MRS2365 than P2Y-siRNA-HIC treatment. Decreased mitochondrial membrane potential (MMP) activity and reduced glutathione (GSH) level show their role in P2Y1R-HIC mediated apoptosis. These in silico and in vitro results confirmed that HIC could induce mitochondrial apoptotic signaling through the P2Y1R activation. Thus, HIC being a potential ligand upon interaction with P2Y1R might have therapeutic value for the treatment of prostate cancer.
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Affiliation(s)
- Hien Thi Thu Le
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland
| | - Akshaya Murugesan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; Department of Biotechnology, Lady Doak College, Thallakulam, Madurai 625002, India
| | - Thiyagarajan Ramesh
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Olli Yli-Harja
- Computational Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; Institute for Systems Biology, 1441N 34th Street, Seattle, WA 98103-8904, USA
| | - Saravanan Konda Mani
- Scigen Research and Innovation Pvt Ltd, Periyar Technology Business Incubator, Thanjavur 613403, Tamil Nadu, India
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland.
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Kalinkovich A, Livshits G. Biased and allosteric modulation of bone cell-expressing G protein-coupled receptors as a novel approach to osteoporosis therapy. Pharmacol Res 2021; 171:105794. [PMID: 34329703 DOI: 10.1016/j.phrs.2021.105794] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 07/25/2021] [Indexed: 12/16/2022]
Abstract
On the cellular level, osteoporosis (OP) is a result of imbalanced bone remodeling, in which osteoclastic bone resorption outcompetes osteoblastic bone formation. Currently available OP medications include both antiresorptive and bone-forming drugs. However, their long-term use in OP patients, mainly in postmenopausal women, is accompanied by severe side effects. Notably, the fundamental coupling between bone resorption and formation processes underlies the existence of an undesirable secondary outcome that bone anabolic or anti-resorptive drugs also reduce bone formation. This drawback requires the development of anti-OP drugs capable of selectively stimulating osteoblastogenesis and concomitantly reducing osteoclastogenesis. We propose that the application of small synthetic biased and allosteric modulators of bone cell receptors, which belong to the G-protein coupled receptors (GPCR) family, could be the key to resolving the undesired anti-OP drug selectivity. This approach is based on the capacity of these GPCR modulators, unlike the natural ligands, to trigger signaling pathways that promote beneficial effects on bone remodeling while blocking potentially deleterious effects. Under the settings of OP, an optimal anti-OP drug should provide fine-tuned regulation of downstream effects, for example, intermittent cyclic AMP (cAMP) elevation, preservation of Ca2+ balance, stimulation of osteoprotegerin (OPG) and estrogen production, suppression of sclerostin secretion, and/or preserved/enhanced canonical β-catenin/Wnt signaling pathway. As such, selective modulation of GPCRs involved in bone remodeling presents a promising approach in OP treatment. This review focuses on the evidence for the validity of our hypothesis.
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Affiliation(s)
- Alexander Kalinkovich
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6905126, Israel
| | - Gregory Livshits
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6905126, Israel; Adelson School of Medicine, Ariel University, Ariel 4077625, Israel.
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Electron paramagnetic resonance spectroscopy on G-protein-coupled receptors: Adopting strategies from related model systems. Curr Opin Struct Biol 2021; 69:177-186. [PMID: 34304006 DOI: 10.1016/j.sbi.2021.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/23/2022]
Abstract
Membrane proteins, including ion channels, transporters and G-protein-coupled receptors (GPCRs), play a significant role in various physiological processes. Many of these proteins are difficult to express in large quantities, imposing crucial experimental restrictions. Nevertheless, there is now a wide variety of studies available utilizing electron paramagnetic resonance (EPR) spectroscopic techniques that expand experimental accessibility by using relatively small quantities of protein. Here, we give an overview starting from basic strategies in EPR on membrane proteins with a focus on GPCRs, while emphasizing several applications from recent years. We highlight how the arsenal of EPR-based techniques may provide significant further contributions to understanding the complex molecular machinery and energetic phenomena responsible for seamless workflow in essential biological processes.
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29
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Structural insights into ligand recognition and activation of angiotensin receptors. Trends Pharmacol Sci 2021; 42:577-587. [PMID: 33985815 DOI: 10.1016/j.tips.2021.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 03/25/2021] [Accepted: 04/19/2021] [Indexed: 01/10/2023]
Abstract
G protein-coupled angiotensin II receptors, AT1R and AT2R, are integral components of the renin-angiotensin system (RAS) that regulates blood pressure and fluid balance in humans. While AT1R is a well-established target of angiotensin receptor blockers (ARBs) for managing hypertension and a prime system for studying biased signaling, AT2R has been recognized as a promising target against neuropathic pain and lung fibrosis. In this review, we discuss how recent structural advances illuminate ligand-binding modes and subtype selectivity, shared and distinct features of the receptors, their transducer-coupling patterns, and downstream signaling responses. We also underscore the key ATR aspects that require further studies to fully appreciate the mechanistic framework that fine-tunes their cellular and physiological functions, providing untapped potential for drug discovery.
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Shaye H, Stauch B, Gati C, Cherezov V. Molecular mechanisms of metabotropic GABA B receptor function. SCIENCE ADVANCES 2021; 7:7/22/eabg3362. [PMID: 34049877 PMCID: PMC8163086 DOI: 10.1126/sciadv.abg3362] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/14/2021] [Indexed: 05/06/2023]
Abstract
Metabotropic γ-aminobutyric acid G protein-coupled receptors (GABAB) represent one of the two main types of inhibitory neurotransmitter receptors in the brain. These receptors act both pre- and postsynaptically by modulating the transmission of neuronal signals and are involved in a range of neurological diseases, from alcohol addiction to epilepsy. A series of recent cryo-EM studies revealed critical details of the activation mechanism of GABAB Structures are now available for the receptor bound to ligands with different modes of action, including antagonists, agonists, and positive allosteric modulators, and captured in different conformational states from the inactive apo to the fully active state bound to a G protein. These discoveries provide comprehensive insights into the activation of the GABAB receptor, which not only broaden our understanding of its structure, pharmacology, and physiological effects but also will ultimately facilitate the discovery of new therapeutic drugs and neuromodulators.
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Affiliation(s)
- Hamidreza Shaye
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
- Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Benjamin Stauch
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
- Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Cornelius Gati
- Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Biosciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
- Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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31
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Bous J, Orcel H, Floquet N, Leyrat C, Lai-Kee-Him J, Gaibelet G, Ancelin A, Saint-Paul J, Trapani S, Louet M, Sounier R, Déméné H, Granier S, Bron P, Mouillac B. Cryo-electron microscopy structure of the antidiuretic hormone arginine-vasopressin V2 receptor signaling complex. SCIENCE ADVANCES 2021; 7:7/21/eabg5628. [PMID: 34020960 PMCID: PMC8139594 DOI: 10.1126/sciadv.abg5628] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/01/2021] [Indexed: 05/08/2023]
Abstract
The antidiuretic hormone arginine-vasopressin (AVP) forms a signaling complex with the V2 receptor (V2R) and the Gs protein, promoting kidney water reabsorption. Molecular mechanisms underlying activation of this critical G protein-coupled receptor (GPCR) signaling system are still unknown. To fill this gap of knowledge, we report here the cryo-electron microscopy structure of the AVP-V2R-Gs complex. Single-particle analysis revealed the presence of three different states. The two best maps were combined with computational and nuclear magnetic resonance spectroscopy constraints to reconstruct two structures of the ternary complex. These structures differ in AVP and Gs binding modes. They reveal an original receptor-Gs interface in which the Gαs subunit penetrates deep into the active V2R. The structures help to explain how V2R R137H or R137L/C variants can lead to two severe genetic diseases. Our study provides important structural insights into the function of this clinically relevant GPCR signaling complex.
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Affiliation(s)
- Julien Bous
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Hélène Orcel
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Nicolas Floquet
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34093 Montpellier cedex 5, France
| | - Cédric Leyrat
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Joséphine Lai-Kee-Him
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Gérald Gaibelet
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Aurélie Ancelin
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Julie Saint-Paul
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Stefano Trapani
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Maxime Louet
- Institut des Biomolécules Max Mousseron, Université de Montpellier, CNRS, ENSCM, 34093 Montpellier cedex 5, France
| | - Rémy Sounier
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France
| | - Hélène Déméné
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Sébastien Granier
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France.
| | - Patrick Bron
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France.
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, 34094 Montpellier cedex 5, France.
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32
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Ma N, Nivedha AK, Vaidehi N. Allosteric communication regulates ligand-specific GPCR activity. FEBS J 2021; 288:2502-2512. [PMID: 33738925 PMCID: PMC9805801 DOI: 10.1111/febs.15826] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/14/2021] [Accepted: 03/17/2021] [Indexed: 01/11/2023]
Abstract
G protein-coupled receptors (GPCRs) are membrane-bound proteins that are ubiquitously expressed in many cell types and take part in mediating multiple signaling pathways. GPCRs are dynamic proteins and exist in an equilibrium between an ensemble of conformational states such as inactive and fully active states. This dynamic nature of GPCRs is one of the factors that confers their basal activity even in the absence of any ligand-mediated activation. Ligands selectively bind and stabilize a subset of the conformations from the ensemble leading to a shift in the equilibrium toward the inactive or the active state depending on the nature of the ligand. This ligand-selective effect is achieved through allosteric communication between the ligand binding site and G protein or β-arrestin coupling site. Similarly, the G protein coupling to the receptor exerts the allosteric effect on the ligand binding region leading to increased binding affinity for agonists and decreased affinity for antagonists or inverse agonists. In this review, we enumerate the current state of our understanding of the mechanism of allosteric communication in GPCRs with a specific focus on the critical role of computational methods in delineating the residues involved in allosteric communication. Analyzing allosteric communication mechanism using molecular dynamics simulations has revealed (a) a structurally conserved mechanism of allosteric communication that regulates the G protein coupling, (b) a rational structure-based approach to designing selective ligands, and (c) an approach to designing allosteric GPCR mutants that are either ligand and G protein or β-arrestin selective.
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Affiliation(s)
- Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010
| | - Anita K. Nivedha
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010
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33
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Mlyniec K, Siodłak D, Doboszewska U, Nowak G. GPCR oligomerization as a target for antidepressants: Focus on GPR39. Pharmacol Ther 2021; 225:107842. [PMID: 33746052 DOI: 10.1016/j.pharmthera.2021.107842] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/15/2021] [Indexed: 11/30/2022]
Abstract
At present most of the evidence for the relevance of oligomerization for the pharmacology of depression comes from in vitro studies which identified oligomers, and from neuropsychopharmacological studies of receptors which participate in oligomerization. For example, behavioural and biochemical studies in knockout animals suggest that GPR39 may mediate the antidepressant action of monoaminergic antidepressants. We have recently found long-lasting antidepressant-like effects of GPR39 agonist, thus suggesting GPR39 as a target for the development of novel antidepressant drugs. In vitro studies have shown that GPR39 oligomerizes with other GPCRs. Oligomerization of GPR39 should thus be considered in relation to the development of new antidepressants targeting this receptor as well as antidepressants targeting other receptors that may form complexes with GPR39. Here, we summarize recent data suggestive of the importance of oligomerization for the pharmacology of depression and discuss approaches for validation of this phenomenon.
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Affiliation(s)
- Katarzyna Mlyniec
- Department of Pharmacobiology, Jagiellonian University Medical College, Medyczna 9, PL 30-688 Krakow, Poland.
| | - Dominika Siodłak
- Department of Pharmacobiology, Jagiellonian University Medical College, Medyczna 9, PL 30-688 Krakow, Poland
| | - Urszula Doboszewska
- Department of Pharmacobiology, Jagiellonian University Medical College, Medyczna 9, PL 30-688 Krakow, Poland
| | - Gabriel Nowak
- Department of Pharmacobiology, Jagiellonian University Medical College, Medyczna 9, PL 30-688 Krakow, Poland; Maj Institute of Pharmacology, Polish Academy of Sciences, Smetna 12, PL 31-343 Kraków, Poland
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34
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Bock A, Bermudez M. Allosteric coupling and biased agonism in G protein‐coupled receptors. FEBS J 2021; 288:2513-2528. [DOI: 10.1111/febs.15783] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/05/2021] [Accepted: 02/22/2021] [Indexed: 12/11/2022]
Affiliation(s)
- Andreas Bock
- Receptor Signaling Lab Max‐Delbrueck‐Center for Molecular Medicine Berlin Germany
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35
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Wada M, Yukawa K, Ogasawara H, Suzawa K, Maekawa T, Yamamoto Y, Ohta T, Lee E, Miki T. GPR52 accelerates fatty acid biosynthesis in a ligand-dependent manner in hepatocytes and in response to excessive fat intake in mice. iScience 2021; 24:102260. [PMID: 33796846 PMCID: PMC7995607 DOI: 10.1016/j.isci.2021.102260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/06/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
Gpr52 is an orphan G-protein-coupled receptor of unknown physiological function. We found that Gpr52-deficient (Gpr52−/−) mice exhibit leanness associated with reduced liver weight, decreased hepatic de novo lipogenesis, and enhanced insulin sensitivity. Treatment of the hepatoma cell line HepG2 cells with c11, the synthetic GPR52 agonist, increased fatty acid biosynthesis, and GPR52 knockdown (KD) abolished the lipogenic action of c11. In addition, c11 induced the expressions of lipogenic enzymes (SCD1 and ELOVL6), whereas these inductions were attenuated by GPR52-KD. In contrast, cholesterol biosynthesis was not increased by c11, but its basal level was significantly suppressed by GPR52-KD. High-fat diet (HFD)-induced increase in hepatic expression of Pparg2 and its targets (Scd1 and Elovl6) was absent in Gpr52−/− mice with alleviated hepatosteatosis. Our present study showed that hepatic GPR52 promotes the biosynthesis of fatty acid and cholesterol in a ligand-dependent and a constitutive manner, respectively, and Gpr52 participates in HFD-induced fatty acid synthesis in liver. Hepatosteatosis is inherently an adaptive response to overnutrition to store energy On the other hand, it can be a pathological condition causing insulin resistance High-fat diet increases PPARγ2 expression and lipogenesis in liver via GPR52 Gpr52 ablation protects mice from developing hepatosteatosis and insulin resistance
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Affiliation(s)
- Mitsuo Wada
- Department of Medical Physiology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan.,Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Yokohama 236-0004, Japan
| | - Kayo Yukawa
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Yokohama 236-0004, Japan
| | - Hiroyuki Ogasawara
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Yokohama 236-0004, Japan
| | - Koichi Suzawa
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki 569-1125, Japan
| | - Tatsuya Maekawa
- Central Pharmaceutical Research Institute, Japan Tobacco Inc., Takatsuki 569-1125, Japan
| | - Yoshihisa Yamamoto
- Pharmaceutical Frontier Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Yokohama 236-0004, Japan
| | - Takeshi Ohta
- Laboratory of Animal Physiology and Functional Anatomy, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Eunyoung Lee
- Department of Medical Physiology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
| | - Takashi Miki
- Department of Medical Physiology, Chiba University, Graduate School of Medicine, Chiba 260-8670, Japan
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A set of common movements within GPCR-G-protein complexes from variability analysis of cryo-EM datasets. J Struct Biol 2021; 213:107699. [PMID: 33545352 DOI: 10.1016/j.jsb.2021.107699] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/05/2021] [Accepted: 01/22/2021] [Indexed: 12/11/2022]
Abstract
G-protein coupled receptors (GPCRs) are among the most versatile signal transducers in the cell. Once activated, GPCRs sample a large conformational space and couple to G-proteins to initiate distinct signaling pathways. The dynamical behavior of GPCR-G-protein complexes is difficult characterize structurally, and it might hinder obtaining routine high-resolution density maps in single-particle reconstructions. Here, we used variability analysis on the rhodopsin-Gi-Fab16 complex cryo-EM dataset, and the results provide insights into the dynamic nature of the receptor-complex interaction. We compare the outcome of this analysis with recent results obtained on the cannabinoid-Gi- and secretin-Gs-receptor complexes. Despite differences related to the biochemical compositions of the three samples, a set of consensus movements emerges. We anticipate that systematic variability analysis on GPCR-G-protein complexes may provide useful information not only at the biological level, but also for improving the preparation of more stable samples for cryo-EM single-particle analysis.
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37
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Liauw BWH, Afsari HS, Vafabakhsh R. Conformational rearrangement during activation of a metabotropic glutamate receptor. Nat Chem Biol 2021; 17:291-297. [PMID: 33398167 PMCID: PMC7904630 DOI: 10.1038/s41589-020-00702-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 10/28/2020] [Indexed: 12/21/2022]
Abstract
G protein-coupled receptors (GPCRs) relay information across cell membranes through conformational coupling between the ligand-binding domain and cytoplasmic signaling domain. In dimeric class C GPCRs, the mechanism of this process, which involves propagation of local ligand-induced conformational changes over 12 nm through three distinct structural domains, is unknown. Here, we used single-molecule FRET (smFRET) and live-cell imaging and found that metabotropic glutamate receptor 2 (mGluR2) interconverts between four conformational states, two of which were previously unknown, and activation proceeds through the conformational selection mechanism. Furthermore, the conformation of the ligand-binding domains and downstream domains are weakly coupled. We show that the intermediate states act as conformational checkpoints for activation and control allosteric modulation of signaling. Our results demonstrate a mechanism for activation of mGluRs where ligand binding controls the proximity of signaling domains, analogous to some receptor kinases. This design principle may be generalizable to other biological allosteric sensors.
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Affiliation(s)
| | | | - Reza Vafabakhsh
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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38
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Kawaguchi K, Park J, Masaki T, Mezaki Y, Ochi S, Matsuura T. Comprehensive gene expression profiling of human astrocytes treated with a hepatic encephalopathy-inducible factor, alpha 1-antichymotripsin. Biochem Biophys Rep 2020; 24:100855. [PMID: 33299931 PMCID: PMC7704407 DOI: 10.1016/j.bbrep.2020.100855] [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: 06/29/2020] [Revised: 09/29/2020] [Accepted: 11/09/2020] [Indexed: 11/22/2022] Open
Abstract
Astrocytes are major glial cells that play a critical role in brain homeostasis. Abnormalities in astrocytic function, such as hepatic encephalopathy (HE) during acute liver failure, can result in brain death following brain edema and the associated astrocyte swelling. Recently, we have identified alpha 1-antichymotripsin (ACT) to be a biomarker candidate for HE. ACT induces astrocyte swelling by upregulating aquaporin 4 (AQP4); however, the causal connection between these proteins is not clear yet. In this study, we utilized a microarray profile to screen the differentially expressed genes (DEGs) in astrocytes treated with ACT. We then performed Gene Ontology, REACTOME, and the comprehensive resource of mammalian protein complexes (CORUM) enrichment analyses of the identified DEGs. The results of these analyses indicated that the DEGs were enriched in pathways activating adenylate cyclase (AC)-coupled G protein-coupled receptors (GPCRs) and therefore were involved in the cyclic adenosine monophosphate (cAMP) signaling. These results indicate that ACT may act as a ligand of Gs-GPCRs and subsequently upregulate cAMP. As cAMP is known to upregulate AQP4 in astrocytes, these results suggest that ACT may upregulate AQP4 by activating AC GPCRs and therefore serve as a therapeutic target for acute HE. The expression of AQP4 is induced by alpha 1-antichymotripsin dependent activation of adenylate cyclase. Combination treatment of alpha 1-antichymotripsin and arginine vasopressin enhance the activation of adenylate cyclase. Alpha 1-antichemotripsin might be a therapeutic target for acute hepatic encephalopathy.
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Affiliation(s)
- Kenji Kawaguchi
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, 105-8461, Japan
| | - Jonghyuk Park
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, 105-8461, Japan
| | - Takahiro Masaki
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, 105-8461, Japan
| | - Yoshihiro Mezaki
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, 105-8461, Japan
| | - Sae Ochi
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, 105-8461, Japan
| | - Tomokazu Matsuura
- Department of Laboratory Medicine, The Jikei University School of Medicine, Minato-ku, Tokyo, 105-8461, Japan
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39
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Statistics for the analysis of molecular dynamics simulations: providing P values for agonist-dependent GPCR activation. Sci Rep 2020; 10:19942. [PMID: 33203907 PMCID: PMC7672096 DOI: 10.1038/s41598-020-77072-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023] Open
Abstract
Molecular dynamics (MD) is the common computational technique for assessing efficacy of GPCR-bound ligands. Agonist efficacy measures the capability of the ligand-bound receptor of reaching the active state in comparison with the free receptor. In this respect, agonists, neutral antagonists and inverse agonists can be considered. A collection of MD simulations of both the ligand-bound and the free receptor are needed to provide reliable conclusions. Variability in the trajectories needs quantification and proper statistical tools for meaningful and non-subjective conclusions. Multiple-factor (time, ligand, lipid) ANOVA with repeated measurements on the time factor is proposed as a suitable statistical method for the analysis of agonist-dependent GPCR activation MD simulations. Inclusion of time factor in the ANOVA model is consistent with the time-dependent nature of MD. Ligand and lipid factors measure agonist and lipid influence on receptor activation. Previously reported MD simulations of adenosine A2a receptor (A2aR) are reanalyzed with this statistical method. TM6–TM3 and TM7–TM3 distances are selected as dependent variables in the ANOVA model. The ligand factor includes the presence or absence of adenosine whereas the lipid factor considers DOPC or DOPG lipids. Statistical analysis of MD simulations shows the efficacy of adenosine and the effect of the membrane lipid composition. Subsequent application of the statistical methodology to NECA A2aR agonist, with resulting P values in consistency with its pharmacological profile, suggests that the method is useful for ligand comparison and potentially for dynamic structure-based virtual screening.
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