1
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Papadourakis M, Sinenka H, Matricon P, Hénin J, Brannigan G, Pérez-Benito L, Pande V, van Vlijmen H, de Graaf C, Deflorian F, Tresadern G, Cecchini M, Cournia Z. Alchemical Free Energy Calculations on Membrane-Associated Proteins. J Chem Theory Comput 2023; 19:7437-7458. [PMID: 37902715 PMCID: PMC11017255 DOI: 10.1021/acs.jctc.3c00365] [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: 03/31/2023] [Indexed: 10/31/2023]
Abstract
Membrane proteins have diverse functions within cells and are well-established drug targets. The advances in membrane protein structural biology have revealed drug and lipid binding sites on membrane proteins, while computational methods such as molecular simulations can resolve the thermodynamic basis of these interactions. Particularly, alchemical free energy calculations have shown promise in the calculation of reliable and reproducible binding free energies of protein-ligand and protein-lipid complexes in membrane-associated systems. In this review, we present an overview of representative alchemical free energy studies on G-protein-coupled receptors, ion channels, transporters as well as protein-lipid interactions, with emphasis on best practices and critical aspects of running these simulations. Additionally, we analyze challenges and successes when running alchemical free energy calculations on membrane-associated proteins. Finally, we highlight the value of alchemical free energy calculations calculations in drug discovery and their applicability in the pharmaceutical industry.
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Affiliation(s)
- Michail Papadourakis
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Hryhory Sinenka
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Pierre Matricon
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Jérôme Hénin
- Laboratoire
de Biochimie Théorique UPR 9080, CNRS and Université Paris Cité, 75005 Paris, France
| | - Grace Brannigan
- Center
for Computational and Integrative Biology, Rutgers University−Camden, Camden, New Jersey 08103, United States of America
- Department
of Physics, Rutgers University−Camden, Camden, New Jersey 08102, United States
of America
| | - Laura Pérez-Benito
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Vineet Pande
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Herman van Vlijmen
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Chris de Graaf
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Francesca Deflorian
- Sosei
Heptares, Steinmetz Building,
Granta Park, Great Abington, Cambridge CB21 6DG, United
Kingdom
| | - Gary Tresadern
- CADD,
In Silico Discovery, Janssen Research &
Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Marco Cecchini
- Institut
de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
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2
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Badshah M, Ibrahim J, Su N, Whiley P, Whittaker M, Exintaris B. The Effects of Age on Prostatic Responses to Oxytocin and the Effects of Antagonists. Biomedicines 2023; 11:2956. [PMID: 38001957 PMCID: PMC10669827 DOI: 10.3390/biomedicines11112956] [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: 09/19/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Benign prostatic hyperplasia (BPH) is an age-related enlargement of the prostate with urethral obstruction that predominantly affects the middle-aged and older male population, resulting in disruptive lower urinary tract symptoms (LUTS), thus creating a profound impact on an individual's quality of life. The development of LUTS may be linked to overexpression of oxytocin receptors (OXTR), resulting in increased baseline myogenic tone within the prostate. Thus, it is hypothesised that targeting OXTR using oxytocin receptor antagonists (atosiban, cligosiban, and β-Mercapto-β,β-cyclopentamethylenepropionyl1, O-Me-Tyr2, Orn8]-Oxytocin (ßMßßC)), may attenuate myogenic tone within the prostate. Organ bath and immunohistochemistry techniques were conducted on prostate tissue from young and older rats. Our contractility studies demonstrated that atosiban significantly decreased the frequency of spontaneous contractions within the prostate of young rats (**** p < 0.0001), and cligosiban (* p < 0.05), and ßMßßC (**** p < 0.0001) in older rats. Additionally, immunohistochemistry findings revealed that nuclear-specific OXTR was predominantly expressed within the epithelium of the prostate of both young (*** p < 0.001) and older rats (**** p < 0.0001). In conclusion, our findings indicate that oxytocin is a key modulator of prostate contractility, and targeting OXTR is a promising avenue in the development of novel BPH drugs.
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Affiliation(s)
- Masroor Badshah
- Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia;
| | - Jibriil Ibrahim
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia (N.S.)
| | - Nguok Su
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia (N.S.)
| | - Penny Whiley
- Hudson Institute of Medical Research, Monash University, Clayton, VIC 3168, Australia;
| | - Michael Whittaker
- Drug, Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia;
| | - Betty Exintaris
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC 3052, Australia (N.S.)
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3
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Mishra S, Rout M, Singh MK, Dehury B, Pati S. Illuminating the structural basis of human neurokinin 1 receptor (NK1R) antagonism through classical all-atoms molecular dynamics simulations. J Cell Biochem 2023; 124:1848-1869. [PMID: 37942587 DOI: 10.1002/jcb.30493] [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: 07/13/2023] [Revised: 09/26/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
Advances in structural biology have bestowed insights into the pleiotropic effects of neurokinin 1 receptors (NK1R) in diverse patho-physiological processes, thereby highlighting the potential therapeutic value of antagonists directed against NK1R. Herein, we investigate the mode of antagonist recognition to discern the obscure atomic facets germane for the function and molecular determinants of NK1R. To commence discernment of potent antagonists and the conformational changes in NK1R, induced upon antagonist binding, state-of-the-art classical all-atoms molecular dynamics (MD) simulations in lipid mimetic bilayers have been utilized. MD simulations of structural ensembles reveals the involvement of TM5 and TM6 in tight anchoring of antagonists through a network of interhelical hydrogen-bonds, while, the extracellular loop 2 (ECL2) governs the overall size and nature of the pocket, thereby modulating NK1R. Consistent comparison between experiments and MD simulation results discerns the predominant role of TM3, TM4, and TM6 in lipid-NK1R interaction. Correlation between hydrophobic index and helicity of TM domains elucidates their importance in maintaining the structural stability in addition to regulating NK1R antagonism. Taken together, we anticipate that our computational study marks a comprehensive structural basis of NK1R antagonism in lipid bilayers, which may facilitate designing of new therapeutics against associated diseases targeting human neurokinin receptors.
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Affiliation(s)
- Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
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4
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Marcus DJ, Bruchas MR. Optical Approaches for Investigating Neuromodulation and G Protein-Coupled Receptor Signaling. Pharmacol Rev 2023; 75:1119-1139. [PMID: 37429736 PMCID: PMC10595021 DOI: 10.1124/pharmrev.122.000584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/06/2023] [Accepted: 05/01/2023] [Indexed: 07/12/2023] Open
Abstract
Despite the fact that roughly 40% of all US Food and Drug Administration (FDA)-approved pharmacological therapeutics target G protein-coupled receptors (GPCRs), there remains a gap in our understanding of the physiologic and functional role of these receptors at the systems level. Although heterologous expression systems and in vitro assays have revealed a tremendous amount about GPCR signaling cascades, how these cascades interact across cell types, tissues, and organ systems remains obscure. Classic behavioral pharmacology experiments lack both the temporal and spatial resolution to resolve these long-standing issues. Over the past half century, there has been a concerted effort toward the development of optical tools for understanding GPCR signaling. From initial ligand uncaging approaches to more recent development of optogenetic techniques, these strategies have allowed researchers to probe longstanding questions in GPCR pharmacology both in vivo and in vitro. These tools have been employed across biologic systems and have allowed for interrogation of everything from specific intramolecular events to pharmacology at the systems level in a spatiotemporally specific manner. In this review, we present a historical perspective on the motivation behind and development of a variety of optical toolkits that have been generated to probe GPCR signaling. Here we highlight how these tools have been used in vivo to uncover the functional role of distinct populations of GPCRs and their signaling cascades at a systems level. SIGNIFICANCE STATEMENT: G protein-coupled receptors (GPCRs) remain one of the most targeted classes of proteins for pharmaceutical intervention, yet we still have a limited understanding of how their unique signaling cascades effect physiology and behavior at the systems level. In this review, we discuss a vast array of optical techniques that have been devised to probe GPCR signaling both in vitro and in vivo.
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Affiliation(s)
- David J Marcus
- Center for the Neurobiology of Addiction, Pain and Emotion (D.J.M., M.R.B.), Department of Anesthesiology and Pain Medicine (D.J.M., M.R.B.), Department of Pharmacology (M.R.B.), and Department of Bioengineering (M.R.B.), University of Washington, Seattle, Washington
| | - Michael R Bruchas
- Center for the Neurobiology of Addiction, Pain and Emotion (D.J.M., M.R.B.), Department of Anesthesiology and Pain Medicine (D.J.M., M.R.B.), Department of Pharmacology (M.R.B.), and Department of Bioengineering (M.R.B.), University of Washington, Seattle, Washington
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5
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Castañeda-Leautaud AC, Vidal-Limon A, Aguila SA. Molecular dynamics and free energy calculations of clozapine bound to D2 and H1 receptors reveal a cardiometabolic mitigated derivative. J Biomol Struct Dyn 2023; 41:9313-9325. [PMID: 36416566 DOI: 10.1080/07391102.2022.2148748] [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: 05/24/2022] [Accepted: 11/12/2022] [Indexed: 11/24/2022]
Abstract
Most atypical antipsychotics derive from a high dropout of drug treatments due to adverse cardiometabolic side effects. These side effects are caused, in part, by the H1 receptor blockade. The current work sought a clozapine derivative with a reduced affinity for the H1 receptor while maintaining its therapeutic effect linked to D2 receptor binding. Explicit molecular dynamics simulations and end-point free energy calculations of clozapine in complex with the D2 and H1 receptors embedded in cholesterol-rich lipid bilayers were performed to analyze the intermolecular interactions and address the relevance of clozapine-functional groups. Based on that, free energy perturbation calculations were performed to measure the change in free energy of clozapine structural modifications. Our results indicate the best clozapine derivative is the iodine atom substitution for chlorine. The latter is mainly due to electrostatic interaction loss for the H1 receptor, while the halogen orientation out of the D2 active site reduces the impact on the affinity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alma C Castañeda-Leautaud
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
- Nanosciences, Center for Scientific Research and Higher Education of Ensenada, Ensenada, B.C., Mexico
| | - Abraham Vidal-Limon
- Instituto de Ecología A.C. (INECOL). Red de Estudios Moleculares Avanzados, Xalapa, Veracruz, México
| | - Sergio A Aguila
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, Mexico
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6
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Zhang X, Wang Y, Supekar S, Cao X, Zhou J, Dang J, Chen S, Jenkins L, Marsango S, Li X, Liu G, Milligan G, Feng M, Fan H, Gong W, Zhang C. Pro-phagocytic function and structural basis of GPR84 signaling. Nat Commun 2023; 14:5706. [PMID: 37709767 PMCID: PMC10502086 DOI: 10.1038/s41467-023-41201-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/26/2023] [Indexed: 09/16/2023] Open
Abstract
GPR84 is a unique orphan G protein-coupled receptor (GPCR) that can be activated by endogenous medium-chain fatty acids (MCFAs). The signaling of GPR84 is largely pro-inflammatory, which can augment inflammatory response, and GPR84 also functions as a pro-phagocytic receptor to enhance phagocytic activities of macrophages. In this study, we show that the activation of GPR84 by the synthetic agonist 6-OAU can synergize with the blockade of CD47 on cancer cells to induce phagocytosis of cancer cells by macrophages. We also determine a high-resolution structure of the GPR84-Gi signaling complex with 6-OAU. This structure reveals an occluded binding pocket for 6-OAU, the molecular basis of receptor activation involving non-conserved structural motifs of GPR84, and an unusual Gi-coupling interface. Together with computational docking and simulations studies, this structure also suggests a mechanism for the high selectivity of GPR84 for MCFAs and a potential routes of ligand binding and dissociation. These results provide a framework for understanding GPR84 signaling and developing new drugs targeting GPR84.
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Affiliation(s)
- Xuan Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yujing Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Shreyas Supekar
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Singapore
| | - Xu Cao
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
| | - Jingkai Zhou
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
| | - Jessica Dang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
| | - Siqi Chen
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA
| | - Laura Jenkins
- Centre for Translational Pharmacology, School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Sara Marsango
- Centre for Translational Pharmacology, School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Xiu Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Guibing Liu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Graeme Milligan
- Centre for Translational Pharmacology, School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.
| | - Mingye Feng
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA.
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, 138671, Singapore.
- Synthetic Biology Translational Research Program and Department of Biochemistry, School of Medicine, National University of Singapore, Singapore, Singapore.
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, Singapore.
| | - Weimin Gong
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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7
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Ahn D, Provasi D, Duc NM, Xu J, Salas-Estrada L, Spasic A, Yun MW, Kang J, Gim D, Lee J, Du Y, Filizola M, Chung KY. Gαs slow conformational transition upon GTP binding and a novel Gαs regulator. iScience 2023; 26:106603. [PMID: 37128611 PMCID: PMC10148139 DOI: 10.1016/j.isci.2023.106603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023] Open
Abstract
G proteins are major signaling partners for G protein-coupled receptors (GPCRs). Although stepwise structural changes during GPCR-G protein complex formation and guanosine diphosphate (GDP) release have been reported, no information is available with regard to guanosine triphosphate (GTP) binding. Here, we used a novel Bayesian integrative modeling framework that combines data from hydrogen-deuterium exchange mass spectrometry, tryptophan-induced fluorescence quenching, and metadynamics simulations to derive a kinetic model and atomic-level characterization of stepwise conformational changes incurred by the β2-adrenergic receptor (β2AR)-Gs complex after GDP release and GTP binding. Our data suggest rapid GTP binding and GTP-induced dissociation of Gαs from β2AR and Gβγ, as opposed to a slow closing of the Gαs α-helical domain (AHD). Yeast-two-hybrid screening using Gαs AHD as bait identified melanoma-associated antigen D2 (MAGE D2) as a novel AHD-binding protein, which was also shown to accelerate the GTP-induced closing of the Gαs AHD.
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Affiliation(s)
- Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jun Xu
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aleksandar Spasic
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Min Woo Yun
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Juyeong Kang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Dongmin Gim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jaecheol Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yang Du
- School of Life and Health Sciences, Kobilka Institute of Innovative Drug Discovery, Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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8
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Zhang X, Wang Y, Supekar S, Cao X, Zhou J, Dang J, Chen S, Jenkins L, Marsango S, Li X, Liu G, Milligan G, Feng M, Fan H, Gong W, Zhang C. Pro-phagocytic function and structural basis of GPR84 signaling. RESEARCH SQUARE 2023:rs.3.rs-2535247. [PMID: 36824923 PMCID: PMC9949259 DOI: 10.21203/rs.3.rs-2535247/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
GPR84 is a unique orphan G protein-coupled receptor (GPCR) that can be activated by endogenous medium-chain fatty acids (MCFAs). The signaling of GPR84 is largely pro-inflammatory, which can augment inflammatory response, and GPR84 also functions as a pro-phagocytic receptor to enhance the phagocytic activities of macrophages. In this study, we first showed that the activation of GPR84 by the synthetic agonist 6-OAU could synergize with the blockade of CD47 on cancer cells to induce phagocytosis of cancer cells by macrophages. Then, we determined a high-resolution structure of the GPR84-Gi signaling complex with 6-OAU. This structure revealed a completely occluded binding pocket for 6-OAU, the molecular basis of receptor activation involving non-conserved structural motifs of GPR84, and an unusual Gi-coupling interface. Together with computational docking and simulations studies, our structure also suggested the mechanism for the high selectivity of GPR84 for MCFAs and the potential routes of ligand binding and dissociation. Our results provide a framework for understanding GPR84 signaling and developing new drugs targeting GPR84.
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Affiliation(s)
- Xuan Zhang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yujing Wang
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Shreyas Supekar
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 138671, Singapore
| | - Xu Cao
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Jingkai Zhou
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Jessica Dang
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Siqi Chen
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Laura Jenkins
- Centre for Translational Pharmacology, School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
| | - Sara Marsango
- Centre for Translational Pharmacology, School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
| | - Xiu Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Guibing Liu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Graeme Milligan
- Centre for Translational Pharmacology, School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, U.K
| | - Mingye Feng
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 138671, Singapore
| | - Weimin Gong
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
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9
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Liu NN, Ren ZY, Ren QD, Chang ZG, Li JL, Li XA, Sun ZY, He JM, Niu QS, Xing XM. Full length transcriptomes analysis of cold-resistance of Apis cerana in Changbai Mountain during overwintering period. Gene 2022; 830:146503. [PMID: 35487395 DOI: 10.1016/j.gene.2022.146503] [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: 12/16/2021] [Revised: 03/21/2022] [Accepted: 04/14/2022] [Indexed: 11/15/2022]
Abstract
Apis cerana in Changbai Mountain is an ecological type of Apis cerana, which is an excellent breeding material with cold-resistant developed by long-term natural selection under the ecological conditions. However, the physiological and molecular mechanisms of Changbai Mountain population under cold stress are still unclear. In this study, the Nanopore sequencing was carried out for the transcriptome of Apis cerana in Changbai Mountain in the coldest period of overwintering, which will provide a reference to the cold-resistant mechanism. We determined 5,941 complete ORF sequences, 1,193 lncRNAs, 619 TFs, 10,866 SSRs and functional annotations of 11,599 new transcripts. Our results showed that the myosin family and the C2H2 zinc finger protein transcription factor family possibly have significant impacts on the response mechanism of cold stress during overwintering. In addition, the cold environment alters genes expression profiles in honeybees via different AS and APA mechanisms. These altered genes in Hippo, Foxo, and MARK pathways help them counter the stress of cold in overwinter period. Our results might provide clues about the response of eastern honeybees to extreme cold, and reflect the possible genetic basis of physiological changes.
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Affiliation(s)
- Nan-Nan Liu
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, Jilin 130112, PR China; Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China.
| | - Zhong-Yuan Ren
- Jilin Institute of Chemical Technology, Jilin, Jilin 132022, PR China
| | - Qing-Dan Ren
- Jilin Provincial Animal Husbandry General Station, Changchun, Jilin 130699, PR China
| | - Zhi-Guang Chang
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Jie-Luan Li
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Xing-An Li
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Zhi-Yu Sun
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Jin-Ming He
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China
| | - Qing-Sheng Niu
- Apiculture Science Institute of Jilin Province, Jilin, Jilin 132108, PR China.
| | - Xiu-Mei Xing
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, Jilin 130112, PR China.
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10
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Elbaradei A, Wang Z, Malmstadt N. Oxidation of Membrane Lipids Alters the Activity of the Human Serotonin 1A Receptor. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6798-6807. [PMID: 35608952 DOI: 10.1021/acs.langmuir.1c03238] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Lipid oxidation has significant effects on lipid bilayer properties; these effects can be expected to extend to interactions between the lipid bilayer and integral membrane proteins. Given that G protein-coupled receptor (GPCR) activity is known to depend on the properties of the surrounding lipid bilayer, these proteins represent an intriguing class of molecules in which the impact of lipid oxidation on protein behavior is studied. Here, we study the effects of lipid oxidation on the human serotonin 1A receptor (5-HT1AR). Giant unilamellar vesicles (GUVs) containing integral 5-HT1AR were fabricated by the hydrogel swelling method; these GUVs contained polyunsaturated 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine (PLinPC) and its oxidation product 1-palmitoyl-2-(9'-oxo-nonanoyl)-sn-glycero-3-phosphocholine (PoxnoPC) at various ratios. 5-HT1AR-integrated GUVs were also fabricated from lipid mixtures that had been oxidized by extended exposure to the atmosphere. Both types of vesicles were used to evaluate 5-HT1AR activity using an assay to quantify GDP-GTP exchange by the coupled G protein α subunit. Results indicated that 5-HT1AR activity increases significantly in bilayers containing oxidized lipids. This work is an important step in understanding how hyperbaric oxidation can change plasma membrane properties and lead to physiological dysfunction.
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11
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Hanson J. [G proteins: privileged transducers of 7-transmembrane spanning receptors]. Biol Aujourdhui 2022; 215:95-106. [PMID: 35275054 DOI: 10.1051/jbio/2021011] [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: 11/04/2021] [Indexed: 06/14/2023]
Abstract
G protein-coupled receptors or GPCR are the most abundant membrane receptors in our genome with around 800 members. They play an essential role in most physiological and pathophysiological phenomena. In addition, they constitute 30% of the targets of currently marketed drugs and remain an important reservoir for new innovative therapies. Their main effectors are heterotrimeric G proteins. These are composed of 3 subunits, α, β and γ, which, upon coupling with a GPCR, dissociate into Gα and Gβγ to activate numerous signaling pathways. This article describes some of the recent advances in understanding the function and role of heterotrimeric G proteins. After a short introduction to GPCRs, the history of the discovery of G proteins is briefly described. Then, the fundamental mechanisms of activation, signaling and regulation of G proteins are reviewed. New paradigms concerning intracellular signaling, specific recognition of G proteins by GPCRs as well as biased signaling are also discussed.
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Affiliation(s)
- Julien Hanson
- Laboratoire de Pharmacologie Moléculaire, GIGA-Molecular Biology of Diseases, Université de Liège, CHU, B34, Tour GIGA (+4), Avenue de l'Hôpital 11, B-4000 Liège, Belgique
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12
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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 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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13
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Jelinek V, Mösslein N, Bünemann M. Structures in G proteins important for subtype selective receptor binding and subsequent activation. Commun Biol 2021; 4:635. [PMID: 34045638 PMCID: PMC8160216 DOI: 10.1038/s42003-021-02143-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/26/2021] [Indexed: 11/09/2022] Open
Abstract
G protein-coupled receptors (GPCRs) selectively couple to specific heterotrimeric G proteins comprised of four subfamilies in order to induce appropriate physiological responses. However, structural determinants in Gα subunits responsible for selective recognition by approximately 800 human GPCRs have remained elusive. Here, we directly compare the influence of subtype-specific Gα structures on the stability of GPCR-G protein complexes and the activation by two Gq-coupled receptors. We used FRET-assays designed to distinguish multiple Go and Gq-based Gα chimeras in their ability to be selectively bound and activated by muscarinic M3 and histaminic H1 receptors. We identify the N-terminus including the αN/β1-hinge, the β2/β3-loop and the α5 helix of Gα to be key selectivity determinants which differ in their impact on selective binding to GPCRs and subsequent activation depending on the specific receptor. Altogether, these findings provide new insights into the molecular basis of G protein-coupling selectivity even beyond the Gα C-terminus.
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Affiliation(s)
- Volker Jelinek
- Institute of Pharmacology and Clinical Pharmacy, Philipps-University Marburg, Marburg, Germany
| | - Nadja Mösslein
- Institute of Pharmacology and Clinical Pharmacy, Philipps-University Marburg, Marburg, Germany
| | - Moritz Bünemann
- Institute of Pharmacology and Clinical Pharmacy, Philipps-University Marburg, Marburg, Germany.
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14
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Patt J, Alenfelder J, Pfeil EM, Voss JH, Merten N, Eryilmaz F, Heycke N, Rick U, Inoue A, Kehraus S, Deupi X, Müller CE, König GM, Crüsemann M, Kostenis E. An experimental strategy to probe Gq contribution to signal transduction in living cells. J Biol Chem 2021; 296:100472. [PMID: 33639168 PMCID: PMC8024710 DOI: 10.1016/j.jbc.2021.100472] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
Heterotrimeric G protein subunits Gαq and Gα11 are inhibited by two cyclic depsipeptides, FR900359 (FR) and YM-254890 (YM), both of which are being used widely to implicate Gq/11 proteins in the regulation of diverse biological processes. An emerging major research question therefore is whether the cellular effects of both inhibitors are on-target, that is, mediated via specific inhibition of Gq/11 proteins, or off-target, that is, the result of nonspecific interactions with other proteins. Here we introduce a versatile experimental strategy to discriminate between these possibilities. We developed a Gαq variant with preserved catalytic activity, but refractory to FR/YM inhibition. A minimum of two amino acid changes were required and sufficient to achieve complete inhibitor resistance. We characterized the novel mutant in HEK293 cells depleted by CRISPR–Cas9 of endogenous Gαq and Gα11 to ensure precise control over the Gα-dependent cellular signaling route. Using a battery of cellular outcomes with known and concealed Gq contribution, we found that FR/YM specifically inhibited cellular signals after Gαq introduction via transient transfection. Conversely, both inhibitors were inert across all assays in cells expressing the drug-resistant variant. These findings eliminate the possibility that inhibition of non-Gq proteins contributes to the cellular effects of the two depsipeptides. We conclude that combined application of FR or YM along with the drug-resistant Gαq variant is a powerful in vitro strategy to discern on-target Gq against off-target non-Gq action. Consequently, it should be of high value for uncovering Gq input to complex biological processes with high accuracy and the requisite specificity.
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Affiliation(s)
- Julian Patt
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Judith Alenfelder
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Eva Marie Pfeil
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Jan Hendrik Voss
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Nicole Merten
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Funda Eryilmaz
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Nina Heycke
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Uli Rick
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Stefan Kehraus
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Xavier Deupi
- Laboratory of Biomolecular Research and Condensed Matter Theory Group, Paul Scherrer Institute, Villigen, Switzerland
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical and Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany.
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15
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Ham D, Ahn D, Ashim J, Cho Y, Kim HR, Yu W, Chung KY. Conformational switch that induces GDP release from Gi. J Struct Biol 2021; 213:107694. [PMID: 33418033 DOI: 10.1016/j.jsb.2020.107694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 12/14/2020] [Accepted: 12/24/2020] [Indexed: 12/26/2022]
Abstract
Heterotrimeric guanine nucleotide-binding proteins (G proteins) are composed of α, β, and γ subunits. Gα switches between guanosine diphosphate (GDP)-bound inactive and guanosine triphosphate (GTP)-bound active states, and Gβγ interacts with the GDP-bound state. The GDP-binding regions are composed of two sites: the phosphate-binding and guanine-binding regions. The turnover of GDP and GTP is induced by guanine nucleotide-exchange factors (GEFs), including G protein-coupled receptors (GPCRs), Ric8A, and GIV/Girdin. However, the key structural factors for stabilizing the GDP-bound state of G proteins and the direct structural event for GDP release remain unclear. In this study, we investigated structural factors affecting GDP release by introducing point mutations in selected, conserved residues in Gαi3. We examined the effects of these mutations on the GDP/GTP turnover rate and the overall conformation of Gαi3 as well as the binding free energy between Gαi3 and GDP. We found that dynamic changes in the phosphate-binding regions are an immediate factor for the release of GDP.
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Affiliation(s)
- Donghee Ham
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Janbolat Ashim
- Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu 42988, Republic of Korea
| | - Yejin Cho
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Wookyung Yu
- Department of Brain and Cognitive Sciences, DGIST, 333 Techno jungang-daero, Daegu 42988, Republic of Korea; Core Protein Resources Center, DGIST, 333 Techno jungang-daero, Daegu 42988, Republic of Korea.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea.
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16
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Kraus S, Benard O, Naor Z, Seger R. C-Src is Activated by the EGF Receptor in a Pathway that Mediates JNK and ERK Activation by Gonadotropin-Releasing Hormone in COS7 Cells. Int J Mol Sci 2020; 21:ijms21228575. [PMID: 33202981 PMCID: PMC7697137 DOI: 10.3390/ijms21228575] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 12/26/2022] Open
Abstract
The key participants in G-protein-coupled receptor (GPCR) signaling are the mitogen-activated protein kinase (MAPK) signaling cascades. The mechanisms involved in the activation of the above cascades by GPCRs are not fully elucidated. The prototypical GPCR is the receptor for gonadotropin-releasing hormone (GnRHR), which serves as a key regulator of the reproductive system. Here, we expressed GnRHR in COS7 cells and found that GnRHR transmits its signals to MAPKs mainly via Gαi and the EGF receptor, without the involvement of Hb-EGF or PKCs. The main pathway that leads to JNK activation downstream of the EGF receptor involves a sequential activation of c-Src and PI3K. ERK activation by GnRHR is mediated by the EGF receptor, which activates Ras either directly or via c-Src. Beside the main pathway, the dissociated Gβγ and β-arrestin may initiate additional (albeit minor) pathways that lead to MAPK activation in the transfected COS7 cells. The pathways detected are significantly different from those in other GnRHR-bearing cells, indicating that GnRH can utilize various signaling mechanisms for MAPK activation. The unique pathway elucidated here, in which c-Src and PI3K are sequentially activated downstream of the EGF receptor, may serve as a prototype of signaling mechanisms by GnRHR and additional GPCRs in various cell types.
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Affiliation(s)
- Sarah Kraus
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel; (S.K.); (O.B.)
| | - Outhiriaradjou Benard
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel; (S.K.); (O.B.)
| | - Zvi Naor
- Department of Biochemistry, Tel Aviv University, Ramat Aviv 69978, Israel;
| | - Rony Seger
- Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 7610001, Israel; (S.K.); (O.B.)
- Correspondence: ; Tel.: +972-8-9343602
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17
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Zhao XF. G protein-coupled receptors function as cell membrane receptors for the steroid hormone 20-hydroxyecdysone. Cell Commun Signal 2020; 18:146. [PMID: 32907599 PMCID: PMC7488307 DOI: 10.1186/s12964-020-00620-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/27/2020] [Indexed: 12/16/2022] Open
Abstract
Abstract G protein-coupled receptors (GPCRs) are cell membrane receptors for various ligands. Recent studies have suggested that GPCRs transmit animal steroid hormone signals. Certain GPCRs have been shown to bind steroid hormones, for example, G protein-coupled estrogen receptor 1 (GPER1) binds estrogen in humans, and Drosophila dopamine/ecdysteroid receptor (DopEcR) binds the molting hormone 20-hydroxyecdysone (20E) in insects. This review summarizes the research progress on GPCRs as animal steroid hormone cell membrane receptors, including the nuclear and cell membrane receptors of steroid hormones in mammals and insects, the 20E signaling cascade via GPCRs, termination of 20E signaling, and the relationship between genomic action and the nongenomic action of 20E. Studies indicate that 20E induces a signal via GPCRs to regulate rapid cellular responses, including rapid Ca2+ release from the endoplasmic reticulum and influx from the extracellular medium, as well as rapid protein phosphorylation and subcellular translocation. 20E via the GPCR/Ca2+/PKC/signaling axis and the GPCR/cAMP/PKA-signaling axis regulates gene transcription by adjusting transcription complex formation and DNA binding activity. GPCRs can bind 20E in the cell membrane and after being isolated, suggesting GPCRs as cell membrane receptors of 20E. This review deepens our understanding of GPCRs as steroid hormone cell membrane receptors and the GPCR-mediated signaling pathway of 20E (20E-GPCR pathway), which will promote further study of steroid hormone signaling via GPCRs, and presents GPCRs as targets to explore new pharmaceutical materials to treat steroid hormone-related diseases or control pest insects. Video abstract
Graphical abstract ![]()
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Affiliation(s)
- Xiao-Fan Zhao
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, 266237, China.
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18
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Kim HR, Xu J, Maeda S, Duc NM, Ahn D, Du Y, Chung KY. Structural mechanism underlying primary and secondary coupling between GPCRs and the Gi/o family. Nat Commun 2020; 11:3160. [PMID: 32572026 PMCID: PMC7308389 DOI: 10.1038/s41467-020-16975-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Heterotrimeric G proteins are categorized into four main families based on their function and sequence, Gs, Gi/o, Gq/11, and G12/13. One receptor can couple to more than one G protein subtype, and the coupling efficiency varies depending on the GPCR-G protein pair. However, the precise mechanism underlying different coupling efficiencies is unknown. Here, we study the structural mechanism underlying primary and secondary Gi/o coupling, using the muscarinic acetylcholine receptor type 2 (M2R) as the primary Gi/o-coupling receptor and the β2-adrenergic receptor (β2AR, which primarily couples to Gs) as the secondary Gi/o-coupling receptor. Hydrogen/deuterium exchange mass spectrometry and mutagenesis studies reveal that the engagement of the distal C-terminus of Gαi/o with the receptor differentiates primary and secondary Gi/o couplings. This study suggests that the conserved hydrophobic residue within the intracellular loop 2 of the receptor (residue 34.51) is not critical for primary Gi/o-coupling; however, it might be important for secondary Gi/o-coupling. G protein-coupled receptors (GPCRs) can couple to more than one G protein subtype, and the coupling efficiency varies depending on the GPCR-G protein pair. Here authors use hydrogen/deuterium exchange mass spectrometry and mutagenesis to study the structural mechanism underlying primary and secondary Gi/o coupling.
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Affiliation(s)
- Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Jun Xu
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Shoji Maeda
- Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, 279 Campus Drive, Stanford, CA, 94305, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.,Division of Precision Medicine, Research Institute, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang, 10408, Republic of Korea
| | - Donghoon Ahn
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Yang Du
- School of Life and Health Sciences, Kobilka Institute of Innovative Drug Discovery, Chinese University of Hong Kong, 2001 Longxiang Ave, Shenzhen, Guangdong, 518172, China.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea.
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19
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Abstract
Heterotrimeric G proteins are the core upstream elements that transduce and amplify the cellular signals from G protein-coupled receptors (GPCRs) to intracellular effectors. GPCRs are the largest family of membrane proteins encoded in the human genome and are the targets of about one-third of prescription medicines. However, to date, no single therapeutic agent exerts its effects via perturbing heterotrimeric G protein function, despite a plethora of evidence linking G protein malfunction to human disease. Several recent studies have brought to light that the Gq family-specific inhibitor FR900359 (FR) is unexpectedly efficacious in silencing the signaling of Gq oncoproteins, mutant Gq variants that mostly exist in the active state. These data not only raise the hope that researchers working in drug discovery may be able to potentially strike Gq oncoproteins from the list of undruggable targets, but also raise questions as to how FR achieves its therapeutic effect. Here, we place emphasis on these recent studies and explain why they expand our pharmacological armamentarium for targeting Gq protein oncogenes as well as broaden our mechanistic understanding of Gq protein oncogene function. We also highlight how this novel insight impacts the significance and utility of using G(q) proteins as targets in drug discovery efforts.
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Affiliation(s)
- Evi Kostenis
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany.
| | - Eva Marie Pfeil
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany
| | - Suvi Annala
- Section of Molecular, Cellular and Pharmacobiology, Institute of Pharmaceutical Biology, Nussallee 6, 53115 Bonn, Germany
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20
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Kang XL, Zhang JY, Wang D, Zhao YM, Han XL, Wang JX, Zhao XF. The steroid hormone 20-hydroxyecdysone binds to dopamine receptor to repress lepidopteran insect feeding and promote pupation. PLoS Genet 2019; 15:e1008331. [PMID: 31412019 PMCID: PMC6693746 DOI: 10.1371/journal.pgen.1008331] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 07/24/2019] [Indexed: 12/11/2022] Open
Abstract
Holometabolous insects stop feeding at the final larval instar stage and then undergo metamorphosis; however, the mechanism is unclear. In the present study, using the serious lepidopteran agricultural pest Helicoverpa armigera as a model, we revealed that 20-hydroxyecdysone (20E) binds to the dopamine receptor (DopEcR), a G protein-coupled receptor, to stop larval feeding and promote pupation. DopEcR was expressed in various tissues and its level increased during metamorphic molting under 20E regulation. The 20E titer was low during larval feeding stages and high during wandering stages. By contrast, the dopamine (DA) titer was high during larval feeding stages and low during the wandering stages. Injection of 20E or blocking dopamine receptors using the inhibitor flupentixol decreased larval food consumption and body weight. Knockdown of DopEcR repressed larval feeding, growth, and pupation. 20E, via DopEcR, promoted apoptosis; and DA, via DopEcR, induced cell proliferation. 20E opposed DA function by repressing DA-induced cell proliferation and AKT phosphorylation. 20E, via DopEcR, induced gene expression and a rapid increase in intracellular calcium ions and cAMP. 20E induced the interaction of DopEcR with G proteins αs and αq. 20E, via DopEcR, induced protein phosphorylation and binding of the EcRB1-USP1 transcription complex to the ecdysone response element. DopEcR could bind 20E inside the cell membrane or after being isolated from the cell membrane. Mutation of DopEcR decreased 20E binding levels and related cellular responses. 20E competed with DA to bind to DopEcR. The results of the present study suggested that 20E, via binding to DopEcR, arrests larval feeding and promotes pupation. The steroid hormone 20-hydroxyecdysone (20E) represses insect larval feeding and promotes metamorphosis; however, the mechanism is unclear. The dopamine receptor plays important roles in animal motor function and reward-motivated behavior. Using the serious lepidopteran agricultural pest Helicoverpa armigera as a model, we revealed that 20E binds to DopEcR to block the dopamine pathway and initiates the 20E pathway. Dopamine (DA) binds to the dopamine receptor (DopEcR), a G protein-coupled receptor (GPCR), to regulate cell proliferation, larval feeding, and growth. However, 20E competes with DA to bind to DopEcR, which represses larval feeding and triggers the 20E-pathway, leading to metamorphosis. The results suggested that 20E, via binding to DopEcR, stops larval feeding and promotes pupation, which presented an example of the steroid hormone regulating dopamine receptor and behavior. Our study showed that GPCRs can bind 20E and function as 20E cell membrane receptors.
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Affiliation(s)
- Xin-Le Kang
- Shandong provincial key laboratory of animal cells and developmental biology, School of life science, Shandong University, Qingdao, China
| | - Jun-Ying Zhang
- Shandong provincial key laboratory of animal cells and developmental biology, School of life science, Shandong University, Qingdao, China
| | - Di Wang
- Shandong provincial key laboratory of animal cells and developmental biology, School of life science, Shandong University, Qingdao, China
| | - Yu-Meng Zhao
- Shandong provincial key laboratory of animal cells and developmental biology, School of life science, Shandong University, Qingdao, China
| | - Xiao-Lin Han
- Shandong provincial key laboratory of animal cells and developmental biology, School of life science, Shandong University, Qingdao, China
| | - Jin-Xing Wang
- Shandong provincial key laboratory of animal cells and developmental biology, School of life science, Shandong University, Qingdao, China
| | - Xiao-Fan Zhao
- Shandong provincial key laboratory of animal cells and developmental biology, School of life science, Shandong University, Qingdao, China
- * E-mail:
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21
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Wang J, Miao Y. Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors. J Phys Chem B 2019; 123:6462-6473. [PMID: 31283874 DOI: 10.1021/acs.jpcb.9b04867] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Coupling between G-protein-coupled receptors (GPCRs) and the G proteins is a key step in cellular signaling. Despite extensive experimental and computational studies, the mechanism of specific GPCR-G protein coupling remains poorly understood. This has greatly hindered effective drug design of GPCRs that are primary targets of ∼1/3 of currently marketed drugs. Here, we have employed all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method to decipher the mechanism of the GPCR-G protein interactions. Adenosine receptors (ARs) were used as model systems based on very recently determined cryo-EM structures of the A1AR and A2AAR coupled with the Gi and Gs proteins, respectively. Changing the Gi protein to the Gs led to increased fluctuations in the A1AR and agonist adenosine (ADO), while agonist 5'-N-ethylcarboxamidoadenosine (NECA) binding in the A2AAR could be still stabilized upon changing the Gs protein to the Gi. Free energy calculations identified one stable low-energy conformation for each of the A1AR-Gi and A2AAR-Gs complexes as in the cryo-EM structures, similarly for the A2AAR-Gi complex. In contrast, the ADO agonist and Gs protein sampled multiple conformations in the A1AR-Gs system. GaMD simulations thus indicated that the A1AR preferred to couple with the Gi protein to the Gs, while the A2AAR could couple with both the Gs and Gi proteins, being highly consistent with experimental findings of the ARs. More importantly, detailed analysis of the atomic simulations showed that the specific AR-G protein coupling resulted from remarkably complementary residue interactions at the protein interface, involving mainly the receptor transmembrane 6 helix and the Gα α5 helix and α4-β6 loop. In summary, the GaMD simulations have provided unprecedented insights into the dynamic mechanism of specific GPCR-G protein interactions at an atomistic level.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences , University of Kansas , Lawrence , Kansas 66047 , United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences , University of Kansas , Lawrence , Kansas 66047 , United States
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22
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Du Y, Duc NM, Rasmussen SGF, Hilger D, Kubiak X, Wang L, Bohon J, Kim HR, Wegrecki M, Asuru A, Jeong KM, Lee J, Chance MR, Lodowski DT, Kobilka BK, Chung KY. Assembly of a GPCR-G Protein Complex. Cell 2019; 177:1232-1242.e11. [PMID: 31080064 DOI: 10.1016/j.cell.2019.04.022] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/25/2019] [Accepted: 04/09/2019] [Indexed: 12/30/2022]
Abstract
The activation of G proteins by G protein-coupled receptors (GPCRs) underlies the majority of transmembrane signaling by hormones and neurotransmitters. Recent structures of GPCR-G protein complexes obtained by crystallography and cryoelectron microscopy (cryo-EM) reveal similar interactions between GPCRs and the alpha subunit of different G protein isoforms. While some G protein subtype-specific differences are observed, there is no clear structural explanation for G protein subtype-selectivity. All of these complexes are stabilized in the nucleotide-free state, a condition that does not exist in living cells. In an effort to better understand the structural basis of coupling specificity, we used time-resolved structural mass spectrometry techniques to investigate GPCR-G protein complex formation and G-protein activation. Our results suggest that coupling specificity is determined by one or more transient intermediate states that serve as selectivity filters and precede the formation of the stable nucleotide-free GPCR-G protein complexes observed in crystal and cryo-EM structures.
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Affiliation(s)
- Yang Du
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Søren G F Rasmussen
- Department of Neuroscience, University of Copenhagen, Copenhagen 2200, Denmark
| | - Daniel Hilger
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Xavier Kubiak
- Department of Neuroscience, University of Copenhagen, Copenhagen 2200, Denmark
| | - Liwen Wang
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jennifer Bohon
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; Case Center for Synchrotron Biosciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Marcin Wegrecki
- Department of Neuroscience, University of Copenhagen, Copenhagen 2200, Denmark
| | - Awuri Asuru
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kyung Min Jeong
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jeongmi Lee
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Mark R Chance
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; Case Center for Synchrotron Biosciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - David T Lodowski
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Brian K Kobilka
- Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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23
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Renault P, Louet M, Marie J, Labesse G, Floquet N. Molecular Dynamics Simulations of the Allosteric Modulation of the Adenosine A2A Receptor by a Mini-G Protein. Sci Rep 2019; 9:5495. [PMID: 30940903 PMCID: PMC6445292 DOI: 10.1038/s41598-019-41980-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 03/19/2019] [Indexed: 01/14/2023] Open
Abstract
Through their coupling to G proteins, G Protein-Coupled Receptors (GPCRs) trigger cellular responses to various signals. Some recent experiments have interestingly demonstrated that the G protein can also act on the receptor by favoring a closed conformation of its orthosteric site, even in the absence of a bound agonist. In this work, we explored such an allosteric modulation by performing extensive molecular dynamics simulations on the adenosine A2 receptor (A2aR) coupled to the Mini-Gs protein. In the presence of the Mini-Gs, we confirmed a restriction of the receptor’s agonist binding site that can be explained by a modulation of the intrinsic network of contacts of the receptor. Of interest, we observed similar effects with the C-terminal helix of the Mini-Gs, showing that the observed effect on the binding pocket results from direct local contacts with the bound protein partner that cause a rewiring of the whole receptor’s interaction network.
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Affiliation(s)
- Pedro Renault
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université de Montpellier, ENSCM, 34090, Montpellier, France.,Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090, Montpellier, France
| | - Maxime Louet
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université de Montpellier, ENSCM, 34090, Montpellier, France
| | - Jacky Marie
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université de Montpellier, ENSCM, 34090, Montpellier, France
| | - Gilles Labesse
- Centre de Biochimie Structurale, Université de Montpellier, CNRS, INSERM, 34090, Montpellier, France
| | - Nicolas Floquet
- Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université de Montpellier, ENSCM, 34090, Montpellier, France.
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24
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Malfacini D, Patt J, Annala S, Harpsøe K, Eryilmaz F, Reher R, Crüsemann M, Hanke W, Zhang H, Tietze D, Gloriam DE, Bräuner-Osborne H, Strømgaard K, König GM, Inoue A, Gomeza J, Kostenis E. Rational design of a heterotrimeric G protein α subunit with artificial inhibitor sensitivity. J Biol Chem 2019; 294:5747-5758. [PMID: 30745359 PMCID: PMC6463727 DOI: 10.1074/jbc.ra118.007250] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/28/2019] [Indexed: 12/31/2022] Open
Abstract
Transmembrane signals initiated by a range of extracellular stimuli converge on members of the Gq family of heterotrimeric G proteins, which relay these signals in target cells. Gq family G proteins comprise Gq, G11, G14, and G16, which upon activation mediate their cellular effects via inositol lipid–dependent and –independent signaling to control fundamental processes in mammalian physiology. To date, highly specific inhibition of Gq/11/14 signaling can be achieved only with FR900359 (FR) and YM-254890 (YM), two naturally occurring cyclic depsipeptides. To further development of FR or YM mimics for other Gα subunits, we here set out to rationally design Gα16 proteins with artificial FR/YM sensitivity by introducing an engineered depsipeptide-binding site. Thereby we permit control of G16 function through ligands that are inactive on the WT protein. Using CRISPR/Cas9-generated Gαq/Gα11-null cells and loss- and gain-of-function mutagenesis along with label-free whole-cell biosensing, we determined the molecular coordinates for FR/YM inhibition of Gq and transplanted these to FR/YM-insensitive G16. Intriguingly, despite having close structural similarity, FR and YM yielded biologically distinct activities: it was more difficult to perturb Gq inhibition by FR and easier to install FR inhibition onto G16 than perturb or install inhibition with YM. A unique hydrophobic network utilized by FR accounted for these unexpected discrepancies. Our results suggest that non-Gq/11/14 proteins should be amenable to inhibition by FR scaffold–based inhibitors, provided that these inhibitors mimic the interaction of FR with Gα proteins harboring engineered FR-binding sites.
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Affiliation(s)
- Davide Malfacini
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Julian Patt
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Suvi Annala
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Funda Eryilmaz
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Raphael Reher
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Max Crüsemann
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Wiebke Hanke
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Hang Zhang
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Daniel Tietze
- Eduard Zintl Institute of Inorganic and Physical Chemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Gabriele M König
- Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Jesus Gomeza
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Evi Kostenis
- From the Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany.
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25
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Modestia SM, Malta de Sá M, Auger E, Trossini GHG, Krieger JE, Rangel-Yagui CDO. Biased Agonist TRV027 Determinants in AT1R by Molecular Dynamics Simulations. J Chem Inf Model 2019; 59:797-808. [PMID: 30668103 DOI: 10.1021/acs.jcim.8b00628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Functional selectivity is a phenomenon observed in G protein-coupled receptors in which intermediate active-state conformations are stabilized by mutations or ligand binding, resulting in different sets of signaling pathways. Peptides capable of selectively activating β-arrestin, known as biased agonists, have already been characterized in vivo and could correspond to a new therapeutic approach for treatment of cardiovascular diseases. Despite the potential of biased agonism, the mechanism involved in selective signaling remains unclear. In this work, molecular dynamics simulations were employed to compare the conformational profile of the angiotensin II type 1 receptor (AT1R) crystal bound to angiotensin II, bound to the biased ligand TRV027, and in the apo form. Our results show that both ligands induce changes near the NPxxY motif in transmembrane domain 7 that are related to receptor activation. However, the biased ligand does not cause the rotamer toggle alternative positioning and displays an exclusive hydrogen-bonding pattern. Our work sheds light on the biased agonism mechanism and will help in the future design of novel biased agonists for AT1R.
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Affiliation(s)
- Silvestre Massimo Modestia
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences , University of São Paulo , Av. Prof. Lineu Prestes 580 , 05508-900 São Paulo - SP , Brazil
| | - Matheus Malta de Sá
- Laboratory of Genetics and Molecular Cardiology, Heart Institute , University of São Paulo Medical School , Av. Dr. Enéas de Carvalho Aguiar 44 , 05403-900 São Paulo - SP , Brazil
| | - Eric Auger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute , University of São Paulo Medical School , Av. Dr. Enéas de Carvalho Aguiar 44 , 05403-900 São Paulo - SP , Brazil
| | - Gustavo Henrique Goulart Trossini
- Department of Pharmacy, School of Pharmaceutical Sciences , University of São Paulo , Av. Prof. Lineu Prestes 580 , 05508-900 São Paulo - SP , Brazil
| | - José Eduardo Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute , University of São Paulo Medical School , Av. Dr. Enéas de Carvalho Aguiar 44 , 05403-900 São Paulo - SP , Brazil
| | - Carlota de Oliveira Rangel-Yagui
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences , University of São Paulo , Av. Prof. Lineu Prestes 580 , 05508-900 São Paulo - SP , Brazil
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26
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Schöppe J, Ehrenmann J, Klenk C, Rucktooa P, Schütz M, Doré AS, Plückthun A. Crystal structures of the human neurokinin 1 receptor in complex with clinically used antagonists. Nat Commun 2019; 10:17. [PMID: 30604743 PMCID: PMC6318301 DOI: 10.1038/s41467-018-07939-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022] Open
Abstract
Neurokinins (or tachykinins) are peptides that modulate a wide variety of human physiology through the neurokinin G protein-coupled receptor family, implicated in a diverse array of pathological processes. Here we report high-resolution crystal structures of the human NK1 receptor (NK1R) bound to two small-molecule antagonist therapeutics – aprepitant and netupitant and the progenitor antagonist CP-99,994. The structures reveal the detailed interactions between clinically approved antagonists and NK1R, which induce a distinct receptor conformation resulting in an interhelical hydrogen-bond network that cross-links the extracellular ends of helices V and VI. Furthermore, the high-resolution details of NK1R bound to netupitant establish a structural rationale for the lack of basal activity in NK1R. Taken together, these co-structures provide a comprehensive structural basis of NK1R antagonism and will facilitate the design of new therapeutics targeting the neurokinin receptor family. Neurokinin receptors are G protein-coupled receptors. Here the authors present three crystal structures of the neurokinin 1 receptor (NK1R) in complex with small-molecule antagonists including aprepitant and netupitant and observe that these clinically approved compounds induce a conformational change in the receptor.
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Affiliation(s)
- Jendrik Schöppe
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Janosch Ehrenmann
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Christoph Klenk
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Prakash Rucktooa
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Marco Schütz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.,Heptares Therapeutics Zürich AG, Grabenstrasse 11a, 8952, Zürich, Switzerland
| | - Andrew S Doré
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
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27
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Wang J, Miao Y. Recent advances in computational studies of GPCR-G protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 116:397-419. [PMID: 31036298 PMCID: PMC6986689 DOI: 10.1016/bs.apcsb.2018.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein-protein interactions are key in cellular signaling. G protein-coupled receptors (GPCRs), the largest superfamily of human membrane proteins, are able to transduce extracellular signals (e.g., hormones and neurotransmitters) to intracellular proteins, in particular the G proteins. Since GPCRs serve as primary targets of ~1/3 of currently marketed drugs, it is important to understand mechanisms of GPCR signaling in order to design selective and potent drug molecules. This chapter focuses on recent advances in computational studies of the GPCR-G protein interactions using bioinformatics, protein-protein docking and molecular dynamics simulation approaches.
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Affiliation(s)
- Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, KS, United States.
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28
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Mackenzie AE, Quon T, Lin LC, Hauser AS, Jenkins L, Inoue A, Tobin AB, Gloriam DE, Hudson BD, Milligan G. Receptor selectivity between the G proteins Gα 12 and Gα 13 is defined by a single leucine-to-isoleucine variation. FASEB J 2019; 33:5005-5017. [PMID: 30601679 PMCID: PMC6436656 DOI: 10.1096/fj.201801956r] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite recent advances in structural definition of GPCR-G protein complexes, the basis of receptor selectivity between G proteins remains unclear. The Gα12 and Gα13 subtypes together form the least studied group of heterotrimeric G proteins. G protein-coupled receptor 35 (GPR35) has been suggested to couple efficiently to Gα13 but weakly to Gα12. Using combinations of cells genome-edited to not express G proteins and bioluminescence resonance energy transfer-based sensors, we confirmed marked selectivity of GPR35 for Gα13. Incorporating Gα12/Gα13 chimeras and individual residue swap mutations into these sensors defined that selectivity between Gα13 and Gα12 was imbued largely by a single leucine-to-isoleucine variation at position G.H5.23. Indeed, leucine could not be substituted by other amino acids in Gα13 without almost complete loss of GPR35 coupling. The critical importance of leucine at G.H5.23 for GPR35-G protein interaction was further demonstrated by introduction of this leucine into Gαq, resulting in the gain of coupling to GPR35. These studies demonstrate that Gα13 is markedly the most effective G protein for interaction with GPR35 and that selection between Gα13 and Gα12 is dictated largely by a single conservative amino acid variation.-Mackenzie, A. E., Quon, T., Lin, L.-C., Hauser, A. S., Jenkins, L., Inoue, A., Tobin, A. B., Gloriam, D. E., Hudson, B. D., Milligan, G. Receptor selectivity between the G proteins Gα12 and Gα13 is defined by a single leucine-to-isoleucine variation.
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Affiliation(s)
- Amanda E Mackenzie
- Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Tezz Quon
- Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Li-Chiung Lin
- Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Alexander S Hauser
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark; and
| | - Laura Jenkins
- Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Andrew B Tobin
- Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark; and
| | - Brian D Hudson
- Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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29
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Gao Y, Erickson JW, Cerione RA, Ramachandran S. Reconstitution of the Rhodopsin-Transducin Complex into Lipid Nanodiscs. Methods Mol Biol 2019; 2009:317-324. [PMID: 31152414 DOI: 10.1007/978-1-4939-9532-5_24] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Transmembrane proteins, such as G protein-coupled receptors (GPCR), require solubilization in detergents prior to purification. The recent development of novel detergents has allowed for the stabilization of GPCRs, which typically have a high degree of structural flexibility and are otherwise subject to denaturation. However, the detergent micelle environment is still very different from the native lipid membrane and the activity of GPCRs can be profoundly affected by interactions with annular lipid molecules. Moreover, GPCRs are often palmitoylated at their intracellular side, and a lipid bilayer environment would allow for proper orientation of these lipid modifications. Therefore, a reconstituted lipid bilayer environment would best mimic the physiological receptor microenvironment for biophysical studies of GPCRs and nanodiscs provide a methodology to address this aim. Nanodiscs are lipid bilayer discs stabilized by amphipathic membrane scaffolding proteins (MSP) where detergent-solubilized transmembrane proteins can be incorporated into them through a self-assembly process. Here we present a method for reconstituting the purified detergent-solubilized rhodopsin-transducin complex, the GPCR-G protein complex in visual phototransduction, into nanodiscs. The resulting complex incorporated into lipid nanodiscs can be used in biophysical studies including small-angle X-ray scattering and electron microscopy. This method is applicable to integral membrane proteins that mediate protein lipidation, including the zDHHC-family of S-acyltransferases and membrane-bound O-acyltransferases.
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Affiliation(s)
- Yang Gao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Jon W Erickson
- Departments of Chemistry and Chemical Biology and Molecular Medicine, Cornell University, Ithaca, NY, USA
| | - Richard A Cerione
- Departments of Chemistry and Chemical Biology and Molecular Medicine, Cornell University, Ithaca, NY, USA
| | - Sekar Ramachandran
- Departments of Chemistry and Chemical Biology and Molecular Medicine, Cornell University, Ithaca, NY, USA.
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30
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Sokolov M, Yadav RP, Brooks C, Artemyev NO. Chaperones and retinal disorders. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:85-117. [PMID: 30635087 DOI: 10.1016/bs.apcsb.2018.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Defects in protein folding and trafficking are a common cause of photoreceptor degeneration, causing blindness. Photoreceptor cells present an unusual challenge to the protein folding and transport machinery due to the high rate of protein synthesis, trafficking and the renewal of the outer segment, a primary cilium that has been modified into a specialized light-sensing compartment. Phototransduction components, such as rhodopsin and cGMP-phosphodiesterase, and multimeric ciliary transport complexes, such as the BBSome, are hotspots for mutations that disrupt proteostasis and lead to the death of photoreceptors. In this chapter, we review recent studies that advance our understanding of the chaperone and transport machinery of phototransduction proteins.
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Affiliation(s)
- Maxim Sokolov
- Department of Ophthalmology, West Virginia University, Morgantown, WV, United States
| | - Ravi P Yadav
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Celine Brooks
- Department of Ophthalmology, West Virginia University, Morgantown, WV, United States
| | - Nikolai O Artemyev
- Department of Molecular Physiology and Biophysics, The University of Iowa Carver College of Medicine, Iowa City, IA, United States; Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA, United States.
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31
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Sun X, Singh S, Blumer KJ, Bowman GR. Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding. eLife 2018; 7:e38465. [PMID: 30289386 PMCID: PMC6224197 DOI: 10.7554/elife.38465] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 10/04/2018] [Indexed: 12/12/2022] Open
Abstract
Activation of heterotrimeric G proteins is a key step in many signaling cascades. However, a complete mechanism for this process, which requires allosteric communication between binding sites that are ~30 Å apart, remains elusive. We construct an atomically detailed model of G protein activation by combining three powerful computational methods: metadynamics, Markov state models (MSMs), and CARDS analysis of correlated motions. We uncover a mechanism that is consistent with a wide variety of structural and biochemical data. Surprisingly, the rate-limiting step for GDP release correlates with tilting rather than translation of the GPCR-binding helix 5. β-Strands 1 - 3 and helix 1 emerge as hubs in the allosteric network that links conformational changes in the GPCR-binding site to disordering of the distal nucleotide-binding site and consequent GDP release. Our approach and insights provide foundations for understanding disease-implicated G protein mutants, illuminating slow events in allosteric networks, and examining unbinding processes with slow off-rates.
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Affiliation(s)
- Xianqiang Sun
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineMissouriUnited States
| | - Sukrit Singh
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineMissouriUnited States
| | - Kendall J Blumer
- Department of Cell Biology and PhysiologyWashington University School of MedicineMissouriUnited States
| | - Gregory R Bowman
- Department of Biochemistry and Molecular BiophysicsWashington University School of MedicineMissouriUnited States
- Center for Biological Systems EngineeringWashington University School of MedicineMissouriUnited States
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Emmerstorfer-Augustin A, Augustin CM, Shams S, Thorner J. Tracking yeast pheromone receptor Ste2 endocytosis using fluorogen-activating protein tagging. Mol Biol Cell 2018; 29:2720-2736. [PMID: 30207829 PMCID: PMC6249837 DOI: 10.1091/mbc.e18-07-0424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To observe internalization of the yeast pheromone receptor Ste2 by fluorescence microscopy in live cells in real time, we visualized only those molecules present at the cell surface at the time of agonist engagement (rather than the total cellular pool) by tagging this receptor at its N-terminus with an exocellular fluorogen-activating protein (FAP). A FAP is a single-chain antibody engineered to bind tightly a nonfluorescent, cell-impermeable dye (fluorogen), thereby generating a fluorescent complex. The utility of FAP tagging to study trafficking of integral membrane proteins in yeast, which possesses a cell wall, had not been examined previously. A diverse set of signal peptides and propeptide sequences were explored to maximize expression. Maintenance of the optimal FAP-Ste2 chimera intact required deletion of two, paralogous, glycosylphosphatidylinositol (GPI)-anchored extracellular aspartyl proteases (Yps1 and Mkc7). FAP-Ste2 exhibited a much brighter and distinct plasma membrane signal than Ste2-GFP or Ste2-mCherry yet behaved quite similarly. Using FAP-Ste2, new information was obtained about the mechanism of its internalization, including novel insights about the roles of the cargo-selective endocytic adaptors Ldb19/Art1, Rod1/Art4, and Rog3/Art7.
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Affiliation(s)
- Anita Emmerstorfer-Augustin
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Christoph M Augustin
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Shadi Shams
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
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Lobysheva E, Taylor CM, Marshall GR, Kisselev OG. Tauroursodeoxycholic acid binds to the G-protein site on light activated rhodopsin. Exp Eye Res 2018; 170:51-57. [PMID: 29454859 PMCID: PMC5983371 DOI: 10.1016/j.exer.2018.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 12/18/2022]
Abstract
The heterotrimeric G-protein binding site on G-protein coupled receptors remains relatively unexplored regarding its potential as a new target of therapeutic intervention or as a secondary site of action by the existing drugs. Tauroursodeoxycholic acid bears structural resemblance to several compounds that were previously identified to specifically bind to the light-activated form of the visual receptor rhodopsin and to inhibit its activation of transducin. We show that TUDCA stabilizes the active form of rhodopsin, metarhodopsin II, and does not display the detergent-like effects of common amphiphilic compounds that share the cholesterol scaffold structure, such as deoxycholic acid. Computer docking of TUDCA to the model of light-activated rhodopsin revealed that it interacts using similar mode of binding to the C-terminal domain of transducin alpha subunit. The ring regions of TUDCA made hydrophobic contacts with loop 3 region of rhodopsin, while the tail of TUDCA is exposed to solvent. The results show that TUDCA interacts specifically with rhodopsin, which may contribute to its wide-ranging effects on retina physiology and as a potential therapeutic compound for retina degenerative diseases.
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Affiliation(s)
- E Lobysheva
- Department of Ophthalmology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - C M Taylor
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - G R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - O G Kisselev
- Department of Ophthalmology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA.
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Iglesias J, Saen‐oon S, Soliva R, Guallar V. Computational structure‐based drug design: Predicting target flexibility. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1367] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | | | | | - Victor Guallar
- Life Science DepartmentBarcelonaSpain
- ICREA, Passeig Lluís Companys 23BarcelonaSpain
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35
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Wild CT, Miszkiel JM, Wold EA, Soto CA, Ding C, Hartley RM, White MA, Anastasio NC, Cunningham KA, Zhou J. Design, Synthesis, and Characterization of 4-Undecylpiperidine-2-carboxamides as Positive Allosteric Modulators of the Serotonin (5-HT) 5-HT 2C Receptor. J Med Chem 2018; 62:288-305. [PMID: 29620897 DOI: 10.1021/acs.jmedchem.8b00401] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
An impaired signaling capacity of the serotonin (5-HT) 5-HT2C receptor (5-HT2CR) has been implicated in the neurobehavioral processes that promote relapse vulnerability in cocaine use disorder (CUD). Restoration of the diminished 5-HT2CR signaling through positive allosteric modulation presents a novel therapeutic approach. Several new molecules with the 4-alkylpiperidine-2-carboxamide scaffold were designed, synthesized, and pharmacologically evaluated, leading to the discovery of selective 5-HT2CR positive allosteric modulators (PAMs). Compound 16 (CYD-1-79) potentiated 5-HT-evoked intracellular calcium release in cells stably expressing the human 5-HT2CR but not the 5-HT2AR cells. A topographically distinct allosteric site was identified based on the newly solved 5-HT2CR structure. Compound 16 modulated 5-HT2CR-mediated spontaneous ambulation, partially substituted for the training dose of the 5-HT2CR agonist WAY163909, synergized with a low dose of WAY163909 to substitute fully for the stimulus effects of WAY163909, and attenuated relapse vulnerability as assessed in a rodent self-administration model, indicating its therapeutic promise for CUD.
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36
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Gao N, Liang T, Yuan Y, Xiao X, Zhao Y, Guo Y, Li M, Pu X. Exploring the mechanism of F282L mutation-caused constitutive activity of GPCR by a computational study. Phys Chem Chem Phys 2018; 18:29412-29422. [PMID: 27735961 DOI: 10.1039/c6cp03710k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
G-protein-coupled receptors (GPCRs) are important drug targets and generally activated by ligands. However, some experiments found that GPCRs also give rise to constitutive activity through some mutations (viz., CAM), which are usually associated with different kinds of diseases. However, the mechanisms of CAMs and their roles in interactions with drug-ligands are unclear in experiments. Herein, we used microsecond molecular dynamics simulations to study the effect of one important F282L mutation on β2AR in order to address the questions above. With the aid of principle component and correlation analysis, our results revealed that the F282L mutation could increase the instability of the overall structure, increase the dramatic fluctuations of NPxxY and extracellular loops, and decrease restraint of the helices through weakening interhelical H-bonding and correlations between residues, which could partly contribute to the constitutive activity reported by the experiments. The observations from the protein structure network (PSN) analysis indicate that the mutant exhibits less information flow than the wild β2AR and weakens the role of TM5 and TM6 in the signal transmission, but it enhances the impact of TM3 on the orthosteric pathway and TM4 on the allosteric one. In addition, the results from the virtual screening reveal that the mutant prefers to select agonists rather than antagonists, similar to the active state but opposite of the inactive state, further confirming that the F282L mutation advances the activation of β2AR. Our observations provide valuable information for understanding the mechanism of the mutation-caused constitutive activity of GPCR and related drug-design.
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Affiliation(s)
- Nan Gao
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Tao Liang
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu 610041, P. R. China
| | - Xiuchan Xiao
- Department of Architecture and Environmental Engineering, Chengdu Technological University, Chengdu, Sichuan 611730, China
| | - Yihuan Zhao
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Yanzhi Guo
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Menglong Li
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Xuemei Pu
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
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37
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Peng Y, McCorvy JD, Harpsøe K, Lansu K, Yuan S, Popov P, Qu L, Pu M, Che T, Nikolajsen LF, Huang XP, Wu Y, Shen L, Bjørn-Yoshimoto WE, Ding K, Wacker D, Han GW, Cheng J, Katritch V, Jensen AA, Hanson MA, Zhao S, Gloriam DE, Roth BL, Stevens RC, Liu ZJ. 5-HT 2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology. Cell 2018; 172:719-730.e14. [PMID: 29398112 DOI: 10.1016/j.cell.2018.01.001] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/25/2017] [Accepted: 01/03/2018] [Indexed: 02/02/2023]
Abstract
Drugs frequently require interactions with multiple targets-via a process known as polypharmacology-to achieve their therapeutic actions. Currently, drugs targeting several serotonin receptors, including the 5-HT2C receptor, are useful for treating obesity, drug abuse, and schizophrenia. The competing challenges of developing selective 5-HT2C receptor ligands or creating drugs with a defined polypharmacological profile, especially aimed at G protein-coupled receptors (GPCRs), remain extremely difficult. Here, we solved two structures of the 5-HT2C receptor in complex with the highly promiscuous agonist ergotamine and the 5-HT2A-C receptor-selective inverse agonist ritanserin at resolutions of 3.0 Å and 2.7 Å, respectively. We analyzed their respective binding poses to provide mechanistic insights into their receptor recognition and opposing pharmacological actions. This study investigates the structural basis of polypharmacology at canonical GPCRs and illustrates how understanding characteristic patterns of ligand-receptor interaction and activation may ultimately facilitate drug design at multiple GPCRs.
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Affiliation(s)
- Yao Peng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - John D McCorvy
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Katherine Lansu
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Shuguang Yuan
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH B3 495 (Bâtiment CH) Station 6, Lausanne 1015, Switzerland
| | - Petr Popov
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Lu Qu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengchen Pu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Tao Che
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Louise F Nikolajsen
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Ling Shen
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Walden E Bjørn-Yoshimoto
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Kang Ding
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Daniel Wacker
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gye Won Han
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Vsevolod Katritch
- Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | | | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Raymond C Stevens
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center, University of Southern California, Los Angeles, CA 90089, USA; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - Zhi-Jie Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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38
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Abstract
G protein-coupled receptors (GPCRs) are critical regulators of human physiology and make up the largest single class of therapeutic drug targets. Although GPCRs regulate highly diverse physiology, they share a common signaling mechanism whereby extracellular stimuli induce conformational changes in the receptor that enable activation of heterotrimeric G proteins and other intracellular effectors. Advances in GPCR structural biology have made it possible to examine ligand-induced GPCR activation at an unprecedented level of detail. Here, we review the structural basis for family A GPCR activation, with a focus on GPCRs for which structures are available in both active or active-like states and inactive states. Crystallographic and other biophysical data show how chemically diverse ligands stabilize highly conserved conformational changes on the intracellular side of the receptors, allowing many different extracellular stimuli to utilize shared downstream signaling molecules. Finally, we discuss the remaining challenges in understanding GPCR activation and signaling and highlight new technologies that may allow unanswered questions to be resolved.
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Affiliation(s)
- Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco , San Francisco, California 94158, United States
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States
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39
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Prosser RS, Ye L, Pandey A, Orazietti A. Activation processes in ligand-activated G protein-coupled receptors: A case study of the adenosine A 2A receptor. Bioessays 2017; 39. [PMID: 28787091 DOI: 10.1002/bies.201700072] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here we review concepts related to an ensemble description of G-protein-coupled receptors (GPCRs). The ensemble is characterized by both inactive and active states, whose equilibrium populations and exchange rates depend sensitively on ligand, environment, and allosteric factors. This review focuses on the adenosine A2 receptor (A2A R), a prototypical class A GPCR. 19 F Nuclear Magnetic Resonance (NMR) studies show that apo A2A R is characterized by a broad ensemble of conformers, spanning inactive to active states, and resembling states defined earlier for rhodopsin. In keeping with ideas associated with a conformational selection mechanism, addition of agonist serves to allosterically restrict the overall degrees of freedom at the G protein binding interface and bias both states and functional dynamics to facilitate G protein binding and subsequent activation. While the ligand does not necessarily "induce" activation, it does bias sampling of states, increase the cooperativity of the activation process and thus, the lifetimes of functional activation intermediates, while restricting conformational dynamics to that needed for activation.
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Affiliation(s)
- R Scott Prosser
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Libin Ye
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON, Canada
| | - Aditya Pandey
- Department of Chemistry, University of Toronto, UTM, Mississauga, ON, Canada
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40
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Budday D, Fonseca R, Leyendecker S, van den Bedem H. Frustration-guided motion planning reveals conformational transitions in proteins. Proteins 2017; 85:1795-1807. [DOI: 10.1002/prot.25333] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 05/19/2017] [Accepted: 06/07/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Dominik Budday
- Chair of Applied Dynamics, University of Erlangen-Nuremberg; Erlangen Germany
| | - Rasmus Fonseca
- Department of Molecular and Cellular Physiology; Stanford University; California Menlo Park
- Biosciences Division; SLAC National Accelerator Laboratory, Stanford University; California Menlo Park
| | - Sigrid Leyendecker
- Chair of Applied Dynamics, University of Erlangen-Nuremberg; Erlangen Germany
| | - Henry van den Bedem
- Biosciences Division; SLAC National Accelerator Laboratory, Stanford University; California Menlo Park
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41
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Andhirka SK, Vignesh R, Aradhyam GK. The nucleotide-free state of heterotrimeric G proteins α-subunit adopts a highly stable conformation. FEBS J 2017. [PMID: 28627018 DOI: 10.1111/febs.14143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Deciphering the mechanism of activation of heterotrimeric G proteins by their cognate receptors continues to be an intriguing area of research. The recently solved crystal structure of the ternary complex captured the receptor-bound α-subunit in an open conformation, without bound nucleotide has improved our understanding of the activation process. Despite these advancements, the mechanism by which the receptor causes GDP release from the α-subunit remains elusive. To elucidate the mechanism of activation, we studied guanine nucleotide-induced structural stability of the α-subunit (in response to thermal/chaotrope-mediated stress). Inherent stabilities of the inactive (GDP-bound) and active (GTP-bound) forms contribute antagonistically to the difference in conformational stability whereas the GDP-bound protein is able to switch to a stable intermediate state, GTP-bound protein loses this ability. Partial perturbation of the protein fold reveals the underlying influence of the bound nucleotide providing an insight into the mechanism of activation. An extra stable, pretransition intermediate, 'empty pocket' state (conformationally active-state like) in the unfolding pathway of GDP-bound protein mimics a gating system - the activation process having to overcome this stable intermediate state. We demonstrate that a relatively more complex conformational fold of the GDP-bound protein is at the core of the gating system. We report capturing this threshold, 'metastable empty pocket' conformation (the gate) of α-subunit of G protein and hypothesize that the receptor activates the G protein by enabling it to achieve this structure through mild structural perturbation.
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Affiliation(s)
- Sai Krishna Andhirka
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Ravichandran Vignesh
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - Gopala Krishna Aradhyam
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
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42
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Ponzoni L, Rossetti G, Maggi L, Giorgetti A, Carloni P, Micheletti C. Unifying view of mechanical and functional hotspots across class A GPCRs. PLoS Comput Biol 2017; 13:e1005381. [PMID: 28158180 PMCID: PMC5315405 DOI: 10.1371/journal.pcbi.1005381] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 02/17/2017] [Accepted: 01/25/2017] [Indexed: 01/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest superfamily of signaling proteins. Their activation process is accompanied by conformational changes that have not yet been fully uncovered. Here, we carry out a novel comparative analysis of internal structural fluctuations across a variety of receptors from class A GPCRs, which currently has the richest structural coverage. We infer the local mechanical couplings underpinning the receptors’ functional dynamics and finally identify those amino acids whose virtual deletion causes a significant softening of the mechanical network. The relevance of these amino acids is demonstrated by their overlap with those known to be crucial for GPCR function, based on static structural criteria. The differences with the latter set allow us to identify those sites whose functional role is more clearly detected by considering dynamical and mechanical properties. Of these sites with a genuine mechanical/dynamical character, the top ranking is amino acid 7x52, a previously unexplored, and experimentally verifiable key site for GPCR conformational response to ligand binding. The biological functionality of several receptors and enzymes depends on their capability to sustain large-scale structural fluctuations and adopt different conformational states in response to ligand binding. This is the case for G protein-coupled receptors (GPCRs), the largest superfamily of signaling proteins in mammals and a primary pharmaceutical target. To better understand the functional dynamics of GPCRs, we have analysed the inter-residue distance variations across the available structures for several receptors of the rhodopsin-like family (class A). We first reconstructed the network of mechanical, rigid-like couplings between nearby amino acids and then identified those acting as dynamical/mechanical hubs. These were the sites whose virtual removal led to a significant softening of the overall mechanical network. After validating the biological relevance of these sites by comparison against known key functional sites, we singled out those regions which emerge as prominent mechanical hubs and yet have an otherwise still unknown functional role. The most relevant of such novel putative functional sites, which could be probed by mutagenesis experiments, is at interface of two transmembrane helices and we expect it to be crucial for assisting GPCRs conformational response to agonist binding.
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Affiliation(s)
| | - Giulia Rossetti
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
- JSC: Division Computational Science – Simulation Laboratory Biology – Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich, Jülich, Germany
- JARA-HPC, Jülich, Germany
- Department of Oncology, Hematology and Stem Cell Transplantation, University Hospital Aachen, RWTH Aachen University, Aachen, Germany
- * E-mail: (LP); (GR)
| | - Luca Maggi
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
| | - Alejandro Giorgetti
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Paolo Carloni
- IAS-5/INM-9: Computational Biomedicine – Institute for Advanced Simulation (IAS) / Institute of Neuroscience and Medicine (INM), Forschungszentrum Jülich, Jülich, Germany
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43
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Ganesan A, Coote ML, Barakat K. Molecular dynamics-driven drug discovery: leaping forward with confidence. Drug Discov Today 2017; 22:249-269. [DOI: 10.1016/j.drudis.2016.11.001] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/22/2016] [Accepted: 11/01/2016] [Indexed: 12/11/2022]
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44
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Duc NM, Kim HR, Chung KY. Recent Progress in Understanding the Conformational Mechanism of Heterotrimeric G Protein Activation. Biomol Ther (Seoul) 2017; 25:4-11. [PMID: 28035078 PMCID: PMC5207459 DOI: 10.4062/biomolther.2016.169] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/26/2016] [Accepted: 09/01/2016] [Indexed: 12/05/2022] Open
Abstract
Heterotrimeric G proteins are key intracellular coordinators that receive signals from cells through activation of cognate G protein-coupled receptors (GPCRs). The details of their atomic interactions and structural mechanisms have been described by many biochemical and biophysical studies. Specifically, a framework for understanding conformational changes in the receptor upon ligand binding and associated G protein activation was provided by description of the crystal structure of the β2-adrenoceptor-Gs complex in 2011. This review focused on recent findings in the conformational dynamics of G proteins and GPCRs during activation processes.
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Affiliation(s)
- Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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45
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Affiliation(s)
- Naomi R. Latorraca
- Department of Computer Science, ‡Biophysics Program, §Department of Molecular
and Cellular
Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - A. J. Venkatakrishnan
- Department of Computer Science, ‡Biophysics Program, §Department of Molecular
and Cellular
Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ron O. Dror
- Department of Computer Science, ‡Biophysics Program, §Department of Molecular
and Cellular
Physiology, and ∥Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
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Drugging specific conformational states of GPCRs: challenges and opportunities for computational chemistry. Drug Discov Today 2016; 21:625-31. [DOI: 10.1016/j.drudis.2016.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/04/2016] [Accepted: 01/19/2016] [Indexed: 01/14/2023]
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Thomas T, Fang Y, Yuriev E, Chalmers DK. Ligand Binding Pathways of Clozapine and Haloperidol in the Dopamine D2 and D3 Receptors. J Chem Inf Model 2016; 56:308-21. [PMID: 26690887 DOI: 10.1021/acs.jcim.5b00457] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The binding of a small molecule ligand to its protein target is most often characterized by binding affinity and is typically viewed as an on/off switch. The more complex reality is that binding involves the ligand passing through a series of intermediate states between the solution phase and the fully bound pose. We have performed a set of 29 unbiased molecular dynamics simulations to model the binding pathways of the dopamine receptor antagonists clozapine and haloperidol binding to the D2 and D3 dopamine receptors. Through these simulations we have captured the binding pathways of clozapine and haloperidol from the extracellular vestibule to the orthosteric binding site and thereby, we also predict the bound pose of each ligand. These are the first long time scale simulations of haloperidol or clozapine binding to dopamine receptors. From these simulations, we have identified several important stages in the binding pathway, including the involvement of Tyr7.35 in a "handover" mechanism that transfers the ligand between the extracellular vestibule and Asp3.32. We have also performed interaction and cluster analyses to determine differences in binding pathways between the D2 and D3 receptors and identified metastable states that may be of use in drug design.
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Affiliation(s)
- Trayder Thomas
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Pde, Parkville, Victoria 3052, Australia
| | - Yu Fang
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Pde, Parkville, Victoria 3052, Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Pde, Parkville, Victoria 3052, Australia
| | - David K Chalmers
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , 381 Royal Pde, Parkville, Victoria 3052, Australia
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Nicole P, Couvineau P, Jamin N, Voisin T, Couvineau A. Crucial role of the orexin-B C-terminus in the induction of OX1 receptor-mediated apoptosis: analysis by alanine scanning, molecular modelling and site-directed mutagenesis. Br J Pharmacol 2015; 172:5211-23. [PMID: 26282891 PMCID: PMC4687804 DOI: 10.1111/bph.13287] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 06/12/2015] [Accepted: 08/11/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND AND PURPOSE Orexins (A and B) are hypothalamic peptides that interact with OX1 and OX2 receptors and are involved in the sleep/wake cycle. We previously demonstrated that OX1 receptors are highly expressed in colon cancer tumours and colonic cancer cell lines where orexins induce apoptosis and inhibit tumour growth in preclinical animal models. The present study explored the structure-function relationships of orexin-B and OX1 receptors. EXPERIMENTAL APPROACH The contribution of all orexin-B residues in orexin-B-induced apoptosis was investigated by alanine scanning. To determine which OX1 receptor domains are involved in orexin-B binding and apoptosis, a 3D model of OX1 receptor docked to the orexin-B C-terminus (AA-20-28) was developed. Substitution of residues present in OX1 receptor transmembrane (TM) domains by site-directed mutagenesis was performed. KEY RESULTS Alanine substitution of orexin-B residues, L(11) , L(15) , A(22) , G(24) , I(25) , L(26) and M(28) , altered orexin-B's binding affinity. Substitution of these residues and of the Q(16) , A(17) , S(18) , N(20) and T(27) residues inhibited apoptosis in CHO-S-OX1 receptor cells. The K(120) , P(123) , Y(124) , N(318) , K(321) , F(340) , T(341) , H(344) and W(345) residues localized in TM2, TM3, TM6 and TM7 of OX1 receptors were shown to play a role in orexin-B recognition and orexin-B/OX1 receptor-induced apoptosis. CONCLUSIONS AND IMPLICATIONS The C-terminus of orexin-B (i) plays an important role in its pro-apoptotic effect; and (ii) interacts with some residues localized in the OX1 receptor TM. This study defines the structure-function relationship for orexin-B recognition by human OX1 receptors and orexin-B/OX1 receptor-induced apoptosis, an important step for the future development of new agonist molecules.
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Affiliation(s)
- Pascal Nicole
- Faculté de Médecine Site Bichat, INSERM U1149/Inflammation Research Center (CRI), Paris‐Diderot UniversityDHU UNITY16, rue H. Huchard75018ParisFrance
| | - Pierre Couvineau
- Faculté de Médecine Site Bichat, INSERM U1149/Inflammation Research Center (CRI), Paris‐Diderot UniversityDHU UNITY16, rue H. Huchard75018ParisFrance
| | - Nadege Jamin
- Laboratoire des Protéines et Systèmes MembranairesCEA, iBiTecS, I2BCF‐91191Gif‐sur‐Yvette CedexFrance
| | - Thierry Voisin
- Faculté de Médecine Site Bichat, INSERM U1149/Inflammation Research Center (CRI), Paris‐Diderot UniversityDHU UNITY16, rue H. Huchard75018ParisFrance
| | - Alain Couvineau
- Faculté de Médecine Site Bichat, INSERM U1149/Inflammation Research Center (CRI), Paris‐Diderot UniversityDHU UNITY16, rue H. Huchard75018ParisFrance
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Kakarala KK, Jamil K. Biased signaling: potential agonist and antagonist of PAR2. J Biomol Struct Dyn 2015; 34:1363-76. [DOI: 10.1080/07391102.2015.1079556] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Flock T, Ravarani CNJ, Sun D, Venkatakrishnan AJ, Kayikci M, Tate CG, Veprintsev DB, Babu MM. Universal allosteric mechanism for Gα activation by GPCRs. Nature 2015; 524:173-179. [PMID: 26147082 PMCID: PMC4866443 DOI: 10.1038/nature14663] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 06/16/2015] [Indexed: 12/25/2022]
Abstract
G protein-coupled receptors (GPCRs) allosterically activate heterotrimeric G proteins and trigger GDP release. Given that there are ∼800 human GPCRs and 16 different Gα genes, this raises the question of whether a universal allosteric mechanism governs Gα activation. Here we show that different GPCRs interact with and activate Gα proteins through a highly conserved mechanism. Comparison of Gα with the small G protein Ras reveals how the evolution of short segments that undergo disorder-to-order transitions can decouple regions important for allosteric activation from receptor binding specificity. This might explain how the GPCR-Gα system diversified rapidly, while conserving the allosteric activation mechanism.
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Affiliation(s)
- Tilman Flock
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | - Dawei Sun
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Melis Kayikci
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Dmitry B. Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - M. Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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