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Rodríguez-Frade JM, González-Granado LI, Santiago CA, Mellado M. The complex nature of CXCR4 mutations in WHIM syndrome. Front Immunol 2024; 15:1406532. [PMID: 39035006 PMCID: PMC11257845 DOI: 10.3389/fimmu.2024.1406532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024] Open
Abstract
Heterozygous autosomal dominant mutations in the CXCR4 gene cause WHIM syndrome, a severe combined immunodeficiency disorder. The mutations primarily affect the C-terminal region of the CXCR4 chemokine receptor, specifically several potential phosphorylation sites critical for agonist (CXCL12)-mediated receptor internalization and desensitization. Mutant receptors have a prolonged residence time on the cell surface, leading to hyperactive signaling that is responsible for some of the symptoms of WHIM syndrome. Recent studies have shown that the situation is more complex than originally thought, as mutant WHIM receptors and CXCR4 exhibit different dynamics at the cell membrane, which also influences their respective cellular functions. This review examines the functional mechanisms of CXCR4 and the impact of WHIM mutations in both physiological and pathological conditions.
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Affiliation(s)
- José Miguel Rodríguez-Frade
- Department of Immunology and Oncology, Chemokine Signaling Group, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - Luis Ignacio González-Granado
- Department of Pediatrics, 12 de Octubre Health Research Institute (imas12), Madrid, Spain
- Department of Public Health School of Medicine, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - César A. Santiago
- X-ray Crystallography Unit, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mario Mellado
- Department of Immunology and Oncology, Chemokine Signaling Group, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
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2
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Wang X, Neale C, Kim SK, Goddard WA, Ye L. Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery. Nat Commun 2023; 14:1325. [PMID: 36899002 PMCID: PMC10006191 DOI: 10.1038/s41467-023-36971-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
Understanding the roles of intermediate states in signaling is pivotal to unraveling the activation processes of G protein-coupled receptors (GPCRs). However, the field is still struggling to define these conformational states with sufficient resolution to study their individual functions. Here, we demonstrate the feasibility of enriching the populations of discrete states via conformation-biased mutants. These mutants adopt distinct distributions among five states that lie along the activation pathway of adenosine A2A receptor (A2AR), a class A GPCR. Our study reveals a structurally conserved cation-π lock between transmembrane helix VI (TM6) and Helix8 that regulates cytoplasmic cavity opening as a "gatekeeper" for G protein penetration. A GPCR activation process based on the well-discerned conformational states is thus proposed, allosterically micro-modulated by the cation-π lock and a previously well-defined ionic interaction between TM3 and TM6. Intermediate-state-trapped mutants will also provide useful information in relation to receptor-G protein signal transduction.
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Affiliation(s)
- Xudong Wang
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, 91125, USA
| | - William A Goddard
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, 91125, USA
| | - Libin Ye
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.
- H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA.
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3
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Ladefoged LK, Koch R, Biggin PC, Schiøtt B. Binding and Activation of Serotonergic G-Protein Coupled Receptors by the Multimodal Antidepressant Vortioxetine. ACS Chem Neurosci 2022; 13:1129-1142. [PMID: 35348335 DOI: 10.1021/acschemneuro.1c00029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are important pharmacological targets. Despite substantial progress, important questions still remain concerning the details of activation: how can a ligand act as an agonist in one receptor but as an antagonist in a homologous receptor, and how can agonists activate a receptor despite lacking polar functional groups able to interact with helix 5 as is the case for the related adrenergic receptors? Studying vortioxetine (VXT), an important multimodal antidepressant drug, may elucidate both questions. Herein, we present a thorough in silico analysis of VXT binding to 5-HT1A, 5-HT1B, and 5-HT7 receptors and compare it with available experimental data. We are able to rationalize the differential mode of action of VXT at different receptors, but also, in the case of the 5-HT1A receptor, we observe the initial steps of activation that inform about an activation mechanism that does not involve polar interaction with helix 5. The results extend our current understanding of agonist and antagonist action at aminergic GPCRs.
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Affiliation(s)
- Lucy Kate Ladefoged
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Rebekka Koch
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
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4
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Liu T, Ji RL, Tao YX. Naturally occurring mutations in G protein-coupled receptors associated with obesity and type 2 diabetes mellitus. Pharmacol Ther 2021; 234:108044. [PMID: 34822948 DOI: 10.1016/j.pharmthera.2021.108044] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 12/12/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of membrane receptors involved in the regulation of almost all known physiological processes. Dysfunctions of GPCR-mediated signaling have been shown to cause various diseases. The prevalence of obesity and type 2 diabetes mellitus (T2DM), two strongly associated disorders, is increasing worldwide, with tremendous economical and health burden. New safer and more efficacious drugs are required for successful weight reduction and T2DM treatment. Multiple GPCRs are involved in the regulation of energy and glucose homeostasis. Mutations in these GPCRs contribute to the development and progression of obesity and T2DM. Therefore, these receptors can be therapeutic targets for obesity and T2DM. Indeed some of these receptors, such as melanocortin-4 receptor and glucagon-like peptide 1 receptor, have provided important new drugs for treating obesity and T2DM. This review will focus on the naturally occurring mutations of several GPCRs associated with obesity and T2DM, especially incorporating recent large genomic data and insights from structure-function studies, providing leads for future investigations.
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Affiliation(s)
- Ting Liu
- Department of Anatomy, Physiology and Pharmacology, Auburn University College of Veterinary Medicine, Auburn, AL 36849, United States
| | - Ren-Lei Ji
- Department of Anatomy, Physiology and Pharmacology, Auburn University College of Veterinary Medicine, Auburn, AL 36849, United States
| | - Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, Auburn University College of Veterinary Medicine, Auburn, AL 36849, United States.
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5
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Ma X, Segura MA, Zarzycka B, Vischer HF, Leurs R. Analysis of Missense Variants in the Human Histamine Receptor Family Reveals Increased Constitutive Activity of E410 6.30×30K Variant in the Histamine H 1 Receptor. Int J Mol Sci 2021; 22:ijms22073702. [PMID: 33918180 PMCID: PMC8038156 DOI: 10.3390/ijms22073702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/19/2021] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
The Exome Aggregation Consortium has collected the protein-encoding DNA sequences of almost 61,000 unrelated humans. Analysis of this dataset for G protein-coupled receptor (GPCR) proteins (available at GPCRdb) revealed a total of 463 naturally occurring genetic missense variations in the histamine receptor family. In this research, we have analyzed the distribution of these missense variations in the four histamine receptor subtypes concerning structural segments and sites important for GPCR function. Four missense variants R1273.52×52H, R13934.57×57H, R4096.29×29H, and E4106.30×30K, were selected for the histamine H1 receptor (H1R) that were hypothesized to affect receptor activity by interfering with the interaction pattern of the highly conserved D(E)RY motif, the so-called ionic lock. The E4106.30×30K missense variant displays higher constitutive activity in G protein signaling as compared to wild-type H1R, whereas the opposite was observed for R1273.52×52H, R13934.57×57H, and R4096.29×29H. The E4106.30×30K missense variant displays a higher affinity for the endogenous agonist histamine than wild-type H1R, whereas antagonist affinity was not affected. These data support the hypothesis that the E4106.30×30K mutation shifts the equilibrium towards active conformations. The study of these selected missense variants gives additional insight into the structural basis of H1R activation and, moreover, highlights that missense variants can result in pharmacologically different behavior as compared to wild-type receptors and should consequently be considered in the drug discovery process.
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6
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Kline JM, Heusinkveld LE, Taranto E, Martin CB, Tomasi AG, Hsu IJ, Cho K, Khillan JS, Murphy PM, Pontejo SM. Structural and functional analysis of Ccr1l1, a Rodentia-restricted eosinophil-selective chemokine receptor homologue. J Biol Chem 2021; 296:100373. [PMID: 33548230 PMCID: PMC7949164 DOI: 10.1016/j.jbc.2021.100373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/26/2021] [Accepted: 02/01/2021] [Indexed: 11/25/2022] Open
Abstract
Mouse Ccr1l1 (Ccr1-like 1) encodes an orphan G-protein-coupled receptor (GPCR) with the highest homology to the inflammatory and highly promiscuous chemokine receptors Ccr1 and Ccr3 (70 and 50% amino acid identity, respectively). Ccr1l1 was first cloned in 1995, yet current knowledge of this putative chemokine receptor is limited to its gene organization and chromosomal localization. Here we report that Ccr1l1 is a Rodentia-specific gene selectively expressed in eosinophils. However, eosinophil phenotypes, development, and responsiveness to chemokines were all normal in naïve Ccr1l1 knockout mice. We demonstrate for the first time that recombinant Ccr1l1 is expressed on the plasma membrane of transfected cells and contains an extracellular N terminus and an intracellular C terminus, consistent with GPCR topology. Using receptor internalization, β-arrestin recruitment, calcium flux, and chemotaxis assays, we excluded all 37 available mouse chemokines, including Ccr1 ligands, and two viral chemokines as Ccr1l1 ligands, and demonstrated that mouse Ccr1, but not Ccr1l1, exhibits constitutive signaling activity. However, sequence analysis and structural modeling revealed that Ccr1l1 is well equipped to act as a classical signaling GPCR, with N-terminal sulfotyrosines as the only signaling and chemokine-binding determinant absent in Ccr1l1. Hereof, we show that a sulfatable N-terminal Ccr1 Y18 residue is essential for chemotaxis and calcium responses induced by Ccl3 and Ccl9/10, but substituting the corresponding Ccr1l1 F19 residue with tyrosine failed to confer responsiveness to Ccr1 ligands. Although Ccr1l1 remains an extreme outlier in the chemokine receptor family, our study supports that it might respond to unidentified mouse chemokine ligands in eosinophil-driven immune responses.
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Affiliation(s)
- Jaclyn M Kline
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Lauren E Heusinkveld
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Eleanor Taranto
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Clare B Martin
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alessandra G Tomasi
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Isabel J Hsu
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kyoungin Cho
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jaspal S Khillan
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Philip M Murphy
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Sergio M Pontejo
- Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
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7
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Yang LK, Tao YX. Alanine Scanning Mutagenesis of the DRYxxI Motif and Intracellular Loop 2 of Human Melanocortin-4 Receptor. Int J Mol Sci 2020; 21:ijms21207611. [PMID: 33076233 PMCID: PMC7589821 DOI: 10.3390/ijms21207611] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/10/2020] [Accepted: 10/11/2020] [Indexed: 12/15/2022] Open
Abstract
The melanocortin-4 receptor (MC4R) is a member of the G-protein-coupled receptor (GPCR) superfamily, which has been extensively studied in obesity pathogenesis due to its critical role in regulating energy homeostasis. Both the Gs-cAMP and ERK1/2 cascades are known as important intracellular signaling pathways initiated by the MC4R. The DRYxxI motif at the end of transmembrane domain 3 and the intracellular loop 2 (ICL2) are thought to be crucial for receptor function in several GPCRs. To study the functions of this domain in MC4R, we performed alanine-scanning mutagenesis on seventeen residues. We showed that one residue was critical for receptor cell surface expression. Eight residues were important for ligand binding. Mutations of three residues impaired Gs-cAMP signaling without changing the binding properties. Investigation on constitutive activities of all the mutants in the cAMP pathway revealed that six residues were involved in constraining the receptor in inactive states and five residues were important for receptor activation in the absence of an agonist. In addition, mutations of four residues impaired the ligand-stimulated ERK1/2 signaling pathway without affecting the binding properties. We also showed that some mutants were biased to the Gs-cAMP or ERK1/2 signaling pathway. In summary, we demonstrated that the DRYxxI motif and ICL2 were important for MC4R function.
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8
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Wang J, Hua T, Liu ZJ. Structural features of activated GPCR signaling complexes. Curr Opin Struct Biol 2020; 63:82-89. [PMID: 32485565 DOI: 10.1016/j.sbi.2020.04.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 12/22/2022]
Abstract
G protein-coupled receptors (GPCRs) couple to diverse heterotrimeric G protein subtypes and then activate downstream signaling pathways in classical GPCR activation. It has also been found that GPCRs transduce signals through different regulatory proteins, such as arrestins. Recently, owing to the breakthroughs in cryo-electron macroscopy (Cryo-EM), numerous structures of GPCR-G protein or GPCR-arrestin complexes have been deciphered. In this review, we summarize most of reported GPCR signaling complex structures, with an emphasis on the structural features of rhodopsin-like GPCR activation and G protein-binding/arrestin-binding modes, to illustrate the activation and signaling mechanism of rhodopsin-like GPCRs.
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Affiliation(s)
- Jingjing Wang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tian Hua
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| | - Zhi-Jie Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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9
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Structural basis of ligand recognition and self-activation of orphan GPR52. Nature 2020; 579:152-157. [PMID: 32076264 DOI: 10.1038/s41586-020-2019-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/23/2020] [Indexed: 11/08/2022]
Abstract
GPR52 is a class-A orphan G-protein-coupled receptor that is highly expressed in the brain and represents a promising therapeutic target for the treatment of Huntington's disease and several psychiatric disorders1,2. Pathological malfunction of GPR52 signalling occurs primarily through the heterotrimeric Gs protein2, but it is unclear how GPR52 and Gs couple for signal transduction and whether a native ligand or other activating input is required. Here we present the high-resolution structures of human GPR52 in three states: a ligand-free state, a Gs-coupled self-activation state and a potential allosteric ligand-bound state. Together, our structures reveal that extracellular loop 2 occupies the orthosteric binding pocket and operates as a built-in agonist, conferring an intrinsically high level of basal activity to GPR523. A fully active state is achieved when Gs is coupled to GPR52 in the absence of an external agonist. The receptor also features a side pocket for ligand binding. These insights into the structure and function of GPR52 could improve our understanding of other self-activated GPCRs, enable the identification of endogenous and tool ligands, and guide drug discovery efforts that target GPR52.
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10
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Díaz Ó, Dalton JAR, Giraldo J. Revealing the Mechanism of Agonist-Mediated Cannabinoid Receptor 1 (CB1) Activation and Phospholipid-Mediated Allosteric Modulation. J Med Chem 2019; 62:5638-5654. [DOI: 10.1021/acs.jmedchem.9b00612] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Óscar Díaz
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| | - James A. R. Dalton
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
| | - Jesús Giraldo
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, 08193 Bellaterra, Spain
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11
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Ragnarsson L, Andersson Å, Thomas WG, Lewis RJ. Mutations in the NPxxY motif stabilize pharmacologically distinct conformational states of the α 1B- and β 2-adrenoceptors. Sci Signal 2019; 12:12/572/eaas9485. [PMID: 30862702 DOI: 10.1126/scisignal.aas9485] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
G protein-coupled receptors (GPCRs) convert extracellular stimuli to intracellular responses that regulate numerous physiological processes. Crystallographic and biophysical advances in GPCR structural analysis have aided investigations of structure-function relationships that clarify our understanding of these dynamic receptors, but the molecular mechanisms associated with activation and signaling for individual GPCRs may be more complex than was previously appreciated. Here, we investigated the proposed water-mediated, hydrogen-bonded activation switch between the conserved NPxxY motif on transmembrane helix 7 (TMH7) and a conserved tyrosine in TMH5, which contributes to α1B-adrenoceptor (α1B-AR) and β2-AR activation. Disrupting this bond by mutagenesis stabilized the α1B-AR and the β2-AR in inactive-state conformations, which displayed decreased agonist potency for stimulating downstream IP1 and cAMP signaling, respectively. Compared to that for wild-type receptors, agonist-mediated β-arrestin recruitment was substantially reduced or abolished for all α1B-AR and β2-AR inactive-state mutants. However, the inactive-state β2-ARs exhibited decreased agonist affinity, whereas the inactive-state α1B-ARs had enhanced agonist affinity. Conversely, antagonist affinity was unchanged for inactive-state conformations of both α1B-AR and β2-AR. Removing the influence of agonist affinity on agonist potency gave a measure of signaling efficacy, which was markedly decreased for the α1B-AR mutants but little altered for the β2-AR mutants. These findings highlight the pharmacological heterogeneity of inactive-state GPCR conformations, which may facilitate the rational design of drugs that target distinct conformational states of GPCRs.
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Affiliation(s)
- Lotten Ragnarsson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Åsa Andersson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Walter G Thomas
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Richard J Lewis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
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12
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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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13
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Martínez-Archundia M, Correa-Basurto J, Montaño S, Rosas-Trigueros JL. Studying the collective motions of the adenosine A2A receptor as a result of ligand binding using principal component analysis. J Biomol Struct Dyn 2019; 37:4685-4700. [DOI: 10.1080/07391102.2018.1564700] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Marlet Martínez-Archundia
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - José Correa-Basurto
- Laboratorio de Modelado Molecular y Bioinformática, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sarita Montaño
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacan, Sinaloa, Mexico
| | - Jorge L. Rosas-Trigueros
- Laboratorio Transdisciplinario de Investigación en Sistemas Evolutivos, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Cómputo, Instituto Politécnico Nacional, Mexico City, Mexico
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14
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García-Cuesta EM, Santiago CA, Vallejo-Díaz J, Juarranz Y, Rodríguez-Frade JM, Mellado M. The Role of the CXCL12/CXCR4/ACKR3 Axis in Autoimmune Diseases. Front Endocrinol (Lausanne) 2019; 10:585. [PMID: 31507535 PMCID: PMC6718456 DOI: 10.3389/fendo.2019.00585] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 08/09/2019] [Indexed: 12/19/2022] Open
Abstract
Chemokine receptors are members of the G protein-coupled receptor superfamily. These receptors are intimately involved in cell movement, and thus play a critical role in several physiological and pathological situations that require the precise regulation of cell positioning. CXCR4 is one of the most studied chemokine receptors and is involved in many functions beyond leukocyte recruitment. During embryogenesis, it plays essential roles in vascular development, hematopoiesis, cardiogenesis, and nervous system organization. It has been also implicated in tumor progression and autoimmune diseases and, together with CD4, is one of the co-receptors used by the HIV-1 virus to infect immune cells. In contrast to other chemokine receptors that are characterized by ligand promiscuity, CXCR4 has a unique ligand-stromal cell-derived factor-1 (SDF1, CXCL12). However, this ligand also binds ACKR3, an atypical chemokine receptor that modulates CXCR4 functions and is overexpressed in multiple cancer types. The CXCL12/CXCR4/ACKR3 axis constitutes a potential therapeutic target for a wide variety of inflammatory diseases, not only by interfering with cell migration but also by modulating immune responses. Thus far, only one antagonist directed against the ligand-binding site of CXCR4, AMD3100, has demonstrated clinical relevance. Here, we review the role of this ligand and its receptors in different autoimmune diseases.
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Affiliation(s)
- Eva M. García-Cuesta
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - César A. Santiago
- Macromolecular X-Ray Crystallography Unit, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - Jesús Vallejo-Díaz
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - Yasmina Juarranz
- Department Cell Biology, Research Institute Hospital 12 de Octubre (i+12), Complutense University of Madrid, Madrid, Spain
| | | | - Mario Mellado
- Department of Immunology and Oncology, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
- *Correspondence: Mario Mellado
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15
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Vass M, Podlewska S, de Esch IJP, Bojarski AJ, Leurs R, Kooistra AJ, de Graaf C. Aminergic GPCR-Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data. J Med Chem 2018; 62:3784-3839. [PMID: 30351004 DOI: 10.1021/acs.jmedchem.8b00836] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The aminergic family of G protein-coupled receptors (GPCRs) plays an important role in various diseases and represents a major drug discovery target class. Structure determination of all major aminergic subfamilies has enabled structure-based ligand design for these receptors. Site-directed mutagenesis data provides an invaluable complementary source of information for elucidating the structural determinants of binding of different ligand chemotypes. The current study provides a comparative analysis of 6692 mutation data points on 34 aminergic GPCR subtypes, covering the chemical space of 540 unique ligands from mutagenesis experiments and information from experimentally determined structures of 52 distinct aminergic receptor-ligand complexes. The integrated analysis enables detailed investigation of structural receptor-ligand interactions and assessment of the transferability of combined binding mode and mutation data across ligand chemotypes and receptor subtypes. An overview is provided of the possibilities and limitations of using mutation data to guide the design of novel aminergic receptor ligands.
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Affiliation(s)
- Márton Vass
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Sabina Podlewska
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Department of Drug Design and Pharmacology , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Sosei Heptares , Steinmetz Building, Granta Park, Great Abington , Cambridge CB21 6DG , U.K
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16
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Nazarko O, Kibrom A, Winkler J, Leon K, Stoveken H, Salzman G, Merdas K, Lu Y, Narkhede P, Tall G, Prömel S, Araç D. A Comprehensive Mutagenesis Screen of the Adhesion GPCR Latrophilin-1/ADGRL1. iScience 2018; 3:264-278. [PMID: 30428326 PMCID: PMC6137404 DOI: 10.1016/j.isci.2018.04.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/16/2018] [Accepted: 04/24/2018] [Indexed: 11/15/2022] Open
Abstract
Adhesion G-protein-coupled receptors (aGPCRs) play critical roles in diverse cellular processes in neurobiology, development, immunity, and numerous diseases. The lack of molecular understanding of their activation mechanisms, especially with regard to the transmembrane domains, hampers further studies to facilitate aGPCR-targeted drug development. Latrophilin-1/ADGRL1 is a model aGPCR that regulates synapse formation and embryogenesis, and its mutations are associated with cancer and attention-deficit/hyperactivity disorder. Here, we established functional assays to monitor latrophilin-1 function and showed the activation of latrophilin-1 by its endogenous agonist peptide. Via a comprehensive mutagenesis screen, we identified transmembrane domain residues essential for latrophilin-1 basal activity and for agonist peptide response. Strikingly, a cancer-associated mutation exhibited increased basal activity and failed to rescue the embryonic developmental phenotype in transgenic worms. These results provide a mechanistic foundation for future aGPCR-targeted drug design.
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Affiliation(s)
- Olha Nazarko
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Amanuel Kibrom
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Jana Winkler
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Katherine Leon
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Hannah Stoveken
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel Salzman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Katarzyna Merdas
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Yue Lu
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Pradnya Narkhede
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Gregory Tall
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - Simone Prömel
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, 04103 Leipzig, Germany
| | - Demet Araç
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, The University of Chicago, Chicago, IL 60637, USA.
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17
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Jończyk J, Malawska B, Bajda M. Hybrid approach to structure modeling of the histamine H3 receptor: Multi-level assessment as a tool for model verification. PLoS One 2017; 12:e0186108. [PMID: 28982153 PMCID: PMC5629032 DOI: 10.1371/journal.pone.0186108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/25/2017] [Indexed: 12/18/2022] Open
Abstract
The crucial role of G-protein coupled receptors and the significant achievements associated with a better understanding of the spatial structure of known receptors in this family encouraged us to undertake a study on the histamine H3 receptor, whose crystal structure is still unresolved. The latest literature data and availability of different software enabled us to build homology models of higher accuracy than previously published ones. The new models are expected to be closer to crystal structures; and therefore, they are much more helpful in the design of potential ligands. In this article, we describe the generation of homology models with the use of diverse tools and a hybrid assessment. Our study incorporates a hybrid assessment connecting knowledge-based scoring algorithms with a two-step ligand-based docking procedure. Knowledge-based scoring employs probability theory for global energy minimum determination based on information about native amino acid conformation from a dataset of experimentally determined protein structures. For a two-step docking procedure two programs were applied: GOLD was used in the first step and Glide in the second. Hybrid approaches offer advantages by combining various theoretical methods in one modeling algorithm. The biggest advantage of hybrid methods is their intrinsic ability to self-update and self-refine when additional structural data are acquired. Moreover, the diversity of computational methods and structural data used in hybrid approaches for structure prediction limit inaccuracies resulting from theoretical approximations or fuzziness of experimental data. The results of docking to the new H3 receptor model allowed us to analyze ligand-receptor interactions for reference compounds.
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Affiliation(s)
- Jakub Jończyk
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Barbara Malawska
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
| | - Marek Bajda
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Krakow, Poland
- * E-mail:
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18
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Chen IS, Furutani K, Kurachi Y. Structural determinants at the M2 muscarinic receptor modulate the RGS4-GIRK response to pilocarpine by impairment of the receptor voltage sensitivity. Sci Rep 2017; 7:6110. [PMID: 28733581 PMCID: PMC5522400 DOI: 10.1038/s41598-017-05128-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/24/2017] [Indexed: 12/23/2022] Open
Abstract
Membrane potential controls the response of the M2 muscarinic receptor to its ligands. Membrane hyperpolarization increases response to the full agonist acetylcholine (ACh) while decreasing response to the partial agonist pilocarpine. We previously have demonstrated that the regulator of G-protein signaling (RGS) 4 protein discriminates between the voltage-dependent responses of ACh and pilocarpine; however, the underlying mechanism remains unclear. Here we show that RGS4 is involved in the voltage-dependent behavior of the M2 muscarinic receptor-mediated signaling in response to pilocarpine. Additionally we revealed structural determinants on the M2 muscarinic receptor underlying the voltage-dependent response. By electrophysiological recording in Xenopus oocytes expressing M2 muscarinic receptor and G-protein-gated inwardly rectifying K+ channels, we quantified voltage-dependent desensitization of pilocarpine-induced current in the presence or absence of RGS4. Hyperpolarization-induced desensitization of the current required for RGS4, also depended on pilocarpine concentration. Mutations of charged residues in the aspartic acid-arginine-tyrosine motif of the M2 muscarinic receptor, but not intracellular loop 3, significantly impaired the voltage-dependence of RGS4 function. Thus, our results demonstrated that voltage-dependence of RGS4 modulation is derived from the M2 muscarinic receptor. These results provide novel insights into how membrane potential impacts G-protein signaling by modulating GPCR communication with downstream effectors.
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Affiliation(s)
- I-Shan Chen
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuharu Furutani
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan. .,Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Yoshihisa Kurachi
- Department of Pharmacology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan. .,Global Center for Medical Engineering and Informatics, Osaka University, Suita, Osaka, 565-0871, Japan.
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19
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Rovati GE, Capra V, Shaw VS, Malik RU, Sivaramakrishnan S, Neubig RR. The DRY motif and the four corners of the cubic ternary complex model. Cell Signal 2017; 35:16-23. [PMID: 28347873 DOI: 10.1016/j.cellsig.2017.03.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/24/2017] [Indexed: 12/14/2022]
Abstract
Recent structural data on GPCRs using a variety of spectroscopic approaches suggest that GPCRs adopt a dynamic conformational landscape, with ligands stabilizing subsets of these states to activate one or more downstream signaling effectors. A key outstanding question posed by this emerging dynamic structural model of GPCRs is what states, active, inactive, or intermediate are captured by the numerous crystal structures of GPCRs complexed with a variety of agonists, partial agonists, and antagonists. In the early nineties the discovery of inverse agonists and constitutive activity led to the idea that the active receptor state (R⁎) is an intrinsic property of the receptor itself rather than of the RG complex, eventually leading to the formulation of the cubic ternary complex model (CTC). Here, by a careful analysis of a series of data obtained with a number of mutants of the highly conserved E/DRY motif, we show evidences for the existence of all the receptor states theorized by the CTC, four 'uncoupled (R, R⁎ and HR and HR⁎), and, consequently four 'coupled' (RG, R⁎G, HRG and HR⁎G). The E/DRY motif located at the cytosolic end of transmembrane helix III of Class A GPCRs has been widely studied and analyzed because it forms a network of interactions believed to lock receptors in the inactive conformation (R), and, thus, to play a key role in receptor activation. Our conclusions are supported by recent crystal and NMR spectra, as well as by results obtained with two prototypical GPCRs using a new FRET technology that de-couples G protein binding to the receptor from signal transduction. Thus, despite its complexity and limitations, we propose that the CTC is a useful framework to reconcile pharmacological, biochemical and structural data.
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Affiliation(s)
- G Enrico Rovati
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy.
| | - Valérie Capra
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy; Department of Health Science, University of Milan, Milano, Italy.
| | - Vincent S Shaw
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Rabia U Malik
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota Twin Cities, Minneapolis, MN, USA.
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota Twin Cities, Minneapolis, MN, USA.
| | - Richard R Neubig
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, USA.
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20
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Bhattacharya S, Salomon-Ferrer R, Lee S, Vaidehi N. Conserved Mechanism of Conformational Stability and Dynamics in G-Protein-Coupled Receptors. J Chem Theory Comput 2016; 12:5575-5584. [PMID: 27709935 DOI: 10.1021/acs.jctc.6b00618] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
G-protein-coupled receptors (GPCRs) are transmembrane receptors involved in diverse biological functions. Despite the diversity in their amino acid sequences, class A GPCRs exhibit a conserved structural topology and possibly a common mechanism of receptor activation. To understand how this high sequence diversity translates to a conserved functional mechanism, we have compared the dynamic behavior of eight class A GPCRs comprised of six biogenic amine receptors, adenosine A2A, and the peptide receptor protease-activated receptor 1. Starting from the crystal structures of the inactive state of these receptors bound to inverse agonists or antagonists, we have performed multiple all-atom MD simulations adding up to several microseconds of simulation. We elucidated the similarities and differences in the dynamic behavior and the conformational ensembles sampled by these eight class A GPCRs. Among the six biogenic amine receptors studied here, β2-adrenergic receptor shows the highest level of fluctuation in the sixth and seventh transmembrane helices, possibly explaining its high basal activity. In contrast, the muscarinic acetylcholine receptors show the lowest fluctuations as well as tight packing and low hydration of the transmembrane domain. All eight GPCRs show several conserved allosteric communication pipelines from the residues in the agonist binding site with the G-protein interface. Positions of the residues along these pipelines that serve as major hubs of allosteric communication are conserved in their respective structures. These findings have important implications in understanding the dynamics and allosteric mechanism of communication in class A GPCRs and hence are useful for designing conformation-specific drugs.
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Affiliation(s)
- Supriyo Bhattacharya
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
| | - Romelia Salomon-Ferrer
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
| | - Sangbae Lee
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
| | - Nagarajan Vaidehi
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
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21
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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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22
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Signal transmission through the CXC chemokine receptor 4 (CXCR4) transmembrane helices. Proc Natl Acad Sci U S A 2016; 113:9928-33. [PMID: 27543332 DOI: 10.1073/pnas.1601278113] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The atomic-level mechanisms by which G protein-coupled receptors (GPCRs) transmit extracellular ligand binding events through their transmembrane helices to activate intracellular G proteins remain unclear. Using a comprehensive library of mutations covering all 352 residues of the GPCR CXC chemokine receptor 4 (CXCR4), we identified 41 amino acids that are required for signaling induced by the chemokine ligand CXCL12 (stromal cell-derived factor 1). CXCR4 variants with each of these mutations do not signal properly but remain folded, based on receptor surface trafficking, reactivity to conformationally sensitive monoclonal antibodies, and ligand binding. When visualized on the structure of CXCR4, the majority of these residues form a continuous intramolecular signaling chain through the transmembrane helices; this chain connects chemokine binding residues on the extracellular side of CXCR4 to G protein-coupling residues on its intracellular side. Integrated into a cohesive model of signal transmission, these CXCR4 residues cluster into five functional groups that mediate (i) chemokine engagement, (ii) signal initiation, (iii) signal propagation, (iv) microswitch activation, and (v) G protein coupling. Propagation of the signal passes through a "hydrophobic bridge" on helix VI that coordinates with nearly every known GPCR signaling motif. Our results agree with known conserved mechanisms of GPCR activation and significantly expand on understanding the structural principles of CXCR4 signaling.
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23
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Venkatakrishnan AJ, Deupi X, Lebon G, Heydenreich FM, Flock T, Miljus T, Balaji S, Bouvier M, Veprintsev DB, Tate CG, Schertler GFX, Babu MM. Diverse activation pathways in class A GPCRs converge near the G-protein-coupling region. Nature 2016; 536:484-7. [PMID: 27525504 DOI: 10.1038/nature19107] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 07/13/2016] [Indexed: 02/06/2023]
Abstract
Class A G-protein-coupled receptors (GPCRs) are a large family of membrane proteins that mediate a wide variety of physiological functions, including vision, neurotransmission and immune responses. They are the targets of nearly one-third of all prescribed medicinal drugs such as beta blockers and antipsychotics. GPCR activation is facilitated by extracellular ligands and leads to the recruitment of intracellular G proteins. Structural rearrangements of residue contacts in the transmembrane domain serve as 'activation pathways' that connect the ligand-binding pocket to the G-protein-coupling region within the receptor. In order to investigate the similarities in activation pathways across class A GPCRs, we analysed 27 GPCRs from diverse subgroups for which structures of active, inactive or both states were available. Here we show that, despite the diversity in activation pathways between receptors, the pathways converge near the G-protein-coupling region. This convergence is mediated by a highly conserved structural rearrangement of residue contacts between transmembrane helices 3, 6 and 7 that releases G-protein-contacting residues. The convergence of activation pathways may explain how the activation steps initiated by diverse ligands enable GPCRs to bind a common repertoire of G proteins.
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24
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Lakkaraju SK, Lemkul JA, Huang J, MacKerell AD. DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR. J Comput Chem 2016; 37:416-25. [PMID: 26558323 PMCID: PMC4756637 DOI: 10.1002/jcc.24231] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 09/10/2015] [Accepted: 10/06/2015] [Indexed: 12/13/2022]
Abstract
The conformational dynamics of a macromolecule can be modulated by a number of factors, including changes in environment, ligand binding, and interactions with other macromolecules, among others. We present a method that quantifies the differences in macromolecular conformational dynamics and automatically extracts the structural features responsible for these changes. Given a set of molecular dynamics (MD) simulations of a macromolecule, the norms of the differences in covariance matrices are calculated for each pair of trajectories. A matrix of these norms thus quantifies the differences in conformational dynamics across the set of simulations. For each pair of trajectories, covariance difference matrices are parsed to extract structural elements that undergo changes in conformational properties. As a demonstration of its applicability to biomacromolecular systems, the method, referred to as DIRECT-ID, was used to identify relevant ligand-modulated structural variations in the β2 -adrenergic (β2 AR) G-protein coupled receptor. Micro-second MD simulations of the β2 AR in an explicit lipid bilayer were run in the apo state and complexed with the ligands: BI-167107 (agonist), epinephrine (agonist), salbutamol (long-acting partial agonist), or carazolol (inverse agonist). Each ligand modulated the conformational dynamics of β2 AR differently and DIRECT-ID analysis of the inverse-agonist vs. agonist-modulated β2 AR identified residues known through previous studies to selectively propagate deactivation/activation information, along with some previously unidentified ligand-specific microswitches across the GPCR. This study demonstrates the utility of DIRECT-ID to rapidly extract functionally relevant conformational dynamics information from extended MD simulations of large and complex macromolecular systems.
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Affiliation(s)
- Sirish Kaushik Lakkaraju
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, MD 21201
| | - Justin A. Lemkul
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, MD 21201
| | - Jing Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, MD 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, MD 21201
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25
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Bhattacharya S, Vaidehi N. Differences in allosteric communication pipelines in the inactive and active states of a GPCR. Biophys J 2015; 107:422-434. [PMID: 25028884 DOI: 10.1016/j.bpj.2014.06.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/02/2014] [Accepted: 06/09/2014] [Indexed: 01/01/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are membrane proteins that allosterically transduce the signal of ligand binding in the extracellular (EC) domain to couple to proteins in the intracellular (IC) domain. However, the complete pathway of allosteric communication from the EC to the IC domain, including the role of individual amino acids in the pathway is not known. Using the correlation in torsion angle movements calculated from microseconds-long molecular-dynamics simulations, we elucidated the allosteric pathways in three different conformational states of β2-adrenergic receptor (β2AR): 1), the inverse-agonist-bound inactive state; 2), the agonist-bound intermediate state; and (3), the agonist- and G-protein-bound fully active state. The inactive state is less dynamic compared with the intermediate and active states, showing dense clusters of allosteric pathways (allosteric pipelines) connecting the EC with the IC domain. The allosteric pipelines from the EC domain to the IC domain are weakened in the intermediate state, thus decoupling the EC domain from the IC domain and making the receptor more dynamic compared with the other states. Also, the orthosteric ligand-binding site becomes the initiator region for allosteric communication in the intermediate state. This finding agrees with the paradigm that the nature of the agonist governs the specific signaling state of the receptor. These results provide an understanding of the mechanism of allosteric communication in class A GPCRs. In addition, our analysis shows that mutations that affect the ligand efficacy, but not the binding affinity, are located in the allosteric pipelines. This clarifies the role of such mutations, which has hitherto been unexplained.
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Affiliation(s)
- Supriyo Bhattacharya
- Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California
| | - Nagarajan Vaidehi
- Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California.
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26
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Burczyk M, Burkhalter MD, Blätte T, Matysik S, Caron MG, Barak LS, Philipp M. Phenotypic regulation of the sphingosine 1-phosphate receptor miles apart by G protein-coupled receptor kinase 2. Biochemistry 2015; 54:765-75. [PMID: 25555130 PMCID: PMC4310627 DOI: 10.1021/bi501061h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
The evolutionarily conserved DRY
motif at the end of the third
helix of rhodopsin-like, class-A G protein-coupled receptors (GPCRs)
is a major regulator of receptor stability, signaling activity, and
β-arrestin-mediated internalization. Substitution of the DRY
arginine with histidine in the human vasopressin receptor results
in a loss-of-function phenotype associated with diabetes insipidus.
The analogous R150H substitution of the DRY motif in zebrafish sphingosine-1
phosphate receptor 2 (S1p2) produces a mutation, miles apart m93 (milm93), that not only disrupts signaling but
also impairs heart field migration. We hypothesized that constitutive
S1p2 desensitization is the underlying cause of this strong zebrafish
developmental defect. We observed in cell assays that the wild-type
S1p2 receptor is at the cell surface whereas in distinct contrast
the S1p2 R150H receptor is found in intracellular vesicles, blocking
G protein but not arrestin signaling activity. Surface S1p2 R150H
expression could be restored by inhibition of G protein-coupled receptor
kinase 2 (GRK2). Moreover, we observed that β-arrestin 2 and
GRK2 colocalize with S1p2 in developing zebrafish embryos and depletion
of GRK2 in the S1p2 R150H miles apart zebrafish partially rescued
cardia bifida. The ability of reduced GRK2 activity to reverse a developmental
phenotype associated with constitutive desensitization supports efforts
to genetically or pharmacologically target this kinase in diseases
involving biased GPCR signaling.
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Affiliation(s)
- Martina Burczyk
- Institute for Biochemistry and Molecular Biology, Ulm University , 89081 Ulm, Germany
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27
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Tehan BG, Bortolato A, Blaney FE, Weir MP, Mason JS. Unifying family A GPCR theories of activation. Pharmacol Ther 2014; 143:51-60. [PMID: 24561131 DOI: 10.1016/j.pharmthera.2014.02.004] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 10/25/2022]
Abstract
Several new pairs of active and inactive GPCR structures have recently been solved enabling detailed structural insight into the activation process, not only of rhodopsin but now also of the β2 adrenergic, M2 muscarinic and adenosine A2A receptors. Combined with structural analyses they have enabled us to examine the different recent theories proposed for GPCR activation and show that they are all indeed parts of the same process, and are intrinsically related through their effect on the central hydrophobic core of GPCRs. This new unifying general process of activation is consistent with the identification of known constitutively active mutants and an in-depth conservational analysis of significant residues implicated in the process.
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Affiliation(s)
- Benjamin G Tehan
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom.
| | - Andrea Bortolato
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
| | - Frank E Blaney
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
| | - Malcolm P Weir
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
| | - Jonathan S Mason
- Heptares Therapeutics BioPark, Broadwater Road, Welwyn Garden City AL7 3AX United Kingdom
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28
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Pruitt MM, Lamm MH, Coffman CR. Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure. BMC STRUCTURAL BIOLOGY 2013; 13:15. [PMID: 24044607 PMCID: PMC3848830 DOI: 10.1186/1472-6807-13-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/16/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND The arginine of the D/E/NRY motif in Rhodopsin family G protein-coupled receptors (GPCRs) is conserved in 96% of these proteins. In some GPCRs, this arginine in transmembrane 3 can form a salt bridge with an aspartic acid or glutamic acid in transmembrane 6. The Drosophila melanogaster GPCR Trapped in endoderm-1 (Tre1) is required for normal primordial germ cell migration. In a mutant form of the protein, Tre1sctt, eight amino acids RYILIACH are missing, resulting in a severe disruption of primordial germ cell development. The impact of the loss of these amino acids on Tre1 structure is unknown. Since the missing amino acids in Tre1sctt include the arginine that is part of the D/E/NRY motif in Tre1, molecular dynamics simulations were performed to explore the hypothesis that these amino acids are involved in salt bridge formation and help maintain Tre1 structure. RESULTS Structural predictions of wild type Tre1 (Tre1+) and Tre1sctt were subjected to over 250 ns of molecular dynamics simulations. The ability of the model systems to form a salt bridge between the arginine of the D/E/NRY motif and an aspartic acid residue in transmembrane 6 was analyzed. The results indicate that a stable salt bridge can form in the Tre1+ systems and a weak salt bridge or no salt bridge, using an alternative arginine, is likely in the Tre1sctt systems. CONCLUSIONS The weak salt bridge or lack of a salt bridge in the Tre1sctt systems could be one possible explanation for the disrupted function of Tre1sctt in primordial germ cell migration. These results provide a framework for studying the importance of the arginine of the D/E/NRY motif in the structure and function of other GPCRs that are involved in cell migration, such as CXCR4 in the mouse, zebrafish, and chicken.
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Affiliation(s)
- Margaret M Pruitt
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Monica H Lamm
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, USA
| | - Clark R Coffman
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
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Study of the selectivity of α1-adrenergic antagonists by molecular modeling of α1a-, α1b-, and α1d-adrenergic receptor subtypes and docking simulations. MONATSHEFTE FUR CHEMIE 2013. [DOI: 10.1007/s00706-013-0966-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Ragnarsson L, Wang CIA, Andersson Å, Fajarningsih D, Monks T, Brust A, Rosengren KJ, Lewis RJ. Conopeptide ρ-TIA defines a new allosteric site on the extracellular surface of the α1B-adrenoceptor. J Biol Chem 2012. [PMID: 23184947 DOI: 10.1074/jbc.m112.430785] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The G protein-coupled receptor (GPCR) superfamily is an important drug target that includes over 1000 membrane receptors that functionally couple extracellular stimuli to intracellular effectors. Despite the potential of extracellular surface (ECS) residues in GPCRs to interact with subtype-specific allosteric modulators, few ECS pharmacophores for class A receptors have been identified. Using the turkey β(1)-adrenergic receptor crystal structure, we modeled the α(1B)-adrenoceptor (α(1B)-AR) to help identify the allosteric site for ρ-conopeptide TIA, an inverse agonist at this receptor. Combining mutational radioligand binding and inositol 1-phosphate signaling studies, together with molecular docking simulations using a refined NMR structure of ρ-TIA, we identified 14 residues on the ECS of the α(1B)-AR that influenced ρ-TIA binding. Double mutant cycle analysis and docking confirmed that ρ-TIA binding was dominated by a salt bridge and cation-π between Arg-4-ρ-TIA and Asp-327 and Phe-330, respectively, and a T-stacking-π interaction between Trp-3-ρ-TIA and Phe-330. Water-bridging hydrogen bonds between Asn-2-ρ-TIA and Val-197, Trp-3-ρ-TIA and Ser-318, and the positively charged N terminus and Glu-186, were also identified. These interactions reveal that peptide binding to the ECS on transmembrane helix 6 (TMH6) and TMH7 at the base of extracellular loop 3 (ECL3) is sufficient to allosterically inhibit agonist signaling at a GPCR. The ligand-accessible ECS residues identified provide the first view of an allosteric inhibitor pharmacophore for α(1)-adrenoceptors and mechanistic insight and a new set of structural constraints for the design of allosteric antagonists at related GPCRs.
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Affiliation(s)
- Lotten Ragnarsson
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
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31
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Gong Y, Fu W, Chen K. Dopamine D1receptor and serotonin 5-HT1Areceptor agonist effects of the natural product (–)-stepholidine: molecular modelling and dynamics simulations. MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2012.679619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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32
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Trzaskowski B, Latek D, Yuan S, Ghoshdastider U, Debinski A, Filipek S. Action of molecular switches in GPCRs--theoretical and experimental studies. Curr Med Chem 2012; 19:1090-109. [PMID: 22300046 PMCID: PMC3343417 DOI: 10.2174/092986712799320556] [Citation(s) in RCA: 336] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 12/30/2011] [Accepted: 01/02/2012] [Indexed: 01/14/2023]
Abstract
G protein coupled receptors (GPCRs), also called 7TM receptors, form a huge superfamily of membrane proteins that, upon activation by extracellular agonists, pass the signal to the cell interior. Ligands can bind either to extracellular N-terminus and loops (e.g. glutamate receptors) or to the binding site within transmembrane helices (Rhodopsin-like family). They are all activated by agonists although a spontaneous auto-activation of an empty receptor can also be observed. Biochemical and crystallographic methods together with molecular dynamics simulations and other theoretical techniques provided models of the receptor activation based on the action of so-called "molecular switches" buried in the receptor structure. They are changed by agonists but also by inverse agonists evoking an ensemble of activation states leading toward different activation pathways. Switches discovered so far include the ionic lock switch, the 3-7 lock switch, the tyrosine toggle switch linked with the nPxxy motif in TM7, and the transmission switch. The latter one was proposed instead of the tryptophan rotamer toggle switch because no change of the rotamer was observed in structures of activated receptors. The global toggle switch suggested earlier consisting of a vertical rigid motion of TM6, seems also to be implausible based on the recent crystal structures of GPCRs with agonists. Theoretical and experimental methods (crystallography, NMR, specific spectroscopic methods like FRET/BRET but also single-molecule-force-spectroscopy) are currently used to study the effect of ligands on the receptor structure, location of stable structural segments/domains of GPCRs, and to answer the still open question on how ligands are binding: either via ensemble of conformational receptor states or rather via induced fit mechanisms. On the other hand the structural investigations of homoand heterodimers and higher oligomers revealed the mechanism of allosteric signal transmission and receptor activation that could lead to design highly effective and selective allosteric or ago-allosteric drugs.
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Affiliation(s)
- B Trzaskowski
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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Shim JY. Understanding functional residues of the cannabinoid CB1. Curr Top Med Chem 2011; 10:779-98. [PMID: 20370713 DOI: 10.2174/156802610791164210] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 10/27/2009] [Indexed: 02/07/2023]
Abstract
The brain cannabinoid (CB(1)) receptor that mediates numerous physiological processes in response to marijuana and other psychoactive compounds is a G protein coupled receptor (GPCR) and shares common structural features with many rhodopsin class GPCRs. For the rational development of therapeutic agents targeting the CB(1) receptor, understanding of the ligand-specific CB(1) receptor interactions responsible for unique G protein signals is crucial. For a more than a decade, a combination of mutagenesis and computational modeling approaches has been successfully employed to study the ligand-specific CB(1) receptor interactions. In this review, after a brief discussion about recent advances in understanding of some structural and functional features of GPCRs commonly applicable to the CB(1) receptor, the CB(1) receptor functional residues reported from mutational studies are divided into three different types, ligand binding (B), receptor stabilization (S) and receptor activation (A) residues, to delineate the nature of the binding pockets of anandamide, CP55940, WIN55212-2 and SR141716A and to describe the molecular events of the ligand-specific CB(1) receptor activation from ligand binding to G protein signaling. Taken these CB(1) receptor functional residues, some of which are unique to the CB(1) receptor, together with the biophysical knowledge accumulated for the GPCR active state, it is possible to propose the early stages of the CB(1) receptor activation process that not only provide some insights into understanding molecular mechanisms of receptor activation but also are applicable for identifying new therapeutic agents by applying the validated structure-based approaches, such as virtual high throughput screening (HTS) and fragment-based approach (FBA).
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Affiliation(s)
- Joong-Youn Shim
- J.L. Chambers Biomedical/Biotechnology Research Institute, North Carolina Central University, 700 George Street, Durham, NC 27707, USA.
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35
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Nikiforovich GV, Marshall GR, Baranski TJ. Simplified modeling approach suggests structural mechanisms for constitutive activation of the C5a receptor. Proteins 2010; 79:787-802. [PMID: 21287612 DOI: 10.1002/prot.22918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 10/11/2010] [Accepted: 10/13/2010] [Indexed: 11/07/2022]
Abstract
Molecular modeling of conformational changes occurring in the transmembrane region of the complement factor 5a receptor (C5aR) during receptor activation was performed by comparing two constitutively active mutants (CAMs) of C5aR, NQ (I124N/L127Q), and F251A, to those of the wild-type C5aR and NQ-N296A (I124N/L127Q/N296A), which have the wild-type phenotype. Modeling involved comprehensive sampling of various rotations of TM helices aligned to the crystal template of the dark-adapted rhodopsin along their long axes. By assuming that the relative energies of the spontaneously activated states of CAMs should be lower or at least comparable to energies characteristic for the ground states, we selected the plausible models for the conformational states associated with constitutive activation in C5aR. The modeling revealed that the hydrogen bonds between the side chains of D82-N119, S85-N119, and S131-C221 characteristic for the ground state were replaced by the hydrogen bonds D82-N296, N296-Y300, and S131-R134, respectively, in the activated states. Also, conformational transitions that occurred upon activation were hindered by contacts between the side chains of L127 and F251. The results rationalize the available data of mutagenesis in C5aR and offer the first specific molecular mechanism for the loss of constitutive activity in NQ-N296A. Our results also contributed to understanding the general structural mechanisms of activation in G-protein-coupled receptors lacking the "ionic lock", R(3.50) and E/D(6.30). Importantly, these results were obtained by modeling approaches that deliberately simplify many elements in order to explore potential conformations of GPCRs involving large-scale molecular movements.
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Abstract
The α1-adrenergic receptor (AR) subtypes (α1a, α1b, and α1d) mediate several physiological effects of epinephrineand norepinephrine. Despite several studies in recombinant systems and insightfrom genetically modified mice, our understanding of the physiological relevance and specificity of the α1-AR subtypes is still limited. Constitutive activity and receptor oligomerization have emerged as potential features regulating receptor function. Another recent paradigm is that βarrestins and G protein-coupled receptors themselves can act as scaffolds binding a variety of proteins and this can result in growing complexity of the receptor-mediated cellular effects. The aim of this review is to summarize our current knowledge on some recently identified functional paradigms and signaling networks that might help to elucidate the functional diversity of the α1-AR subtypes in various organs.
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Affiliation(s)
- Susanna Cotecchia
- Dipartimento di Fisiologia Generale e Ambientale, Università di Bari, Italy.
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37
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Carrieri A, Piergentili A, Bello FD, Giannella M, Pigini M, Leonardi A, Fanelli F, Quaglia W. Structure–activity relationships in 1,4-benzodioxan-related compounds. 10. Novel α1-adrenoreceptor antagonists related to openphendioxan: Synthesis, biological evaluation, and α1d computational study. Bioorg Med Chem 2010; 18:7065-77. [DOI: 10.1016/j.bmc.2010.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 07/28/2010] [Accepted: 08/02/2010] [Indexed: 01/03/2023]
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38
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Swaminath G, Jaeckel P, Guo Q, Cardozo M, Weiszmann J, Lindberg R, Wang Y, Schwandner R, Li Y. Allosteric rescuing of loss-of-function FFAR2 mutations. FEBS Lett 2010; 584:4208-14. [PMID: 20837008 DOI: 10.1016/j.febslet.2010.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/08/2010] [Accepted: 09/03/2010] [Indexed: 10/19/2022]
Abstract
FFAR2 (GPR43) is a receptor for short-chain fatty acids (SCFAs), acetate and propionate. In the current study, we investigate the molecular determinants contributing to receptor activation by endogenous ligands. Mutational analysis revealed several important residues located in transmembrane domains (TM) 3, 4, 5, 6, and 7 for acetate binding. Interestingly, mutations that abolished acetate activity, including the mutation in the well-conserved D(E)RY motif, could be rescued by a recently identified synthetic allosteric agonist. These findings provide additional insight into agonist binding and activation which may aid in designing allosteric ligands for targeting receptor function in various diseases.
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39
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An evolutionarily conserved arginine is essential for Tre1 G protein-coupled receptor function during germ cell migration in Drosophila melanogaster. PLoS One 2010; 5:e11839. [PMID: 20676220 PMCID: PMC2911388 DOI: 10.1371/journal.pone.0011839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 06/29/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND G protein-coupled receptors (GPCRs) play central roles in mediating cellular responses to environmental signals leading to changes in cell physiology and behaviors, including cell migration. Numerous clinical pathologies including metastasis, an invasive form of cell migration, have been linked to abnormal GPCR signaling. While the structures of some GPCRs have been defined, the in vivo roles of conserved amino acid residues and their relationships to receptor function are not fully understood. Trapped in endoderm 1 (Tre1) is an orphan receptor of the rhodopsin class that is necessary for primordial germ cell migration in Drosophila melanogaster embryos. In this study, we employ molecular genetic approaches to identify residues in Tre1 that are critical to its functions in germ cell migration. METHODOLOGY/PRINCIPAL FINDINGS First, we show that the previously reported scattershot mutation is an allele of tre1. The scattershot allele results in an in-frame deletion of 8 amino acids at the junction of the third transmembrane domain and the second intracellular loop of Tre1 that dramatically impairs the function of this GPCR in germ cell migration. To further refine the molecular basis for this phenotype, we assayed the effects of single amino acid substitutions in transgenic animals and determined that the arginine within the evolutionarily conserved E/N/DRY motif is critical for receptor function in mediating germ cell migration within an intact developing embryo. CONCLUSIONS/SIGNIFICANCE These structure-function studies of GPCR signaling in native contexts will inform future studies into the basic biology of this large and clinically important family of receptors.
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40
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A conserved protonation-induced switch can trigger "ionic-lock" formation in adrenergic receptors. J Mol Biol 2010; 397:1339-49. [PMID: 20132827 DOI: 10.1016/j.jmb.2010.01.060] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 01/19/2010] [Accepted: 01/25/2010] [Indexed: 11/23/2022]
Abstract
The mechanism of signal transduction in G-protein-coupled receptors (GPCRs) is a crucial step in cell signaling. However, the molecular details of this process are still largely undetermined. Carrying out submicrosecond molecular dynamics simulations of beta-adrenergic receptors, we found that cooperation between a number of highly conserved residues is crucial to alter the equilibrium between the active state and the inactive state of diffusible ligand GPCRs. In particular, "ionic-lock" formation in beta-adrenergic receptors is directly correlated with the protonation state of a highly conserved aspartic acid residue [Asp(2.50)] even though the two sites are located more than 20 A away from each other. Internal polar residues, acting as local microswitches, cooperate to propagate the signal from Asp(2.50) to the G-protein interaction site at the helix III-helix VI interface. Evolutionarily conserved differences between opsin and non-opsin GPCRs in the surrounding of Asp(2.50) influence the acidity of this residue and can thus help in rationalizing the differences in constitutive activity of class A GPCRs.
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41
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Cotecchia S. Constitutive activity and inverse agonism at the α(₁a) and α(₁b) adrenergic receptor subtypes. Methods Enzymol 2010; 485:123-38. [PMID: 21050914 DOI: 10.1016/b978-0-12-381296-4.00007-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The α(1b)-adrenergic receptor (AR) was, after rhodopsin, the first G protein-coupled receptor (GPCR) in which point mutations were shown to trigger constitutive (agonist-independent) activity. Constitutively activating mutations have been found in other AR subtypes as well as in several GPCRs. This chapter briefly summarizes the main findings on constitutively active mutants of the α(1a)- and α(1b)-AR subtypes and the methods used to predict activating mutations, to measure constitutive activity of Gq-coupled receptors and to investigate inverse agonism. In addition, it highlights the implications of studies on constitutively active AR mutants on elucidating the molecular mechanisms of receptor activation and drug action.
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Affiliation(s)
- Susanna Cotecchia
- Department of General and Environmental Physiology, University of Bari, Italy
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42
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Nikiforovich GV, Baranski TJ. Computational Modeling of Constitutively Active Mutants of GPCRs. Methods Enzymol 2010; 485:369-91. [DOI: 10.1016/b978-0-12-381296-4.00021-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Tao YX, Segaloff DL. Follicle stimulating hormone receptor mutations and reproductive disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 89:115-31. [PMID: 20374735 DOI: 10.1016/s1877-1173(09)89005-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The follicle stimulating hormone receptor (FSHR) plays a critical role in reproductive function. In the males, FSH supports spermatogenesis, whereas in females, FSH is absolutely required for ovarian follicle growth. In females, inactivating mutations in the FSHR result in ovarian dysgenesis with amenorrhea and infertility. The few males reported with severe inactivating mutations exhibited varying spermatogenic defects, but not azoospermia. While these findings may potentially suggest that FSH action is not absolutely required for spermatogenesis, it cannot be ruled out that these individuals have some residual FSHR activity. Gain-of-function mutations in the FSHR cause spontaneous ovarian hyperstimulation syndrome in females due to the inappropriate stimulation of the mutant FSHR by human choriogonadotropin.
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Affiliation(s)
- Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, College of Veterinary Medicine, Auburn University, Alabama 36849, USA
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44
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Madathil S, Fahmy K. Lipid protein interactions couple protonation to conformation in a conserved cytosolic domain of G protein-coupled receptors. J Biol Chem 2009; 284:28801-9. [PMID: 19706606 DOI: 10.1074/jbc.m109.002030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The visual photoreceptor rhodopsin is a prototypical class I (rhodopsin-like) G protein-coupled receptor. Photoisomerization of the covalently bound ligand 11-cis-retinal leads to restructuring of the cytosolic face of rhodopsin. The ensuing protonation of Glu-134 in the class-conserved D(E)RY motif at the C-terminal end of transmembrane helix-3 promotes the formation of the G protein-activating state. Using transmembrane segments derived from helix-3 of bovine rhodopsin, we show that lipid protein interactions play a key role in this cytosolic "proton switch." Infrared and fluorescence spectroscopic pK(a) determinations reveal that the D(E)RY motif is an autonomous functional module coupling side chain neutralization to conformation and helix positioning as evidenced by side chain to lipid headgroup Foerster resonance energy transfer. The free enthalpies of helix stabilization and hydrophobic burial of the neutral carboxyl shift the side chain pK(a) into the range typical of Glu-134 in photoactivated rhodopsin. The lipid-mediated coupling mechanism is independent of interhelical contacts allowing its conservation without interference with the diversity of ligand-specific interactions in class I G protein-coupled receptors.
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Affiliation(s)
- Sineej Madathil
- Division of Biophysics, Institute of Radiochemistry, Forschungszentrum Dresden-Rossendorf, PF 510119, D-01314 Dresden, Germany
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Vanni S, Neri M, Tavernelli I, Rothlisberger U. Observation of "ionic lock" formation in molecular dynamics simulations of wild-type beta 1 and beta 2 adrenergic receptors. Biochemistry 2009; 48:4789-97. [PMID: 19378975 DOI: 10.1021/bi900299f] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
G protein coupled receptors (GPCRs) are a large family of integral membrane proteins involved in signal transduction pathways, making them appealing drug targets for a wide spectrum of diseases. The recently crystallized structures of two engineered adrenergic receptors have opened new avenues for the understanding of the molecular mechanisms of action of GPCRs. Taking the two crystal structures as a starting point, we carried out submicrosecond molecular dynamics simulations of wild-type beta(1) and beta(2) adrenergic receptors in a lipid bilayer under physiological conditions. These simulations give access to structural and dynamic properties of the receptors in pseudo in vivo conditions. For both systems the overall fold properties of the transmembrane region as well as the binding pocket remain close to the crystal structure of the engineered systems, thus suggesting that the ligand binding mode is not affected by the introduced modifications. Both simulations indicate the presence of one or two internal water molecules absent in both crystal structures and essential for the stabilization of the binding pocket at the interface between transmembrane helices III, IV, and V. The different interactions arising from the substitution of Tyr308 in beta(2)AR into Phe325 in beta(1)AR induce different conformations of the homologous Asn(6.55) inside the binding pockets of the two receptors, suggesting a possible origin of receptor specificity in agonist binding. The equilibrated structures of both receptors recover all of the previously suggested features of inactive GPCRs including formation of a salt bridge between the cytoplasmatic moieties of helices III and VI ("ionic lock") that is absent in the crystal structures.
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Affiliation(s)
- Stefano Vanni
- Laboratory of Computational Chemistry and Biochemistry, Federal Institute of Technology, EPFL, CH-1015 Lausanne, Switzerland
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Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. Proc Natl Acad Sci U S A 2009; 106:4689-94. [PMID: 19258456 DOI: 10.1073/pnas.0811065106] [Citation(s) in RCA: 245] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fully understanding the mechanisms of signaling proteins such as G protein-coupled receptors (GPCRs) will require the characterization of their conformational states and the pathways connecting those states. The recent crystal structures of the beta(2)- and beta(1)-adrenergic receptors in a nominally inactive state constituted a major advance toward this goal, but also raised new questions. Although earlier biochemical observations had suggested that these receptors possessed a set of contacts between helices 3 and 6, known as the ionic lock, which was believed to form a molecular switch for receptor activation, the crystal structures lacked these contacts. The unexpectedly broken ionic lock has raised questions about the true conformation(s) of the inactive state and the role of the ionic lock in receptor activation and signaling. To address these questions, we performed microsecond-timescale molecular dynamics simulations of the beta(2)-adrenergic receptor (beta(2)AR) in multiple wild-type and mutant forms. In wild-type simulations, the ionic lock formed reproducibly, bringing the intracellular ends of helices 3 and 6 together to adopt a conformation similar to that found in inactive rhodopsin. Our results suggest that inactive beta(2)AR exists in equilibrium between conformations with the lock formed and the lock broken, whether or not the cocrystallized ligand is present. These findings, along with the formation of several secondary structural elements in the beta(2)AR loops during our simulations, may provide a more comprehensive picture of the inactive state of the beta-adrenergic receptors, reconciling the crystal structures with biochemical studies.
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Sum CS, Tikhonova IG, Costanzi S, Gershengorn MC. Two arginine-glutamate ionic locks near the extracellular surface of FFAR1 gate receptor activation. J Biol Chem 2008; 284:3529-36. [PMID: 19068482 DOI: 10.1074/jbc.m806987200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Activation of a number of class A G protein-coupled receptors (GPCRs) is thought to involve two molecular switches, a rotamer toggle switch within the transmembrane domain and an ionic lock at the cytoplasmic surface of the receptor; however, the mechanism by which agonist binding changes these molecular interactions is not understood. Importantly, 80% of GPCRs including free fatty acid receptor 1 (FFAR1) lack the complement of amino acid residues implicated in either or both of these two switches; the mechanism of activation of these GPCRs is therefore less clear. By homology modeling, we identified two Glu residues (Glu-145 and Glu-172) in the second extracellular loop of FFAR1 that form putative interactions individually with two transmembrane Arg residues (Arg-183(5.39) and Arg-258(7.35)) to create two ionic locks. Molecular dynamics simulations showed that binding of agonists to FFAR1 leads to breakage of these Glu-Arg interactions. In mutagenesis experiments, breakage of these two putative interactions by substituting Ala for Glu-145 and Glu-172 caused constitutive receptor activation. Our results therefore reveal a molecular switch for receptor activation present on the extracellular surface of FFAR1 that is broken by agonist binding. Similar ionic locks between the transmembrane domains and the extracellular loops may constitute a mechanism common to other class A GPCRs also.
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Affiliation(s)
- Chi Shing Sum
- Clinical Endocrinology Branch, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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Chee MJS, Mörl K, Lindner D, Merten N, Zamponi GW, Light PE, Beck-Sickinger AG, Colmers WF. The third intracellular loop stabilizes the inactive state of the neuropeptide Y1 receptor. J Biol Chem 2008; 283:33337-46. [PMID: 18812316 PMCID: PMC2662261 DOI: 10.1074/jbc.m804671200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 09/15/2008] [Indexed: 11/06/2022] Open
Abstract
Constitutively active G-protein-coupled receptors (GPCRs) can signal even in the absence of ligand binding. Most Class I GPCRs are stabilized in the resting conformation by intramolecular interactions involving transmembrane domain (TM) 3 and TM6, particularly at loci 6.30 and 6.34 of TM6. Signaling by Gi/Go-coupled receptors such as the Neuropeptide Y1 receptor decreases already low basal metabolite levels. Thus, we examined constitutive activity using a biochemical assay mediated by a Gi/Gq chimeric protein and a more direct electrophysiological assay. Wild-type (WT-Y1) receptors express no measurable, agonist-independent activation, while mu-opioid receptors (MOR) and P2Y12 purinoceptors showed clear evidence of constitutive activation, especially in the electrophysiological assay. Neither point mutations at TM6 (T6.30A or N6.34A) nor substitution of the entire TM3 and TM6 regions from the MOR into the Y1 receptor increased basal WT-Y1 activation. By contrast, chimeric substitution of the third intracellular loop (ICL3) generated a constitutively active, Y1-ICL3-MOR chimera. Furthermore, the loss of stabilizing interactions from the native ICL3 enhanced the role of surrounding residues to permit basal receptor activation; because constitutive activity of the Y1-ICL3-MOR chimera was further increased by point mutation at locus 6.34, which did not alter WT-Y1 receptor activity. Our results indicate that the ICL3 stabilizes the Y1 receptor in the inactive state and confers structural properties critical for regulating Y receptor activation and signal transduction. These studies reveal the active participation of the ICL3 in the stabilization and activation of Class I GPCRs.
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MESH Headings
- Animals
- COS Cells
- Chlorocebus aethiops
- GTP-Binding Protein alpha Subunits, Gi-Go/genetics
- GTP-Binding Protein alpha Subunits, Gi-Go/metabolism
- GTP-Binding Protein alpha Subunits, Gq-G11/genetics
- GTP-Binding Protein alpha Subunits, Gq-G11/metabolism
- Humans
- Point Mutation
- Protein Structure, Secondary/physiology
- Protein Structure, Tertiary/physiology
- Receptors, Neuropeptide Y/genetics
- Receptors, Neuropeptide Y/metabolism
- Receptors, Opioid, mu/genetics
- Receptors, Opioid, mu/metabolism
- Receptors, Purinergic P2/genetics
- Receptors, Purinergic P2/metabolism
- Receptors, Purinergic P2Y12
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Signal Transduction/physiology
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Affiliation(s)
- Melissa J S Chee
- Department of Pharmacology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Tao YX. Constitutive activation of G protein-coupled receptors and diseases: insights into mechanisms of activation and therapeutics. Pharmacol Ther 2008; 120:129-48. [PMID: 18768149 DOI: 10.1016/j.pharmthera.2008.07.005] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 07/22/2008] [Indexed: 01/17/2023]
Abstract
The existence of constitutive activity for G protein-coupled receptors (GPCRs) was first described in 1980s. In 1991, the first naturally occurring constitutively active mutations in GPCRs that cause diseases were reported in rhodopsin. Since then, numerous constitutively active mutations that cause human diseases were reported in several additional receptors. More recently, loss of constitutive activity was postulated to also cause diseases. Animal models expressing some of these mutants confirmed the roles of these mutations in the pathogenesis of the diseases. Detailed functional studies of these naturally occurring mutations, combined with homology modeling using rhodopsin crystal structure as the template, lead to important insights into the mechanism of activation in the absence of crystal structure of GPCRs in active state. Search for inverse agonists on these receptors will be critical for correcting the diseases cause by activating mutations in GPCRs. Theoretically, these inverse agonists are better therapeutics than neutral antagonists in treating genetic diseases caused by constitutively activating mutations in GPCRs.
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Affiliation(s)
- Ya-Xiong Tao
- Department of Anatomy, Physiology and Pharmacology, 212 Greene Hall, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USA.
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Artigas RA, Gonzalez A, Riquelme E, Carvajal CA, Cattani A, Martínez-Aguayo A, Kalergis AM, Pérez-Acle T, Fardella CE. A novel adrenocorticotropin receptor mutation alters its structure and function, causing familial glucocorticoid deficiency. J Clin Endocrinol Metab 2008; 93:3097-105. [PMID: 18492762 DOI: 10.1210/jc.2008-0048] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
CONTEXT Familial glucocorticoid deficiency (FGD) is an autosomal recessive disorder characterized by unresponsiveness to ACTH. In this study, two mutations of the ACTH receptor (MC2R) gene are reported in this FGD clinical case. OBJECTIVE The objective of the study was to characterize a novel MC2R gene mutation in a compound heterozygous patient with FGD phenotype. DESIGN This was a clinical case description, biochemical, molecular, and bioinformatics analysis to describe a novel MC2R gene mutation. PATIENTS The subject of the study was a male diagnosed with primary adrenal insufficiency. The family history showed nonconsanguineous healthy parents, three healthy siblings, and one brother affected with FGD. MAIN OUTCOME MEASURES The mutant MC2R-Ala126Ser showed significantly lower activity when it was stimulated with ACTH-(1-24) than did cells transfected with wild-type MC2R. RESULTS The molecular studies demonstrated the presence of an adenine heterozygous insertion (InsA1347) in the MC2R gene (G217fs) in the patient. This insertion was due to a frame shift mutation in one allele and a premature stop codon codifying an aberrant receptor of 247 residues (27.2 kDa). We also found a novel heterozygous mutation alanine 126 by serine. Molecular dynamic simulations showed that serine 126 side chain fluctuates forming a noncanonical intrahelical hydrogen bond in the transmembrane helix 3 of the mutated receptor. This produces a structural rearrangement of the MC2R internal cavities that may affect the ligand recognition and signal transduction throughout the G protein. CONCLUSIONS We propose a molecular explanation for the reduced activity exhibited by the MC2R alanine 126 by serine mutant.
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Affiliation(s)
- Rocío A Artigas
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Lira 85, 5 degrees piso, 8330074 Santiago, Chile
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