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Tiss A, Ben Boubaker R, Henrion D, Guissouma H, Chabbert M. Homology Modeling of Class A G-Protein-Coupled Receptors in the Age of the Structure Boom. Methods Mol Biol 2021; 2315:73-97. [PMID: 34302671 DOI: 10.1007/978-1-0716-1468-6_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
With 700 members, G protein-coupled receptors (GPCRs) of the rhodopsin family (class A) form the largest membrane receptor family in humans and are the target of about 30% of presently available pharmaceutical drugs. The recent boom in GPCR structures led to the structural resolution of 57 unique receptors in different states (39 receptors in inactive state only, 2 receptors in active state only and 16 receptors in different activation states). In spite of these tremendous advances, most computational studies on GPCRs, including molecular dynamics simulations, virtual screening and drug design, rely on GPCR models obtained by homology modeling. In this protocol, we detail the different steps of homology modeling with the MODELLER software, from template selection to model evaluation. The present structure boom provides closely related templates for most receptors. If, in these templates, some of the loops are not resolved, in most cases, the numerous available structures enable to find loop templates with similar length for equivalent loops. However, simultaneously, the large number of putative templates leads to model ambiguities that may require additional information based on multiple sequence alignments or molecular dynamics simulations to be resolved. Using the modeling of the human bradykinin receptor B1 as a case study, we show how several templates are managed by MODELLER, and how the choice of template(s) and of template fragments can improve the quality of the models. We also give examples of how additional information and tools help the user to resolve ambiguities in GPCR modeling.
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Affiliation(s)
- Asma Tiss
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.,Laboratoire de Génétique, Immunologie et Pathologies Humaines, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Rym Ben Boubaker
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Daniel Henrion
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Hajer Guissouma
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Département de Biologie, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Marie Chabbert
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.
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2
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Worth CL, Kreuchwig F, Tiemann JKS, Kreuchwig A, Ritschel M, Kleinau G, Hildebrand PW, Krause G. GPCR-SSFE 2.0-a fragment-based molecular modeling web tool for Class A G-protein coupled receptors. Nucleic Acids Res 2019; 45:W408-W415. [PMID: 28582569 PMCID: PMC5570183 DOI: 10.1093/nar/gkx399] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/03/2017] [Indexed: 11/14/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are key players in signal transduction and therefore a large proportion of pharmaceutical drugs target these receptors. Structural data of GPCRs are sparse yet important for elucidating the molecular basis of GPCR-related diseases and for performing structure-based drug design. To ameliorate this problem, GPCR-SSFE 2.0 (http://www.ssfa-7tmr.de/ssfe2/), an intuitive web server dedicated to providing three-dimensional Class A GPCR homology models has been developed. The updated web server includes 27 inactive template structures and incorporates various new functionalities. Uniquely, it uses a fingerprint correlation scoring strategy for identifying the optimal templates, which we demonstrate captures structural features that sequence similarity alone is unable to do. Template selection is carried out separately for each helix, allowing both single-template models and fragment-based models to be built. Additionally, GPCR-SSFE 2.0 stores a comprehensive set of pre-calculated and downloadable homology models and also incorporates interactive loop modeling using the tool SL2, allowing knowledge-based input by the user to guide the selection process. For visual analysis, the NGL viewer is embedded into the result pages. Finally, blind-testing using two recently published structures shows that GPCR-SSFE 2.0 performs comparably or better than other state-of-the art GPCR modeling web servers.
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Affiliation(s)
- Catherine L Worth
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), D-13125 Berlin, Germany
| | - Franziska Kreuchwig
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), D-13125 Berlin, Germany
| | - Johanna K S Tiemann
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, D-10117 Berlin, Germany
| | - Annika Kreuchwig
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), D-13125 Berlin, Germany
| | - Michele Ritschel
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, D-10117 Berlin, Germany
| | - Gunnar Kleinau
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, D-10117 Berlin, Germany.,Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin, D-13353 Berlin, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, D-10117 Berlin, Germany.,Institute of Medical Physics and Biophysics, Leipzig University, D-04107 Leipzig, Germany
| | - Gerd Krause
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), D-13125 Berlin, Germany
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3
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GPCR-SAS: A web application for statistical analyses on G protein-coupled receptors sequences. PLoS One 2018; 13:e0199843. [PMID: 30044824 PMCID: PMC6059404 DOI: 10.1371/journal.pone.0199843] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/14/2018] [Indexed: 11/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are one of the largest protein families in mammals. They mediate signal transduction across cell membranes and are important targets for the pharmaceutical industry. The G Protein-Coupled Receptors-Sequence Analysis and Statistics (GPCR-SAS) web application provides a set of tools to perform comparative analysis of sequence positions between receptors, based on a curated structural-informed multiple sequence alignment. The analysis tools include: (i) percentage of occurrence of an amino acid or motif and entropy at a position or range of positions, (ii) covariance of two positions, (iii) correlation between two amino acids in two positions (or two sequence motifs in two ranges of positions), and (iv) snake-plot representation for a specific receptor or for the consensus sequence of a group of selected receptors. The analysis of conservation of residues and motifs across transmembrane (TM) segments may guide the design of more selective ligands or help to rationalize activation mechanisms, among others. As an example, here we analyze the amino acids of the "transmission switch", that initiates receptor activation following ligand binding. The tool is freely accessible at http://lmc.uab.cat/gpcrsas/.
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Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M. Evolution of chemokine receptors is driven by mutations in the sodium binding site. PLoS Comput Biol 2018; 14:e1006209. [PMID: 29912865 PMCID: PMC6037435 DOI: 10.1371/journal.pcbi.1006209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 07/09/2018] [Accepted: 05/16/2018] [Indexed: 12/22/2022] Open
Abstract
Chemokines and their receptors (members of the GPCR super-family) are involved in a wide variety of physiological processes and diseases; thus, understanding the specificity of the chemokine receptor family could help develop new receptor specific drugs. Here, we explore the evolutionary mechanisms that led to the emergence of the chemokine receptors. Based on GPCR hierarchical classification, we analyzed nested GPCR sets with an eigen decomposition approach of the sequence covariation matrix and determined three key residues whose mutation was crucial for the emergence of the chemokine receptors and their subsequent divergence into homeostatic and inflammatory receptors. These residues are part of the allosteric sodium binding site. Their structural and functional roles were investigated by molecular dynamics simulations of CXCR4 and CCR5 as prototypes of homeostatic and inflammatory chemokine receptors, respectively. This study indicates that the three mutations crucial for the evolution of the chemokine receptors dramatically altered the sodium binding mode. In CXCR4, the sodium ion is tightly bound by four protein atoms and one water molecule. In CCR5, the sodium ion is mobile within the binding pocket and moves between different sites involving from one to three protein atoms and two to five water molecules. Analysis of chemokine receptor evolution reveals that a highly constrained sodium binding site characterized most ancient receptors, and that the constraints were subsequently loosened during the divergence of this receptor family. We discuss the implications of these findings for the evolution of the chemokine receptor functions and mechanisms of action.
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Affiliation(s)
- Bruck Taddese
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Madeline Deniaud
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Antoine Garnier
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Asma Tiss
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Hajer Guissouma
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Hervé Abdi
- The University of Texas at Dallas, School of Behavioral and Brain Sciences, Dallas, Texas, United States of America
| | - Daniel Henrion
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Marie Chabbert
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
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Castel H, Desrues L, Joubert JE, Tonon MC, Prézeau L, Chabbert M, Morin F, Gandolfo P. The G Protein-Coupled Receptor UT of the Neuropeptide Urotensin II Displays Structural and Functional Chemokine Features. Front Endocrinol (Lausanne) 2017; 8:76. [PMID: 28487672 PMCID: PMC5403833 DOI: 10.3389/fendo.2017.00076] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/28/2017] [Indexed: 12/16/2022] Open
Abstract
The urotensinergic system was previously considered as being linked to numerous physiopathological states, including atherosclerosis, heart failure, hypertension, pre-eclampsia, diabetes, renal disease, as well as brain vascular lesions. Thus, it turns out that the actions of the urotensin II (UII)/G protein-coupled receptor UT system in animal models are currently not predictive enough in regard to their effects in human clinical trials and that UII analogs, established to target UT, were not as beneficial as expected in pathological situations. Thus, many questions remain regarding the overall signaling profiles of UT leading to complex involvement in cardiovascular and inflammatory responses as well as cancer. We address the potential UT chemotactic structural and functional definition under an evolutionary angle, by the existence of a common conserved structural feature among chemokine receptorsopioïdergic receptors and UT, i.e., a specific proline position in the transmembrane domain-2 TM2 (P2.58) likely responsible for a kink helical structure that would play a key role in chemokine functions. Even if the last decade was devoted to the elucidation of the cardiovascular control by the urotensinergic system, we also attempt here to discuss the role of UII on inflammation and migration, likely providing a peptide chemokine status for UII. Indeed, our recent work established that activation of UT by a gradient concentration of UII recruits Gαi/o and Gα13 couplings in a spatiotemporal way, controlling key signaling events leading to chemotaxis. We think that this new vision of the urotensinergic system should help considering UT as a chemotactic therapeutic target in pathological situations involving cell chemoattraction.
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Affiliation(s)
- Hélène Castel
- Normandie University, UNIROUEN, INSERM, DC2N, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
- *Correspondence: Hélène Castel,
| | - Laurence Desrues
- Normandie University, UNIROUEN, INSERM, DC2N, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Jane-Eileen Joubert
- Normandie University, UNIROUEN, INSERM, DC2N, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Marie-Christine Tonon
- Normandie University, UNIROUEN, INSERM, DC2N, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Laurent Prézeau
- CNRS UMR 5203, INSERM U661, Institute of Functional Genomic (IGF), University of Montpellier 1 and 2, Montpellier, France
| | - Marie Chabbert
- UMR CNRS 6214, INSERM 1083, Faculté de Médecine 3, Angers, France
| | - Fabrice Morin
- Normandie University, UNIROUEN, INSERM, DC2N, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Pierrick Gandolfo
- Normandie University, UNIROUEN, INSERM, DC2N, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
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Caillon A, Grenier C, Grimaud L, Vessieres E, Guihot AL, Blanchard S, Lelievre E, Chabbert M, Foucher ED, Jeannin P, Beauvillain C, Abraham P, Loufrani L, Delneste Y, Henrion D. The angiotensin II type 2 receptor activates flow-mediated outward remodelling through T cells-dependent interleukin-17 production. Cardiovasc Res 2016; 112:515-25. [PMID: 27328880 DOI: 10.1093/cvr/cvw172] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 06/09/2016] [Indexed: 12/11/2022] Open
Abstract
AIMS The angiotensin II type 1 receptor (AT1R) through the activation of immune cells plays a key role in arterial inward remodelling and reduced blood flow in cardiovascular disorders. On the other side, flow (shear stress)-mediated outward remodelling (FMR), involved in collateral arteries growth in ischaemic diseases, allows revascularization. We hypothesized that the type 2 receptor (AT2R), described as opposing the effects of AT1R, could be involved in FMR. METHODS AND RESULTS We studied FMR using a model of ligation of feed arteries supplying collateral pathways in the mouse mesenteric arterial bed in vivo. Seven days after ligation, diameter increased by 30% in high flow (HF) arteries compared with normal flow vessels. FMR was absent in mice lacking AT2R. At Day 2, T lymphocytes expressing AT2R were present preferentially around HF arteries. FMR did not occur in athymic (nude) mice lacking T cells and in mice treated with anti-CD3ε antibodies. AT2R activation induced interleukin-17 production by memory T cells. Treatment of nude mice or AT2R-deficient mice with interleukin-17 restored diameter enlargement in HF arteries. Interleukin-17 increased NO-dependent relaxation and matrix metalloproteinases activity, both important in FMR. Remodelling of feeding arteries in the skin flap model of ischaemia was also absent in AT2R-deficient mice and in anti-interleukin-17-treated mice. Finally, remodelling, absent in 12-month-old mice, was restored by a treatment with the AT2R non-peptidic agonist C21. CONCLUSION AT2R-dependent interleukin-17 production by T lymphocyte is necessary for collateral artery growth and could represent a new therapeutic target in ischaemic disorders.
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Affiliation(s)
- Antoine Caillon
- MITOVASC Institute, UMR CNRS 6214, INSERM U1083, Angers University, F-49045 Angers, France UMR CNRS 6299, UMR INSERM 892, Angers University, F-49045 Angers, France
| | - Céline Grenier
- MITOVASC Institute, UMR CNRS 6214, INSERM U1083, Angers University, F-49045 Angers, France
| | - Linda Grimaud
- MITOVASC Institute, UMR CNRS 6214, INSERM U1083, Angers University, F-49045 Angers, France
| | - Emilie Vessieres
- MITOVASC Institute, UMR CNRS 6214, INSERM U1083, Angers University, F-49045 Angers, France Cardiovascular Functions In Vitro (CARFI) Facility, Angers University, F-49045 Angers, France
| | - Anne-Laure Guihot
- MITOVASC Institute, UMR CNRS 6214, INSERM U1083, Angers University, F-49045 Angers, France
| | - Simon Blanchard
- UMR CNRS 6299, UMR INSERM 892, Angers University, F-49045 Angers, France Department of Immunology and Allergology, University Hospital, F-49045 Angers, France
| | - Eric Lelievre
- MITOVASC Institute, UMR CNRS 6214, INSERM U1083, Angers University, F-49045 Angers, France
| | - Marie Chabbert
- MITOVASC Institute, UMR CNRS 6214, INSERM U1083, Angers University, F-49045 Angers, France
| | - Etienne D Foucher
- UMR CNRS 6299, UMR INSERM 892, Angers University, F-49045 Angers, France
| | - Pascale Jeannin
- UMR CNRS 6299, UMR INSERM 892, Angers University, F-49045 Angers, France Department of Immunology and Allergology, University Hospital, F-49045 Angers, France
| | - Céline Beauvillain
- UMR CNRS 6299, UMR INSERM 892, Angers University, F-49045 Angers, France Department of Immunology and Allergology, University Hospital, F-49045 Angers, France
| | - Pierre Abraham
- MITOVASC Institute, UMR CNRS 6214, INSERM U1083, Angers University, F-49045 Angers, France Department of Vascular Medicine, University Hospital, F-49045 Angers, France
| | - Laurent Loufrani
- MITOVASC Institute, UMR CNRS 6214, INSERM U1083, Angers University, F-49045 Angers, France
| | - Yves Delneste
- UMR CNRS 6299, UMR INSERM 892, Angers University, F-49045 Angers, France Department of Immunology and Allergology, University Hospital, F-49045 Angers, France
| | - Daniel Henrion
- MITOVASC Institute, UMR CNRS 6214, INSERM U1083, Angers University, F-49045 Angers, France Cardiovascular Functions In Vitro (CARFI) Facility, Angers University, F-49045 Angers, France Department of Vascular Medicine, University Hospital, F-49045 Angers, France
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Chantreau V, Taddese B, Munier M, Gourdin L, Henrion D, Rodien P, Chabbert M. Molecular Insights into the Transmembrane Domain of the Thyrotropin Receptor. PLoS One 2015; 10:e0142250. [PMID: 26545118 PMCID: PMC4636318 DOI: 10.1371/journal.pone.0142250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/20/2015] [Indexed: 12/12/2022] Open
Abstract
The thyrotropin receptor (TSHR) is a G protein-coupled receptor (GPCR) that is member of the leucine-rich repeat subfamily (LGR). In the absence of crystal structure, the success of rational design of ligands targeting the receptor internal cavity depends on the quality of the TSHR models built. In this subfamily, transmembrane helices (TM) 2 and 5 are characterized by the absence of proline compared to most receptors, raising the question of the structural conformation of these helices. To gain insight into the structural properties of these helices, we carried out bioinformatics and experimental studies. Evolutionary analysis of the LGR family revealed a deletion in TM5 but provided no information on TM2. Wild type residues at positions 2.58, 2.59 or 2.60 in TM2 and/or at position 5.50 in TM5 were substituted to proline. Depending on the position of the proline substitution, different effects were observed on membrane expression, glycosylation, constitutive cAMP activity and responses to thyrotropin. Only proline substitution at position 2.59 maintained complex glycosylation and high membrane expression, supporting occurrence of a bulged TM2. The TSHR transmembrane domain was modeled by homology with the orexin 2 receptor, using a protocol that forced the deletion of one residue in the TM5 bulge of the template. The stability of the model was assessed by molecular dynamics simulations. TM5 straightened during the equilibration phase and was stable for the remainder of the simulations. Our data support a structural model of the TSHR transmembrane domain with a bulged TM2 and a straight TM5 that is specific of glycoprotein hormone receptors.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Computational Biology
- Cyclic AMP/metabolism
- Evolution, Molecular
- Glycosylation
- HEK293 Cells
- Humans
- Models, Molecular
- Molecular Dynamics Simulation
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Phylogeny
- Protein Structure, Tertiary
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/classification
- Receptors, G-Protein-Coupled/genetics
- Receptors, Thyrotropin/chemistry
- Receptors, Thyrotropin/genetics
- Receptors, Thyrotropin/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Deletion
- Sequence Homology, Amino Acid
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Affiliation(s)
- Vanessa Chantreau
- UMR CNRS 6214 –INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology, University of Angers, Angers, France
| | - Bruck Taddese
- UMR CNRS 6214 –INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology, University of Angers, Angers, France
| | - Mathilde Munier
- UMR CNRS 6214 –INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology, University of Angers, Angers, France
| | - Louis Gourdin
- UMR CNRS 6214 –INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology, University of Angers, Angers, France
- Reference Centre for the pathologies of hormonal receptivity, Department of Endocrinology, Centre Hospitalier Universitaire of Angers, Angers, France
| | - Daniel Henrion
- UMR CNRS 6214 –INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology, University of Angers, Angers, France
| | - Patrice Rodien
- UMR CNRS 6214 –INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology, University of Angers, Angers, France
- Reference Centre for the pathologies of hormonal receptivity, Department of Endocrinology, Centre Hospitalier Universitaire of Angers, Angers, France
| | - Marie Chabbert
- UMR CNRS 6214 –INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology, University of Angers, Angers, France
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van der Kant R, Vriend G. Alpha-bulges in G protein-coupled receptors. Int J Mol Sci 2014; 15:7841-64. [PMID: 24806342 PMCID: PMC4057707 DOI: 10.3390/ijms15057841] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/02/2014] [Accepted: 04/09/2014] [Indexed: 12/31/2022] Open
Abstract
Agonist binding is related to a series of motions in G protein-coupled receptors (GPCRs) that result in the separation of transmembrane helices III and VI at their cytosolic ends and subsequent G protein binding. A large number of smaller motions also seem to be associated with activation. Most helices in GPCRs are highly irregular and often contain kinks, with extensive literature already available about the role of prolines in kink formation and the precise function of these kinks. GPCR transmembrane helices also contain many α-bulges. In this article we aim to draw attention to the role of these α-bulges in ligand and G-protein binding, as well as their role in several aspects of the mobility associated with GPCR activation. This mobility includes regularization and translation of helix III in the extracellular direction, a rotation of the entire helix VI, an inward movement of the helices near the extracellular side, and a concerted motion of the cytosolic ends of the helices that makes their orientation appear more circular and that opens up space for the G protein to bind. In several cases, α-bulges either appear or disappear as part of the activation process.
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Affiliation(s)
- Rob van der Kant
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.
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Pelé J, Moreau M, Abdi H, Rodien P, Castel H, Chabbert M. Comparative analysis of sequence covariation methods to mine evolutionary hubs: Examples from selected GPCR families. Proteins 2014; 82:2141-56. [DOI: 10.1002/prot.24570] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 03/11/2014] [Accepted: 03/19/2014] [Indexed: 01/26/2023]
Affiliation(s)
- Julien Pelé
- UMR CNRS 6214-INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology; University of Angers; 49045 Angers France
| | - Matthieu Moreau
- UMR CNRS 6214-INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology; University of Angers; 49045 Angers France
| | - Hervé Abdi
- The University of Texas at Dallas; School of Behavioral and Brain Sciences; Richardson, TX 75080-3021 USA
| | - Patrice Rodien
- UMR CNRS 6214-INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology; University of Angers; 49045 Angers France
- Department of Endocrinology, Reference Centre for the pathologies of hormonal receptivity; Centre Hospitalier Universitaire of Angers; 4 rue Larrey 49933 Angers France
| | - Hélène Castel
- INSERM U982, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, DC2N; University of Rouen; 76821 Mont-Saint-Aignan France
| | - Marie Chabbert
- UMR CNRS 6214-INSERM 1083, Laboratory of Integrated Neurovascular and Mitochondrial Biology; University of Angers; 49045 Angers France
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10
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Stäubert C, Le Duc D, Schöneberg T. Examining the Dynamic Evolution of G Protein-Coupled Receptors. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-62703-779-2_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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11
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Gonzalez A, Cordomí A, Matsoukas M, Zachmann J, Pardo L. Modeling of G Protein-Coupled Receptors Using Crystal Structures: From Monomers to Signaling Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:15-33. [DOI: 10.1007/978-94-007-7423-0_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Deupi X. Quantification of structural distortions in the transmembrane helices of GPCRs. Methods Mol Biol 2013; 914:219-35. [PMID: 22976031 DOI: 10.1007/978-1-62703-023-6_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
A substantial part of the structural and much of the functional information about G protein-coupled receptors (GPCRs) comes from studies on rhodopsin. Thus, analysis tools for detailed structure comparison are key to see to what extent this information can be extended to other GPCRs. Among the methods to evaluate protein structures and, in particular, helix distortions, HELANAL has the advantage that it provides data (local bend and twist angles) that can be easily translated to structural effects, as a local opening/tightening of the helix.In this work I show how HELANAL can be used to extract detailed structural information of the transmembrane bundle of GPCRs, and I provide some examples on how these data can be interpreted to study basic principles of protein structure, to compare homologous proteins and to study mechanisms of receptor activation. Also, I show how in combination with the sequence analysis tools provided by the program GMoS, distortions in individual receptors can be put in the context of the whole Class A GPCR family. Specifically, quantification of the strong proline-induced distortions in the transmembrane bundle of rhodopsin shows that they are not standard proline kinks. Moreover, the helix distortions in transmembrane helix (TMH) 5 and TMH 6 of rhodopsin are also present in the rest of GPCR crystal structures obtained so far, and thus, rhodopsin-based homology models have modeled correctly these strongly distorted helices. While in some cases the inherent "rhodopsin bias" of many of the GPCR models to date has not been a disadvantage, the availability of more templates will clearly result in better homology models. This type of analysis can be, of course, applied to any protein, and it may be particularly useful for the structural analysis of other membrane proteins. A detailed knowledge of the local structural changes related to ligand binding and how they are translated into larger-scale movements of transmembrane domains is key to understand receptor activation.
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Affiliation(s)
- Xavier Deupi
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland.
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Bécu JM, Pelé J, Rodien P, Abdi H, Chabbert M. Structural evolution of G-protein-coupled receptors: a sequence space approach. Methods Enzymol 2013; 520:49-66. [PMID: 23332695 DOI: 10.1016/b978-0-12-391861-1.00003-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Class A G-protein-coupled receptors (GPCRs) provide a fascinating example of evolutionary success. In this review, we discuss how metric multidimensional scaling (MDS), a multivariate analysis method, complements traditional tree-based phylogenetic methods and helps decipher the mechanisms that drove the evolution of class A GPCRs. MDS provides low-dimensional representations of a distance matrix. Applied to a multiple sequence alignment, MDS represents the sequences in a Euclidean space as points whose interdistances are as close as possible to the distances in the alignment (the so-called sequence space). We detail how to perform the MDS analysis of a multiple sequence alignment and how to analyze and interpret the resulting sequence space. We also show that the projection of supplementary data (a property of the MDS method) can be used to straightforwardly monitor the evolutionary drift of specific subfamilies. The sequence space of class A GPCRs reveals the key role of mutations at the level of the TM2 and TM5 proline residues in the evolution of class A GPCRs.
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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: 333] [Impact Index Per Article: 27.8] [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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15
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Abstract
GPCRs (G-protein-coupled receptors) are seven-transmembrane helix proteins that transduce exogenous and endogenous signals to modulate the activity of downstream effectors inside the cell. Despite the relevance of these proteins in human physiology and pharmaceutical research, we only recently started to understand the structural basis of their activation mechanism. In the period 2008-2011, nine active-like structures of GPCRs were solved. Among them, we have determined the structure of light-activated rhodopsin with all the features of the active metarhodopsin-II, which represents so far the most native-like model of an active GPCR. This structure, together with the structures of other inactive, intermediate and active states of rhodopsin constitutes a unique structural framework on which to understand the conserved aspects of the activation mechanism of GPCRs. This mechanism can be summarized as follows: retinal isomerization triggers a series of local structural changes in the binding site that are amplified into three intramolecular activation pathways through TM (transmembrane helix) 5/TM3, TM6 and TM7/TM2. Sequence analysis strongly suggests that these pathways are conserved in other GPCRs. Differential activation of these pathways by ligands could be translated into the stabilization of different active states of the receptor with specific signalling properties.
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Pelé J, Bécu JM, Abdi H, Chabbert M. Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling. BMC Bioinformatics 2012; 13:133. [PMID: 22702410 PMCID: PMC3403911 DOI: 10.1186/1471-2105-13-133] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 06/15/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The distance matrix computed from multiple alignments of homologous sequences is widely used by distance-based phylogenetic methods to provide information on the evolution of protein families. This matrix can also be visualized in a low dimensional space by metric multidimensional scaling (MDS). Applied to protein families, MDS provides information complementary to the information derived from tree-based methods. Moreover, MDS gives a unique opportunity to compare orthologous sequence sets because it can add supplementary elements to a reference space. RESULTS The R package bios2mds (from BIOlogical Sequences to MultiDimensional Scaling) has been designed to analyze multiple sequence alignments by MDS. Bios2mds starts with a sequence alignment, builds a matrix of distances between the aligned sequences, and represents this matrix by MDS to visualize a sequence space. This package also offers the possibility of performing K-means clustering in the MDS derived sequence space. Most importantly, bios2mds includes a function that projects supplementary elements (a.k.a. "out of sample" elements) onto the space defined by reference or "active" elements. Orthologous sequence sets can thus be compared in a straightforward way. The data analysis and visualization tools have been specifically designed for an easy monitoring of the evolutionary drift of protein sub-families. CONCLUSIONS The bios2mds package provides the tools for a complete integrated pipeline aimed at the MDS analysis of multiple sets of orthologous sequences in the R statistical environment. In addition, as the analysis can be carried out from user provided matrices, the projection function can be widely used on any kind of data.
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Affiliation(s)
- Julien Pelé
- CNRS UMR 6214 – INSERM 1083, Faculté de Médecine, 3 rue Haute de Reculée, Angers, 49045, France
| | - Jean-Michel Bécu
- CNRS UMR 6214 – INSERM 1083, Faculté de Médecine, 3 rue Haute de Reculée, Angers, 49045, France
| | - Hervé Abdi
- The University of Texas at Dallas, School of Behavioral and Brain Sciences, 800 West Campbell Road, Richardson, TX, 75080-3021, USA
| | - Marie Chabbert
- CNRS UMR 6214 – INSERM 1083, Faculté de Médecine, 3 rue Haute de Reculée, Angers, 49045, France
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Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 2011; 19:1108-26. [PMID: 21827947 DOI: 10.1016/j.str.2011.05.012] [Citation(s) in RCA: 228] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 05/24/2011] [Accepted: 05/28/2011] [Indexed: 12/19/2022]
Abstract
The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule antagonists and CXCR4 with a synthetic cyclopeptide. Thirty-five groups submitted their receptor-ligand complex structure predictions prior to the release of the crystallographic coordinates. With closely related homology modeling templates, as for dopamine D3 receptor, and with incorporation of biochemical and QSAR data, modern computational techniques predicted complex details with accuracy approaching experimental. In contrast, CXCR4 complexes that had less-characterized interactions and only distant homology to the known GPCR structures still remained very challenging. The assessment results provide guidance for modeling and crystallographic communities in method development and target selection for further expansion of the structural coverage of the GPCR universe.
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Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92039, USA
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Porter ML, Blasic JR, Bok MJ, Cameron EG, Pringle T, Cronin TW, Robinson PR. Shedding new light on opsin evolution. Proc Biol Sci 2011; 279:3-14. [PMID: 22012981 DOI: 10.1098/rspb.2011.1819] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function.
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Affiliation(s)
- Megan L Porter
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250, USA.
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Pelé J, Abdi H, Moreau M, Thybert D, Chabbert M. Multidimensional scaling reveals the main evolutionary pathways of class A G-protein-coupled receptors. PLoS One 2011; 6:e19094. [PMID: 21544207 PMCID: PMC3081337 DOI: 10.1371/journal.pone.0019094] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 03/16/2011] [Indexed: 11/21/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) constitute the largest family of transmembrane receptors in the human genome. Understanding the mechanisms which drove the evolution of such a large family would help understand the specificity of each GPCR sub-family with applications to drug design. To gain evolutionary information on class A GPCRs, we explored their sequence space by metric multidimensional scaling analysis (MDS). Three-dimensional mapping of human sequences shows a non-uniform distribution of GPCRs, organized in clusters that lay along four privileged directions. To interpret these directions, we projected supplementary sequences from different species onto the human space used as a reference. With this technique, we can easily monitor the evolutionary drift of several GPCR sub-families from cnidarians to humans. Results support a model of radiative evolution of class A GPCRs from a central node formed by peptide receptors. The privileged directions obtained from the MDS analysis are interpretable in terms of three main evolutionary pathways related to specific sequence determinants. The first pathway was initiated by a deletion in transmembrane helix 2 (TM2) and led to three sub-families by divergent evolution. The second pathway corresponds to the differentiation of the amine receptors. The third pathway corresponds to parallel evolution of several sub-families in relation with a covarion process involving proline residues in TM2 and TM5. As exemplified with GPCRs, the MDS projection technique is an important tool to compare orthologous sequence sets and to help decipher the mutational events that drove the evolution of protein families.
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Affiliation(s)
- Julien Pelé
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
| | - Hervé Abdi
- School of Behavioral and Brain Sciences, The University of Texas at Dallas, Richardson, Texas, United States of America
| | - Matthieu Moreau
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
| | - David Thybert
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
| | - Marie Chabbert
- CNRS UMR 6214 – INSERM 771, Faculté de Médecine, Angers, France
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Deflorian F, Jacobson KA. Comparison of three GPCR structural templates for modeling of the P2Y12 nucleotide receptor. J Comput Aided Mol Des 2011; 25:329-38. [PMID: 21461952 PMCID: PMC3157290 DOI: 10.1007/s10822-011-9423-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 03/20/2011] [Indexed: 11/26/2022]
Abstract
The P2Y(12) receptor (P2Y(12)R) is an ADP-activated G protein-coupled receptor (GPCR) that is an important target for antithrombotic drugs. Three homology models of P2Y(12)R were compared, based on different GPCR structural templates: bovine rhodopsin (bRHO), human A(2A) adenosine receptor (A(2A)AR), and human C-X-C chemokine receptor type 4 (CXCR4). By criteria of sequence analysis (25.6% identity in transmembrane region), deviation from helicity in the second transmembrane helix (TM2), docked poses of ligands highlighting the role of key residues, accessibility of a conserved disulfide bridge that is reactive toward irreversibly-binding antagonists, and the presence of a shared disulfide bridge between the third extracellular loop (EL3) and the N-terminus, the CXCR4-based model appeared to be the most consistent with known characteristics of P2Y(12)R. The docked poses of agonist 2MeSADP and charged anthraquinone antagonist PSB-0739 in the binding pocket of P2Y(12)R-CXC agree with previously published site-directed mutagenesis studies of Arg256 and Lys280. A sulfonate at position 2 of the anthraquinone core created a strong interaction with the Lys174(EL2) side chain. The docking poses of the irreversibly-binding, active metabolite (existing as two diastereoisomers in vivo) of the clinically utilized antagonist Clopidogrel were compared. The free thiol group of the 4S diastereoisomer, but not the 4R isomer, was found in close proximity (~4.7 Å) to the sulfur atom of a disulfide bridge involving Cys175, suggesting greater activity in covalent binding. Therefore, ligand docking to the CXCR4-based model of the P2Y(12)R predicted poses of both reversibly and irreversibly-binding small molecules, consistent with observed pharmacology and mutagenesis studies.
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MESH Headings
- Amino Acid Sequence
- Animals
- Binding Sites
- Cattle
- Humans
- Ligands
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleotides/chemistry
- Protein Structure, Secondary
- Receptor, Adenosine A2A/chemistry
- Receptors, CXCR4/chemistry
- Receptors, Purinergic P2Y12/chemistry
- Receptors, Purinergic P2Y12/genetics
- Receptors, Purinergic P2Y12/metabolism
- Rhodopsin/chemistry
- Sequence Homology, Nucleic Acid
- Structural Homology, Protein
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Affiliation(s)
- Francesca Deflorian
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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Rosenkilde MM, Benned-Jensen T, Frimurer TM, Schwartz TW. The minor binding pocket: a major player in 7TM receptor activation. Trends Pharmacol Sci 2010; 31:567-74. [PMID: 20870300 DOI: 10.1016/j.tips.2010.08.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 08/21/2010] [Accepted: 08/27/2010] [Indexed: 01/09/2023]
Abstract
From the deep part of the main ligand-binding crevice, a minor, often shallower pocket extends between the extracellular ends of transmembrane domains (TM)-I, II, III and VII of 7TM receptors. This minor binding pocket is defined by a highly conserved kink in TM-II that is induced by a proline residue located in one of two adjacent positions. Here we argue that this minor binding pocket is important for receptor activation. Functional coupling of the receptors seems to be mediated through the hydrogen bond network located between the intracellular segments of these TMs, with the allosteric interface between TM-II and TM-VII being of particular significance. Importantly, the minor binding pocket, especially the proline-kink in TM-II, is involved in G protein versus arrestin pathway-biased signaling, for example in the angiotensin AT1 system. Consequently, this pocket could be specifically targeted in the development of functionally biased drugs.
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Affiliation(s)
- Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Institute for Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark.
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Rey J, Deville J, Chabbert M. Structural determinants stabilizing helical distortions related to proline. J Struct Biol 2010; 171:266-76. [DOI: 10.1016/j.jsb.2010.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 04/29/2010] [Accepted: 05/02/2010] [Indexed: 10/19/2022]
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Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models. PLoS One 2009; 4:e7011. [PMID: 19756152 PMCID: PMC2738427 DOI: 10.1371/journal.pone.0007011] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 08/10/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Up until recently the only available experimental (high resolution) structure of a G-protein-coupled receptor (GPCR) was that of bovine rhodopsin. In the past few years the determination of GPCR structures has accelerated with three new receptors, as well as squid rhodopsin, being successfully crystallized. All share a common molecular architecture of seven transmembrane helices and can therefore serve as templates for building molecular models of homologous GPCRs. However, despite the common general architecture of these structures key differences do exist between them. The choice of which experimental GPCR structure(s) to use for building a comparative model of a particular GPCR is unclear and without detailed structural and sequence analyses, could be arbitrary. The aim of this study is therefore to perform a systematic and detailed analysis of sequence-structure relationships of known GPCR structures. METHODOLOGY We analyzed in detail conserved and unique sequence motifs and structural features in experimentally-determined GPCR structures. Deeper insight into specific and important structural features of GPCRs as well as valuable information for template selection has been gained. Using key features a workflow has been formulated for identifying the most appropriate template(s) for building homology models of GPCRs of unknown structure. This workflow was applied to a set of 14 human family A GPCRs suggesting for each the most appropriate template(s) for building a comparative molecular model. CONCLUSIONS The available crystal structures represent only a subset of all possible structural variation in family A GPCRs. Some GPCRs have structural features that are distributed over different crystal structures or which are not present in the templates suggesting that homology models should be built using multiple templates. This study provides a systematic analysis of GPCR crystal structures and a consistent method for identifying suitable templates for GPCR homology modelling that will help to produce more reliable three-dimensional models.
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