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Conformational states of the full-length glucagon receptor. Nat Commun 2015; 6:7859. [PMID: 26227798 PMCID: PMC4532856 DOI: 10.1038/ncomms8859] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 06/18/2015] [Indexed: 01/06/2023] Open
Abstract
Class B G protein-coupled receptors are composed of an extracellular domain (ECD) and a seven-transmembrane (7TM) domain, and their signalling is regulated by peptide hormones. Using a hybrid structural biology approach together with the ECD and 7TM domain crystal structures of the glucagon receptor (GCGR), we examine the relationship between full-length receptor conformation and peptide ligand binding. Molecular dynamics (MD) and disulfide crosslinking studies suggest that apo-GCGR can adopt both an open and closed conformation associated with extensive contacts between the ECD and 7TM domain. The electron microscopy (EM) map of the full-length GCGR shows how a monoclonal antibody stabilizes the ECD and 7TM domain in an elongated conformation. Hydrogen/deuterium exchange (HDX) studies and MD simulations indicate that an open conformation is also stabilized by peptide ligand binding. The combined studies reveal the open/closed states of GCGR and suggest that glucagon binds to GCGR by a conformational selection mechanism.
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52
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Roth S, Kholodenko BN, Smit MJ, Bruggeman FJ. G Protein-Coupled Receptor Signaling Networks from a Systems Perspective. Mol Pharmacol 2015; 88:604-16. [PMID: 26162865 DOI: 10.1124/mol.115.100057] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/10/2015] [Indexed: 12/20/2022] Open
Abstract
The signal-transduction network of a mammalian cell integrates internal and external cues to initiate adaptive responses. Among the cell-surface receptors are the G protein-coupled receptors (GPCRs), which have remarkable signal-integrating capabilities. Binding of extracellular signals stabilizes intracellular-domain conformations that selectively activate intracellular proteins. Hereby, multiple signaling routes are activated simultaneously to degrees that are signal-combination dependent. Systems-biology studies indicate that signaling networks have emergent processing capabilities that go far beyond those of single proteins. Such networks are spatiotemporally organized and capable of gradual, oscillatory, all-or-none, and subpopulation-generating responses. Protein-protein interactions, generating feedback and feedforward circuitry, are generally required for these spatiotemporal phenomena. Understanding of information processing by signaling networks therefore requires network theories in addition to biochemical and biophysical concepts. Here we review some of the key signaling systems behaviors that have been discovered recurrently across signaling networks. We emphasize the role of GPCRs, so far underappreciated receptors in systems-biology research.
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Affiliation(s)
- S Roth
- Systems Bioinformatics (S.R., F.J.B.) and Amsterdam Institute for Molecules, Medicines & Systems, VU University, Amsterdam, The Netherlands (M.J.S.); and Systems Biology Ireland, University College Dublin, Dublin, Ireland (B.N.K.)
| | - B N Kholodenko
- Systems Bioinformatics (S.R., F.J.B.) and Amsterdam Institute for Molecules, Medicines & Systems, VU University, Amsterdam, The Netherlands (M.J.S.); and Systems Biology Ireland, University College Dublin, Dublin, Ireland (B.N.K.)
| | - M J Smit
- Systems Bioinformatics (S.R., F.J.B.) and Amsterdam Institute for Molecules, Medicines & Systems, VU University, Amsterdam, The Netherlands (M.J.S.); and Systems Biology Ireland, University College Dublin, Dublin, Ireland (B.N.K.)
| | - F J Bruggeman
- Systems Bioinformatics (S.R., F.J.B.) and Amsterdam Institute for Molecules, Medicines & Systems, VU University, Amsterdam, The Netherlands (M.J.S.); and Systems Biology Ireland, University College Dublin, Dublin, Ireland (B.N.K.)
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Conformational thermostabilisation of corticotropin releasing factor receptor 1. Sci Rep 2015; 5:11954. [PMID: 26159865 PMCID: PMC4498186 DOI: 10.1038/srep11954] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/11/2015] [Indexed: 01/16/2023] Open
Abstract
Recent technical advances have greatly facilitated G-protein coupled receptors crystallography as evidenced by the number of successful x-ray structures that have been reported recently. These technical advances include novel detergents, specialised crystallography techniques as well as protein engineering solutions such as fusions and conformational thermostabilisation. Using conformational thermostabilisation, it is possible to generate variants of GPCRs that exhibit significantly increased stability in detergent micelles whilst preferentially occupying a single conformation. In this paper we describe for the first time the application of this technique to a member of a class B GPCR, the corticotropin releasing factor receptor 1 (CRF1R). Mutational screening in the presence of the inverse agonist, CP-376395, resulted in the identification of a construct with twelve point mutations that exhibited significantly increased thermal stability in a range of detergents. We further describe the subsequent construct engineering steps that eventually yielded a crystallisation-ready construct which recently led to the solution of the first x-ray structure of a class B receptor. Finally, we have used molecular dynamic simulation to provide structural insight into CRF1R instability as well as the stabilising effects of the mutants, which may be extended to other class B receptors considering the high degree of structural conservation.
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54
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Piscitelli CL, Kean J, de Graaf C, Deupi X. A Molecular Pharmacologist's Guide to G Protein-Coupled Receptor Crystallography. Mol Pharmacol 2015; 88:536-51. [PMID: 26152196 DOI: 10.1124/mol.115.099663] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/07/2015] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptor (GPCR) structural biology has progressed dramatically in the last decade. There are now over 120 GPCR crystal structures deposited in the Protein Data Bank of 32 different receptors from families scattered across the phylogenetic tree, including class B, C, and Frizzled GPCRs. These structures have been obtained in combination with a wide variety of ligands and captured in a range of conformational states. This surge in structural knowledge has enlightened research into the molecular recognition of biologically active molecules, the mechanisms of receptor activation, the dynamics of functional selectivity, and fueled structure-based drug design efforts for GPCRs. Here we summarize the innovations in both protein engineering/molecular biology and crystallography techniques that have led to these advances in GPCR structural biology and discuss how they may influence the resulting structural models. We also provide a brief molecular pharmacologist's guide to GPCR X-ray crystallography, outlining some key aspects in the process of structure determination, with the goal to encourage noncrystallographers to interrogate structures at the molecular level. Finally, we show how chemogenomics approaches can be used to marry the wealth of existing receptor pharmacology data with the expanding repertoire of structures, providing a deeper understanding of the mechanistic details of GPCR function.
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Affiliation(s)
- Chayne L Piscitelli
- Laboratory of Biomolecular Research, Department of Biology and Chemistry (C.L.P., X.D.), and Condensed Matter Theory Group, Department of Research with Neutrons and Muons (X.D.), Paul Scherrer Institute, Villigen, Switzerland; Heptares Therapeutics Ltd., Welwyn Garden City, United Kingdom (J.K.); and Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems, VU University of Amsterdam, Amsterdam, The Netherlands (C.G.)
| | - James Kean
- Laboratory of Biomolecular Research, Department of Biology and Chemistry (C.L.P., X.D.), and Condensed Matter Theory Group, Department of Research with Neutrons and Muons (X.D.), Paul Scherrer Institute, Villigen, Switzerland; Heptares Therapeutics Ltd., Welwyn Garden City, United Kingdom (J.K.); and Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems, VU University of Amsterdam, Amsterdam, The Netherlands (C.G.)
| | - Chris de Graaf
- Laboratory of Biomolecular Research, Department of Biology and Chemistry (C.L.P., X.D.), and Condensed Matter Theory Group, Department of Research with Neutrons and Muons (X.D.), Paul Scherrer Institute, Villigen, Switzerland; Heptares Therapeutics Ltd., Welwyn Garden City, United Kingdom (J.K.); and Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems, VU University of Amsterdam, Amsterdam, The Netherlands (C.G.)
| | - Xavier Deupi
- Laboratory of Biomolecular Research, Department of Biology and Chemistry (C.L.P., X.D.), and Condensed Matter Theory Group, Department of Research with Neutrons and Muons (X.D.), Paul Scherrer Institute, Villigen, Switzerland; Heptares Therapeutics Ltd., Welwyn Garden City, United Kingdom (J.K.); and Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems, VU University of Amsterdam, Amsterdam, The Netherlands (C.G.)
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Pachov DV, van den Bedem H. Nullspace Sampling with Holonomic Constraints Reveals Molecular Mechanisms of Protein Gαs. PLoS Comput Biol 2015; 11:e1004361. [PMID: 26218073 PMCID: PMC4517867 DOI: 10.1371/journal.pcbi.1004361] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 05/22/2015] [Indexed: 11/19/2022] Open
Abstract
Proteins perform their function or interact with partners by exchanging between conformational substates on a wide range of spatiotemporal scales. Structurally characterizing these exchanges is challenging, both experimentally and computationally. Large, diffusional motions are often on timescales that are difficult to access with molecular dynamics simulations, especially for large proteins and their complexes. The low frequency modes of normal mode analysis (NMA) report on molecular fluctuations associated with biological activity. However, NMA is limited to a second order expansion about a minimum of the potential energy function, which limits opportunities to observe diffusional motions. By contrast, kino-geometric conformational sampling (KGS) permits large perturbations while maintaining the exact geometry of explicit conformational constraints, such as hydrogen bonds. Here, we extend KGS and show that a conformational ensemble of the α subunit Gαs of heterotrimeric stimulatory protein Gs exhibits structural features implicated in its activation pathway. Activation of protein Gs by G protein-coupled receptors (GPCRs) is associated with GDP release and large conformational changes of its α-helical domain. Our method reveals a coupled α-helical domain opening motion while, simultaneously, Gαs helix α5 samples an activated conformation. These motions are moderated in the activated state. The motion centers on a dynamic hub near the nucleotide-binding site of Gαs, and radiates to helix α4. We find that comparative NMA-based ensembles underestimate the amplitudes of the motion. Additionally, the ensembles fall short in predicting the accepted direction of the full activation pathway. Taken together, our findings suggest that nullspace sampling with explicit, holonomic constraints yields ensembles that illuminate molecular mechanisms involved in GDP release and protein Gs activation, and further establish conformational coupling between key structural elements of Gαs.
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Affiliation(s)
- Dimitar V. Pachov
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Henry van den Bedem
- Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Stanford University, Stanford, California, United States of America
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Vaudry H, Leprince J, Chatenet D, Fournier A, Lambert DG, Le Mével JC, Ohlstein EH, Schwertani A, Tostivint H, Vaudry D. International Union of Basic and Clinical Pharmacology. XCII. Urotensin II, urotensin II-related peptide, and their receptor: from structure to function. Pharmacol Rev 2015; 67:214-58. [PMID: 25535277 DOI: 10.1124/pr.114.009480] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Urotensin II (UII) is a cyclic neuropeptide that was first isolated from the urophysis of teleost fish on the basis of its ability to contract the hindgut. Subsequently, UII was characterized in tetrapods including humans. Phylogenetic studies and synteny analysis indicate that UII and its paralogous peptide urotensin II-related peptide (URP) belong to the somatostatin/cortistatin superfamily. In mammals, the UII and URP genes are primarily expressed in cholinergic neurons of the brainstem and spinal cord. UII and URP mRNAs are also present in various organs notably in the cardiovascular, renal, and endocrine systems. UII and URP activate a common G protein-coupled receptor, called UT, that exhibits relatively high sequence identity with somatostatin, opioid, and galanin receptors. The UT gene is widely expressed in the central nervous system (CNS) and in peripheral tissues including the retina, heart, vascular bed, lung, kidney, adrenal medulla, and skeletal muscle. Structure-activity relationship studies and NMR conformational analysis have led to the rational design of a number of peptidic and nonpeptidic UT agonists and antagonists. Consistent with the wide distribution of UT, UII has now been shown to exert a large array of biologic activities, in particular in the CNS, the cardiovascular system, and the kidney. Here, we review the current knowledge concerning the pleiotropic actions of UII and discusses the possible use of antagonists for future therapeutic applications.
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Affiliation(s)
- Hubert Vaudry
- Institut National de la Santé et de la Recherche Médicale, U982, Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan, France (H.V., J.L., D.V.), University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.V.); Institut National de la Recherche Scientifique-Institut Armand Frappier, Laval, Québec, Canada (D.C., A.F.); International Associated Laboratory Samuel de Champlain, University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.C., A.F., D.V.); Department of Cardiovascular Sciences, Division of Anaesthesia, Critical Care and Pain Management, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, United Kingdom (D.G.L.); Institut National de la Santé et de la Recherche Médicale, U1101, Laboratoire de Traitement de l'Information Médicale, Laboratoire de Neurophysiologie, Université Européenne de Bretagne, Brest, France (J.-C.L.M.); AltheRx Pharmaceuticals, Malvern, Pennsylvania (E.H.O.); Division of Cardiology, Montreal General Hospital, McGill University Health Center, Montreal, Québec, Canada (A.S.); and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7221, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, Paris, France (H.T.)
| | - Jérôme Leprince
- Institut National de la Santé et de la Recherche Médicale, U982, Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan, France (H.V., J.L., D.V.), University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.V.); Institut National de la Recherche Scientifique-Institut Armand Frappier, Laval, Québec, Canada (D.C., A.F.); International Associated Laboratory Samuel de Champlain, University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.C., A.F., D.V.); Department of Cardiovascular Sciences, Division of Anaesthesia, Critical Care and Pain Management, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, United Kingdom (D.G.L.); Institut National de la Santé et de la Recherche Médicale, U1101, Laboratoire de Traitement de l'Information Médicale, Laboratoire de Neurophysiologie, Université Européenne de Bretagne, Brest, France (J.-C.L.M.); AltheRx Pharmaceuticals, Malvern, Pennsylvania (E.H.O.); Division of Cardiology, Montreal General Hospital, McGill University Health Center, Montreal, Québec, Canada (A.S.); and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7221, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, Paris, France (H.T.)
| | - David Chatenet
- Institut National de la Santé et de la Recherche Médicale, U982, Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan, France (H.V., J.L., D.V.), University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.V.); Institut National de la Recherche Scientifique-Institut Armand Frappier, Laval, Québec, Canada (D.C., A.F.); International Associated Laboratory Samuel de Champlain, University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.C., A.F., D.V.); Department of Cardiovascular Sciences, Division of Anaesthesia, Critical Care and Pain Management, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, United Kingdom (D.G.L.); Institut National de la Santé et de la Recherche Médicale, U1101, Laboratoire de Traitement de l'Information Médicale, Laboratoire de Neurophysiologie, Université Européenne de Bretagne, Brest, France (J.-C.L.M.); AltheRx Pharmaceuticals, Malvern, Pennsylvania (E.H.O.); Division of Cardiology, Montreal General Hospital, McGill University Health Center, Montreal, Québec, Canada (A.S.); and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7221, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, Paris, France (H.T.)
| | - Alain Fournier
- Institut National de la Santé et de la Recherche Médicale, U982, Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan, France (H.V., J.L., D.V.), University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.V.); Institut National de la Recherche Scientifique-Institut Armand Frappier, Laval, Québec, Canada (D.C., A.F.); International Associated Laboratory Samuel de Champlain, University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.C., A.F., D.V.); Department of Cardiovascular Sciences, Division of Anaesthesia, Critical Care and Pain Management, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, United Kingdom (D.G.L.); Institut National de la Santé et de la Recherche Médicale, U1101, Laboratoire de Traitement de l'Information Médicale, Laboratoire de Neurophysiologie, Université Européenne de Bretagne, Brest, France (J.-C.L.M.); AltheRx Pharmaceuticals, Malvern, Pennsylvania (E.H.O.); Division of Cardiology, Montreal General Hospital, McGill University Health Center, Montreal, Québec, Canada (A.S.); and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7221, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, Paris, France (H.T.)
| | - David G Lambert
- Institut National de la Santé et de la Recherche Médicale, U982, Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan, France (H.V., J.L., D.V.), University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.V.); Institut National de la Recherche Scientifique-Institut Armand Frappier, Laval, Québec, Canada (D.C., A.F.); International Associated Laboratory Samuel de Champlain, University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.C., A.F., D.V.); Department of Cardiovascular Sciences, Division of Anaesthesia, Critical Care and Pain Management, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, United Kingdom (D.G.L.); Institut National de la Santé et de la Recherche Médicale, U1101, Laboratoire de Traitement de l'Information Médicale, Laboratoire de Neurophysiologie, Université Européenne de Bretagne, Brest, France (J.-C.L.M.); AltheRx Pharmaceuticals, Malvern, Pennsylvania (E.H.O.); Division of Cardiology, Montreal General Hospital, McGill University Health Center, Montreal, Québec, Canada (A.S.); and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7221, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, Paris, France (H.T.)
| | - Jean-Claude Le Mével
- Institut National de la Santé et de la Recherche Médicale, U982, Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan, France (H.V., J.L., D.V.), University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.V.); Institut National de la Recherche Scientifique-Institut Armand Frappier, Laval, Québec, Canada (D.C., A.F.); International Associated Laboratory Samuel de Champlain, University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.C., A.F., D.V.); Department of Cardiovascular Sciences, Division of Anaesthesia, Critical Care and Pain Management, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, United Kingdom (D.G.L.); Institut National de la Santé et de la Recherche Médicale, U1101, Laboratoire de Traitement de l'Information Médicale, Laboratoire de Neurophysiologie, Université Européenne de Bretagne, Brest, France (J.-C.L.M.); AltheRx Pharmaceuticals, Malvern, Pennsylvania (E.H.O.); Division of Cardiology, Montreal General Hospital, McGill University Health Center, Montreal, Québec, Canada (A.S.); and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7221, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, Paris, France (H.T.)
| | - Eliot H Ohlstein
- Institut National de la Santé et de la Recherche Médicale, U982, Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan, France (H.V., J.L., D.V.), University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.V.); Institut National de la Recherche Scientifique-Institut Armand Frappier, Laval, Québec, Canada (D.C., A.F.); International Associated Laboratory Samuel de Champlain, University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.C., A.F., D.V.); Department of Cardiovascular Sciences, Division of Anaesthesia, Critical Care and Pain Management, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, United Kingdom (D.G.L.); Institut National de la Santé et de la Recherche Médicale, U1101, Laboratoire de Traitement de l'Information Médicale, Laboratoire de Neurophysiologie, Université Européenne de Bretagne, Brest, France (J.-C.L.M.); AltheRx Pharmaceuticals, Malvern, Pennsylvania (E.H.O.); Division of Cardiology, Montreal General Hospital, McGill University Health Center, Montreal, Québec, Canada (A.S.); and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7221, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, Paris, France (H.T.)
| | - Adel Schwertani
- Institut National de la Santé et de la Recherche Médicale, U982, Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan, France (H.V., J.L., D.V.), University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.V.); Institut National de la Recherche Scientifique-Institut Armand Frappier, Laval, Québec, Canada (D.C., A.F.); International Associated Laboratory Samuel de Champlain, University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.C., A.F., D.V.); Department of Cardiovascular Sciences, Division of Anaesthesia, Critical Care and Pain Management, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, United Kingdom (D.G.L.); Institut National de la Santé et de la Recherche Médicale, U1101, Laboratoire de Traitement de l'Information Médicale, Laboratoire de Neurophysiologie, Université Européenne de Bretagne, Brest, France (J.-C.L.M.); AltheRx Pharmaceuticals, Malvern, Pennsylvania (E.H.O.); Division of Cardiology, Montreal General Hospital, McGill University Health Center, Montreal, Québec, Canada (A.S.); and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7221, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, Paris, France (H.T.)
| | - Hervé Tostivint
- Institut National de la Santé et de la Recherche Médicale, U982, Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan, France (H.V., J.L., D.V.), University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.V.); Institut National de la Recherche Scientifique-Institut Armand Frappier, Laval, Québec, Canada (D.C., A.F.); International Associated Laboratory Samuel de Champlain, University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.C., A.F., D.V.); Department of Cardiovascular Sciences, Division of Anaesthesia, Critical Care and Pain Management, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, United Kingdom (D.G.L.); Institut National de la Santé et de la Recherche Médicale, U1101, Laboratoire de Traitement de l'Information Médicale, Laboratoire de Neurophysiologie, Université Européenne de Bretagne, Brest, France (J.-C.L.M.); AltheRx Pharmaceuticals, Malvern, Pennsylvania (E.H.O.); Division of Cardiology, Montreal General Hospital, McGill University Health Center, Montreal, Québec, Canada (A.S.); and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7221, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, Paris, France (H.T.)
| | - David Vaudry
- Institut National de la Santé et de la Recherche Médicale, U982, Institute for Research and Innovation in Biomedicine, Mont-Saint-Aignan, France (H.V., J.L., D.V.), University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.V.); Institut National de la Recherche Scientifique-Institut Armand Frappier, Laval, Québec, Canada (D.C., A.F.); International Associated Laboratory Samuel de Champlain, University of Rouen, Mont-Saint-Aignan, France (H.V., J.L., D.C., A.F., D.V.); Department of Cardiovascular Sciences, Division of Anaesthesia, Critical Care and Pain Management, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, United Kingdom (D.G.L.); Institut National de la Santé et de la Recherche Médicale, U1101, Laboratoire de Traitement de l'Information Médicale, Laboratoire de Neurophysiologie, Université Européenne de Bretagne, Brest, France (J.-C.L.M.); AltheRx Pharmaceuticals, Malvern, Pennsylvania (E.H.O.); Division of Cardiology, Montreal General Hospital, McGill University Health Center, Montreal, Québec, Canada (A.S.); and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7221, Evolution des Régulations Endocriniennes, Muséum National d'Histoire Naturelle, Paris, France (H.T.)
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Hisano Y, Inoue A, Taimatsu K, Ota S, Ohga R, Kotani H, Muraki M, Aoki J, Kawahara A. Comprehensive analysis of sphingosine-1-phosphate receptor mutants during zebrafish embryogenesis. Genes Cells 2015; 20:647-58. [PMID: 26094551 DOI: 10.1111/gtc.12259] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 05/11/2015] [Indexed: 12/19/2022]
Abstract
The lipid mediator sphingosine-1-phosphate (S1P) regulates various physiological and pathological phenomena such as angiogenesis and oncogenesis. Secreted S1P associates with the G-protein-coupled S1P receptors (S1PRs), leading to the activation of downstream signaling molecules. In mammals, five S1prs have been identified and the genetic disruption of a single S1pr1 gene causes vascular defects. In zebrafish, seven s1prs have been isolated. We found that individual s1prs showed unique expression patterns with some overlapping expression domains during early embryogenesis. We generated all s1pr single-mutant zebrafish by introducing premature stop codons in their coding regions using transcription activator-like effector nucleases and analyzed their phenotypes during early embryogenesis. Zygotic s1pr1, s1pr3a, s1pr3b, s1pr4, s1pr5a and s1pr5b mutants showed no developmental defects and grew into adults, whereas zygotic s1pr2 mutant showed embryonic lethality with a cardiac defect, showing quite distinct embryonic phenotypes for individual S1pr mutants between zebrafish and mouse. We further generated maternal-zygotic s1pr1, s1pr3a, s1pr3b, s1pr4, s1pr5a and s1pr5b mutants and found that these maternal-zygotic mutants also showed no obvious developmental defects, presumably suggesting the redundant functions of the S1P receptor-mediated signaling in zebrafish.
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Affiliation(s)
- Yu Hisano
- Laboratory for Developmental Gene Regulation, Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Laboratory for Cardiovascular Molecular Dynamics, Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0074, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-8613, Japan
| | - Kiyohito Taimatsu
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Satoshi Ota
- Laboratory for Cardiovascular Molecular Dynamics, Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0074, Japan.,Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Rie Ohga
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Hirohito Kotani
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
| | - Michiko Muraki
- Laboratory for Cardiovascular Molecular Dynamics, Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0074, Japan
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,CREST, Japan Science and Technology Agency, Kawaguchi, 332-8613, Japan
| | - Atsuo Kawahara
- Laboratory for Cardiovascular Molecular Dynamics, Quantitative Biology Center, RIKEN, 6-2-3 Furuedai, Suita, Osaka, 565-0074, Japan.,Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, 1110 Shimokato, Chuo, Yamanashi, 409-3898, Japan
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58
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Duc NM, Kim HR, Chung KY. Structural mechanism of G protein activation by G protein-coupled receptor. Eur J Pharmacol 2015; 763:214-22. [PMID: 25981300 DOI: 10.1016/j.ejphar.2015.05.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/03/2015] [Accepted: 05/11/2015] [Indexed: 12/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are a family of membrane receptors that regulate physiology and pathology of various organs. Consequently, about 40% of drugs in the market targets GPCRs. Heterotrimeric G proteins are composed of α, β, and γ subunits, and act as the key downstream signaling molecules of GPCRs. The structural mechanism of G protein activation by GPCRs has been of a great interest, and a number of biochemical and biophysical studies have been performed since the late 80's. These studies investigated the interface between GPCR and G proteins and the structural mechanism of GPCR-induced G protein activation. Recently, arrestins are also reported to be important molecular switches in GPCR-mediated signal transduction, and the physiological output of arrestin-mediated signal transduction is different from that of G protein-mediated signal transduction. Understanding the structural mechanism of the activation of G proteins and arrestins would provide fundamental information for the downstream signaling-selective GPCR-targeting drug development. This review will discuss the structural mechanism of GPCR-induced G protein activation by comparing previous biochemical and biophysical studies.
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Affiliation(s)
- Nguyen Minh Duc
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 440-746, Republic of Korea
| | - Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 440-746, Republic of Korea
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 440-746, Republic of Korea.
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59
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Shang Y, Filizola M. Opioid receptors: Structural and mechanistic insights into pharmacology and signaling. Eur J Pharmacol 2015; 763:206-13. [PMID: 25981301 DOI: 10.1016/j.ejphar.2015.05.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 03/02/2015] [Accepted: 05/11/2015] [Indexed: 01/18/2023]
Abstract
Opioid receptors are important drug targets for pain management, addiction, and mood disorders. Although substantial research on these important subtypes of G protein-coupled receptors has been conducted over the past two decades to discover ligands with higher specificity and diminished side effects, currently used opioid therapeutics remain suboptimal. Luckily, recent advances in structural biology of opioid receptors provide unprecedented insights into opioid receptor pharmacology and signaling. We review here a few recent studies that have used the crystal structures of opioid receptors as a basis for revealing mechanistic details of signal transduction mediated by these receptors, and for the purpose of drug discovery.
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Affiliation(s)
- Yi Shang
- Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology, One Gustave, L. Levy Place, Box 1677, New York, NY 10029, USA
| | - Marta Filizola
- Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology, One Gustave, L. Levy Place, Box 1677, New York, NY 10029, USA.
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60
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Dalton JAR, Lans I, Giraldo J. Quantifying conformational changes in GPCRs: glimpse of a common functional mechanism. BMC Bioinformatics 2015; 16:124. [PMID: 25902715 PMCID: PMC4422131 DOI: 10.1186/s12859-015-0567-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/09/2015] [Indexed: 12/12/2022] Open
Abstract
Background G-protein-coupled receptors (GPCRs) are important drug targets and a better understanding of their molecular mechanisms would be desirable. The crystallization rate of GPCRs has accelerated in recent years as techniques have become more sophisticated, particularly with respect to Class A GPCRs interacting with G-proteins. These developments have made it possible for a quantitative analysis of GPCR geometrical features and binding-site conformations, including a statistical comparison between Class A GPCRs in active (agonist-bound) and inactive (antagonist-bound) states. Results Here we implement algorithms for the analysis of interhelical angles, distances, interactions and binding-site volumes in the transmembrane domains of 25 Class A GPCRs (7 active and 18 inactive). Two interhelical angles change in a statistically significant way between average inactive and active states: TM3-TM6 (by -9°) and TM6-TM7 (by +12°). A third interhelical angle: TM5-TM6 shows a trend, changing by -9°. In the transition from inactive to active states, average van der Waals interactions between TM3 and TM7 significantly increase as the average distance between them decreases by >2 Å. Average H-bonding between TM3 and TM6 decreases but is seemingly compensated by an increase in H-bonding between TM5 and TM6. In five Class A GPCRs, crystallized in both active and inactive states, increased H-bonding of agonists to TM6 and TM7, relative to antagonists, is observed. These protein-agonist interactions likely favour a change in the TM6-TM7 angle, which creates a narrowing in the binding pocket of activated receptors and an average ~200 Å3 reduction in volume. Conclusions In terms of similar conformational changes and agonist binding pattern, Class A GPCRs appear to share a common mechanism of activation, which can be exploited in future drug development. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0567-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James A R Dalton
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Isaias Lans
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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61
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Bacterial chemoreceptor dynamics correlate with activity state and are coupled over long distances. Proc Natl Acad Sci U S A 2015; 112:2455-60. [PMID: 25675479 DOI: 10.1073/pnas.1414155112] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Dynamics are hypothesized to play an important role in the transmission of signals across membranes by receptors. Bacterial chemoreceptors are long helical proteins that consist of a periplasmic ligand-binding domain; a transmembrane region; a cytoplasmic HAMP (histidine kinase, adenylyl cyclases, methyl-accepting chemotaxis proteins, and phosphatases) domain; and a kinase-control module (KCM). The KCM is further composed of adaptation, hinge, and protein interaction regions (PIRs), the latter of which binds the histidine kinase CheA and adaptor CheW. Fusions of the Escherichia coli aspartate receptor KCM to HAMP domains of defined structure (H1-Tar vs. H1-2-Tar) give opposite responses in phosphotransfer and cellular assays, despite similar binding to CheA and CheW. Pulsed dipolar ESR spectroscopy (PDS) of these isolated on and off dimeric effectors reveals that, in the kinase-on state, the HAMP is more conformationally destabilized compared with the PIR, whereas in the kinase-off state, the HAMP is more compact, and the PIR samples a greater breadth of conformations. On and off HAMP states produce different conformational effects at the KCM junction, but these differences decrease through the adaptation region and into the hinge only to return with the inverted relationship in the PIR. Continuous wave-ESR of the spin-labeled proteins confirms that broader PDS distance distributions correlate with increased rates of dynamics. Conformational breadth in the adaptation region changes with charge alterations caused by modification enzymes. Activating modifications broaden the HAMP conformational ensemble but correspondingly, compact the PIR. Thus, chemoreceptors behave as coupled units, in which dynamics in regions proximal and distal to the membrane change coherently but with opposite sign.
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62
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Gorbunov EA, Ertuzun IA, Kachaeva EV, Tarasov SA, Epstein OI. In vitro screening of major neurotransmitter systems possibly involved in the mechanism of action of antibodies to S100 protein in released-active form. Neuropsychiatr Dis Treat 2015; 11:2837-46. [PMID: 26604768 PMCID: PMC4639559 DOI: 10.2147/ndt.s92456] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Experimentally and clinically, it was shown that released-active form of antibodies to S100 protein (RAF of Abs to S100) exerts a wide range of pharmacological activities: anxiolytic, antiasthenic, antiaggressive, stress-protective, antihypoxic, antiischemic, neuroprotective, and nootropic. The purpose of this study was to determine the influence of RAF of Abs to S100 on major neurotransmitter systems (serotoninergic, GABAergic, dopaminergic, and on sigma receptors as well) which are possibly involved in its mechanism of pharmacological activity. Radioligand binding assays were used for assessment of the drug influence on ligand-receptor interaction. [(35)S]GTPγS binding assay, cyclic adenosine monophosphate HTRF™, cellular dielectric spectroscopy assays, and assays based on measurement of intracellular concentration of Ca(2+) ions were used for assessment of agonist or antagonist properties of the drug toward receptors. RAF of Abs to S100 increased radioligand binding to 5-HT1F, 5-HT2B, 5-HT2Cedited, 5-HT3, and to D3 receptors by 142.0%, 131.9%, 149.3%, 120.7%, and 126.3%, respectively. Also, the drug significantly inhibited specific binding of radioligands to GABAB1A/B2 receptors by 25.8%, and to both native and recombinant human sigma1 receptors by 75.3% and 40.32%, respectively. In the functional assays, it was shown that the drug exerted antagonism at 5-HT1B, D3, and GABAB1A/B2 receptors inhibiting agonist-induced responses by 23.24%, 32.76%, and 30.2%, respectively. On the contrary, the drug exerted an agonist effect at 5-HT1A receptors enhancing receptor functional activity by 28.0%. The pharmacological profiling of RAF of Abs to S100 among 27 receptor provides evidence for drug-related modification of major neurotransmitter systems.
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Affiliation(s)
| | - Irina A Ertuzun
- OOO "NPF "MATERIA MEDICA HOLDING", Moscow, Russian Federation
| | | | | | - Oleg I Epstein
- OOO "NPF "MATERIA MEDICA HOLDING", Moscow, Russian Federation
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63
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Tautermann CS, Seeliger D, Kriegl JM. What can we learn from molecular dynamics simulations for GPCR drug design? Comput Struct Biotechnol J 2014; 13:111-21. [PMID: 25709761 PMCID: PMC4334948 DOI: 10.1016/j.csbj.2014.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/28/2014] [Accepted: 12/03/2014] [Indexed: 01/05/2023] Open
Abstract
Recent years have seen a tremendous progress in the elucidation of experimental structural information for G-protein coupled receptors (GPCRs). Although for the vast majority of pharmaceutically relevant GPCRs structural information is still accessible only by homology models the steadily increasing amount of structural information fosters the application of structure-based drug design tools for this important class of drug targets. In this article we focus on the application of molecular dynamics (MD) simulations in GPCR drug discovery programs. Typical application scenarios of MD simulations and their scope and limitations will be described on the basis of two selected case studies, namely the binding of small molecule antagonists to the human CC chemokine receptor 3 (CCR3) and a detailed investigation of the interplay between receptor dynamics and solvation for the binding of small molecules to the human muscarinic acetylcholine receptor 3 (hM3R).
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Affiliation(s)
| | | | - Jan M. Kriegl
- Boehringer Ingelheim Pharma GmbH & Co. KG, Lead Identification and Optimization Support, Birkendorfer Str. 65, D-88397 Biberach a.d. Riss, Germany
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64
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Perez-Aguilar JM, Shan J, LeVine M, Khelashvili G, Weinstein H. A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2. J Am Chem Soc 2014; 136:16044-54. [PMID: 25314362 PMCID: PMC4235374 DOI: 10.1021/ja508394x] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Indexed: 01/16/2023]
Abstract
With recent progress in determination of G protein-coupled receptor (GPCR) structure with crystallography, a variety of other experimental approaches (e.g., NMR spectroscopy, fluorescent-based assays, mass spectrometry techniques) are also being used to characterize state-specific and ligand-specific conformational states. MD simulations offer a powerful complementary approach to elucidate the dynamic features associated with ligand-specific GPCR conformations. To shed light on the conformational elements and dynamics of the important aspect of GPCR functional selectivity, we carried out unbiased microsecond-length MD simulations of the human serotonin 2A receptor (5-HT(2A)R) in the absence of ligand and bound to four distinct serotonergic agonists. The 5-HT(2A)R is a suitable system to study the structural features involved in the ligand-dependent conformational heterogeneity of GPCRs because it is well-characterized experimentally and exhibits a strong agonist-specific phenotype in that some 5-HT(2A)R agonists induce LSD-like hallucinations, while others lack this psychoactive property entirely. Here we report evidence for structural and dynamic differences in 5-HT(2A)R interacting with such pharmacologically distinct ligands, hallucinogens, and nonhallucinogens obtained from all-atom MD simulations. Differential ligand binding contacts were identified for structurally similar hallucinogens and nonhallucinogens and found to correspond to different conformations in the intracellular loop 2 (ICL2). From the different ICL2 conformations, functional selective phenotypes are suggested through effects on dimerization and/or distinct direct interaction with effector proteins. The findings are presented in the context of currently proposed hallucinogenesis mechanisms, and ICL2 is proposed as a fine-tuning selective switch that can differentiates modes of 5-HT(2A)R activation.
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Affiliation(s)
- Jose Manuel Perez-Aguilar
- Department
of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal
Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Jufang Shan
- Department
of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal
Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Michael
V. LeVine
- Department
of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal
Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - George Khelashvili
- Department
of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal
Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Harel Weinstein
- Department
of Physiology and Biophysics and The HRH Prince Alwaleed Bin Talal
Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York 10065, United States
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65
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Palczewski K. Chemistry and biology of the initial steps in vision: the Friedenwald lecture. Invest Ophthalmol Vis Sci 2014; 55:6651-72. [PMID: 25338686 DOI: 10.1167/iovs.14-15502] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Visual transduction is the process in the eye whereby absorption of light in the retina is translated into electrical signals that ultimately reach the brain. The first challenge presented by visual transduction is to understand its molecular basis. We know that maintenance of vision is a continuous process requiring the activation and subsequent restoration of a vitamin A-derived chromophore through a series of chemical reactions catalyzed by enzymes in the retina and retinal pigment epithelium (RPE). Diverse biochemical approaches that identified key proteins and reactions were essential to achieve a mechanistic understanding of these visual processes. The three-dimensional arrangements of these enzymes' polypeptide chains provide invaluable insights into their mechanisms of action. A wealth of information has already been obtained by solving high-resolution crystal structures of both rhodopsin and the retinoid isomerase from pigment RPE (RPE65). Rhodopsin, which is activated by photoisomerization of its 11-cis-retinylidene chromophore, is a prototypical member of a large family of membrane-bound proteins called G protein-coupled receptors (GPCRs). RPE65 is a retinoid isomerase critical for regeneration of the chromophore. Electron microscopy (EM) and atomic force microscopy have provided insights into how certain proteins are assembled to form much larger structures such as rod photoreceptor cell outer segment membranes. A second challenge of visual transduction is to use this knowledge to devise therapeutic approaches that can prevent or reverse conditions leading to blindness. Imaging modalities like optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO) applied to appropriate animal models as well as human retinal imaging have been employed to characterize blinding diseases, monitor their progression, and evaluate the success of therapeutic agents. Lately two-photon (2-PO) imaging, together with biochemical assays, are revealing functional aspects of vision at a new molecular level. These multidisciplinary approaches combined with suitable animal models and inbred mutant species can be especially helpful in translating provocative cell and tissue culture findings into therapeutic options for further development in animals and eventually in humans. A host of different approaches and techniques is required for substantial progress in understanding fundamental properties of the visual system.
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Affiliation(s)
- Krzysztof Palczewski
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, United States
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66
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Martí-Solano M, Sanz F, Pastor M, Selent J. A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity. PLoS One 2014; 9:e109312. [PMID: 25313636 PMCID: PMC4196896 DOI: 10.1371/journal.pone.0109312] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 09/02/2014] [Indexed: 11/19/2022] Open
Abstract
Functional selectivity is a property of G protein-coupled receptors that allows them to preferentially couple to particular signaling partners upon binding of biased agonists. Publication of the X-ray crystal structure of serotonergic 5-HT1B and 5-HT2B receptors in complex with ergotamine, a drug capable of activating G protein coupling and β-arrestin signaling at the 5-HT1B receptor but clearly favoring β-arrestin over G protein coupling at the 5-HT2B subtype, has recently provided structural insight into this phenomenon. In particular, these structures highlight the importance of specific residues, also called micro-switches, for differential receptor activation. In our work, we apply classical molecular dynamics simulations and enhanced sampling approaches to analyze the behavior of these micro-switches and their impact on the stabilization of particular receptor conformational states. Our analysis shows that differences in the conformational freedom of helix 6 between both receptors could explain their different G protein-coupling capacity. In particular, as compared to the 5-HT1B receptor, helix 6 movement in the 5-HT2B receptor can be constrained by two different mechanisms. On the one hand, an anchoring effect of ergotamine, which shows an increased capacity to interact with the extracellular part of helices 5 and 6 and stabilize them, hinders activation of a hydrophobic connector region at the center of the receptor. On the other hand, this connector region in an inactive conformation is further stabilized by unconserved contacts extending to the intracellular part of the 5-HT2B receptor, which hamper opening of the G protein binding site. This work highlights the importance of considering receptor capacity to adopt different conformational states from a dynamic perspective in order to underpin the structural basis of functional selectivity.
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MESH Headings
- Binding Sites
- Databases, Protein
- Ergotamine/chemistry
- Ergotamine/metabolism
- Hydrophobic and Hydrophilic Interactions
- Molecular Dynamics Simulation
- Protein Stability
- Protein Structure, Tertiary
- Receptor, Serotonin, 5-HT1B/chemistry
- Receptor, Serotonin, 5-HT1B/metabolism
- Receptor, Serotonin, 5-HT2B/chemistry
- Receptor, Serotonin, 5-HT2B/metabolism
- Serotonin Receptor Agonists/chemistry
- Serotonin Receptor Agonists/metabolism
- Thermodynamics
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Affiliation(s)
- Maria Martí-Solano
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Ferran Sanz
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Manuel Pastor
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
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67
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Roth S, Bruggeman FJ. A conformation-equilibrium model captures ligand-ligand interactions and ligand-biased signalling by G-protein coupled receptors. FEBS J 2014; 281:4659-71. [DOI: 10.1111/febs.12970] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 07/07/2014] [Accepted: 08/11/2014] [Indexed: 12/31/2022]
Affiliation(s)
- Susanne Roth
- Systems Bioinformatics; VU University; Amsterdam The Netherlands
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68
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Shang Y, LeRouzic V, Schneider S, Bisignano P, Pasternak G, Filizola M. Mechanistic insights into the allosteric modulation of opioid receptors by sodium ions. Biochemistry 2014; 53:5140-9. [PMID: 25073009 PMCID: PMC4131901 DOI: 10.1021/bi5006915] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/21/2014] [Indexed: 01/09/2023]
Abstract
The idea of sodium ions altering G-protein-coupled receptor (GPCR) ligand binding and signaling was first suggested for opioid receptors (ORs) in the 1970s and subsequently extended to other GPCRs. Recently published ultra-high-resolution crystal structures of GPCRs, including that of the δ-OR subtype, have started to shed light on the mechanism underlying sodium control in GPCR signaling by revealing details of the sodium binding site. Whether sodium accesses different receptor subtypes from the extra- or intracellular sides, following similar or different pathways, is still an open question. Earlier experiments in brain homogenates suggested a differential sodium regulation of ligand binding to the three major OR subtypes, in spite of their high degree of sequence similarity. Intrigued by this possibility, we explored the dynamic nature of sodium binding to δ-OR, μ-OR, and κ-OR by means of microsecond-scale, all-atom molecular dynamics (MD) simulations. Rapid sodium permeation was observed exclusively from the extracellular milieu, and following similar binding pathways in all three ligand-free OR systems, notwithstanding extra densities of sodium observed near nonconserved residues of κ-OR and δ-OR, but not in μ-OR. We speculate that these differences may be responsible for the differential increase in antagonist binding affinity of μ-OR by sodium resulting from specific ligand binding experiments in transfected cells. On the other hand, sodium reduced the level of binding of subtype-specific agonists to all OR subtypes. Additional biased and unbiased MD simulations were conducted using the δ-OR ultra-high-resolution crystal structure as a model system to provide a mechanistic explanation for this experimental observation.
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MESH Headings
- Animals
- Binding Sites
- Crystallography, X-Ray
- Humans
- Ligands
- Mice
- Models, Molecular
- Molecular Dynamics Simulation
- Protein Conformation
- Radioligand Assay
- Receptors, Opioid/chemistry
- Receptors, Opioid/metabolism
- Receptors, Opioid, delta/antagonists & inhibitors
- Receptors, Opioid, delta/chemistry
- Receptors, Opioid, delta/metabolism
- Receptors, Opioid, kappa/chemistry
- Receptors, Opioid, kappa/metabolism
- Receptors, Opioid, mu/chemistry
- Receptors, Opioid, mu/metabolism
- Sodium/metabolism
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Affiliation(s)
- Yi Shang
- Department
of Structural and Chemical Biology, Icahn
School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Valerie LeRouzic
- Molecular
Pharmacology and Chemistry Program, Memorial
Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - Sebastian Schneider
- Department
of Structural and Chemical Biology, Icahn
School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Paola Bisignano
- Department
of Structural and Chemical Biology, Icahn
School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Gavril
W. Pasternak
- Molecular
Pharmacology and Chemistry Program, Memorial
Sloan-Kettering Cancer Center, New York, New York 10065, United States
| | - Marta Filizola
- Department
of Structural and Chemical Biology, Icahn
School of Medicine at Mount Sinai, New York, New York 10029, United States
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69
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70
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Maeda S, Sun D, Singhal A, Foggetta M, Schmid G, Standfuss J, Hennig M, Dawson RJP, Veprintsev DB, Schertler GFX. Crystallization scale preparation of a stable GPCR signaling complex between constitutively active rhodopsin and G-protein. PLoS One 2014; 9:e98714. [PMID: 24979345 PMCID: PMC4076187 DOI: 10.1371/journal.pone.0098714] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/07/2014] [Indexed: 11/29/2022] Open
Abstract
The activation of the G-protein transducin (Gt) by rhodopsin (Rho) has been intensively studied for several decades. It is the best understood example of GPCR activation mechanism and serves as a template for other GPCRs. The structure of the Rho/G protein complex, which is transiently formed during the signaling reaction, is of particular interest. It can help understanding the molecular details of how retinal isomerization leads to the G protein activation, as well as shed some light on how GPCR recognizes its cognate G protein. The native Rho/Gt complex isolated from bovine retina suffers from low stability and loss of the retinal ligand. Recently, we reported that constitutively active mutant of rhodopsin E113Q forms a Rho/Gt complex that is stable in detergent solution. Here, we introduce methods for a large scale preparation of the complex formed by the thermo-stabilized and constitutively active rhodopsin mutant N2C/M257Y/D282C(RhoM257Y) and the native Gt purified from bovine retinas. We demonstrate that the light-activated rhodopsin in this complex contains a covalently bound unprotonated retinal and therefore corresponds to the active metarhodopin II state; that the isolated complex is active and dissociates upon addition of GTPγS; and that the stoichiometry corresponds to a 1∶1 molar ratio of rhodopsin to the heterotrimeric G-protein. And finally, we show that the rhodopsin also forms stable complex with Gi. This complex has significantly higher thermostability than RhoM257Y/Gt complex and is resistant to a variety of detergents. Overall, our data suggest that the RhoM257Y/Gi complex is an ideal target for future structural and mechanistic studies of signaling in the visual system.
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Affiliation(s)
- Shoji Maeda
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Dawei Sun
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ankita Singhal
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Marcello Foggetta
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Georg Schmid
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Joerg Standfuss
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Michael Hennig
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Roger J. P. Dawson
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Dmitry B. Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
- * E-mail: (DBV); (GFXS)
| | - Gebhard F. X. Schertler
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen, Switzerland and Department of Biology, ETH Zurich, Zurich, Switzerland
- * E-mail: (DBV); (GFXS)
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71
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Janero DR. The future of drug discovery: enabling technologies for enhancing lead characterization and profiling therapeutic potential. Expert Opin Drug Discov 2014; 9:847-58. [PMID: 24965547 DOI: 10.1517/17460441.2014.925876] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Technology often serves as a handmaiden and catalyst of invention. The discovery of safe, effective medications depends critically upon experimental approaches capable of providing high-impact information on the biological effects of drug candidates early in the discovery pipeline. This information can enable reliable lead identification, pharmacological compound differentiation and successful translation of research output into clinically useful therapeutics. The shallow preclinical profiling of candidate compounds promulgates a minimalistic understanding of their biological effects and undermines the level of value creation necessary for finding quality leads worth moving forward within the development pipeline with efficiency and prognostic reliability sufficient to help remediate the current pharma-industry productivity drought. Three specific technologies discussed herein, in addition to experimental areas intimately associated with contemporary drug discovery, appear to hold particular promise for strengthening the preclinical valuation of drug candidates by deepening lead characterization. These are: i) hydrogen-deuterium exchange mass spectrometry for characterizing structural and ligand-interaction dynamics of disease-relevant proteins; ii) activity-based chemoproteomics for profiling the functional diversity of mammalian proteomes; and iii) nuclease-mediated precision gene editing for developing more translatable cellular and in vivo models of human diseases. When applied in an informed manner congruent with the clinical understanding of disease processes, technologies such as these that span levels of biological organization can serve as valuable enablers of drug discovery and potentially contribute to reducing the current, unacceptably high rates of compound clinical failure.
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Affiliation(s)
- David R Janero
- Northeastern University, Bouvé College of Health Sciences, Center for Drug Discovery, Department of Pharmaceutical Sciences, Health Sciences Entrepreneurs , 360 Huntington Avenue, 116 Mugar Life Sciences Hall, Boston, MA 02115-5000 , USA +1 617 373 2208 ; +1 617 373 7493 ;
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72
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Kling RC, Tschammer N, Lanig H, Clark T, Gmeiner P. Active-state model of a dopamine D2 receptor-Gαi complex stabilized by aripiprazole-type partial agonists. PLoS One 2014; 9:e100069. [PMID: 24932547 PMCID: PMC4059746 DOI: 10.1371/journal.pone.0100069] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/20/2014] [Indexed: 11/18/2022] Open
Abstract
Partial agonists exhibit a submaximal capacity to enhance the coupling of one receptor to an intracellular binding partner. Although a multitude of studies have reported different ligand-specific conformations for a given receptor, little is known about the mechanism by which different receptor conformations are connected to the capacity to activate the coupling to G-proteins. We have now performed molecular-dynamics simulations employing our recently described active-state homology model of the dopamine D2 receptor-Gαi protein-complex coupled to the partial agonists aripiprazole and FAUC350, in order to understand the structural determinants of partial agonism better. We have compared our findings with our model of the D2R-Gαi-complex in the presence of the full agonist dopamine. The two partial agonists are capable of inducing different conformations of important structural motifs, including the extracellular loop regions, the binding pocket and, in particular, intracellular G-protein-binding domains. As G-protein-coupling to certain intracellular epitopes of the receptor is considered the key step of allosterically triggered nucleotide-exchange, it is tempting to assume that impaired coupling between the receptor and the G-protein caused by distinct ligand-specific conformations is a major determinant of partial agonist efficacy.
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Affiliation(s)
- Ralf C. Kling
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Erlangen, Germany
- Department of Chemistry and Pharmacy, Computer Chemistry Center, Friedrich Alexander University, Erlangen, Germany
| | - Nuska Tschammer
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Erlangen, Germany
| | - Harald Lanig
- Department of Chemistry and Pharmacy, Computer Chemistry Center, Friedrich Alexander University, Erlangen, Germany
- Central Institute for Scientific Computing, Friedrich Alexander University, Erlangen, Germany
| | - Timothy Clark
- Department of Chemistry and Pharmacy, Computer Chemistry Center, Friedrich Alexander University, Erlangen, Germany
- Centre for Molecular Design, University of Portsmouth, King Henry Building, Portsmouth, United Kingdom
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Erlangen, Germany
- * E-mail:
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73
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Mnpotra JS, Qiao Z, Cai J, Lynch DL, Grossfield A, Leioatts N, Hurst DP, Pitman MC, Song ZH, Reggio PH. Structural basis of G protein-coupled receptor-Gi protein interaction: formation of the cannabinoid CB2 receptor-Gi protein complex. J Biol Chem 2014; 289:20259-72. [PMID: 24855641 DOI: 10.1074/jbc.m113.539916] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In this study, we applied a comprehensive G protein-coupled receptor-Gαi protein chemical cross-linking strategy to map the cannabinoid receptor subtype 2 (CB2)-Gαi interface and then used molecular dynamics simulations to explore the dynamics of complex formation. Three cross-link sites were identified using LC-MS/MS and electrospray ionization-MS/MS as follows: 1) a sulfhydryl cross-link between C3.53(134) in TMH3 and the Gαi C-terminal i-3 residue Cys-351; 2) a lysine cross-link between K6.35(245) in TMH6 and the Gαi C-terminal i-5 residue, Lys-349; and 3) a lysine cross-link between K5.64(215) in TMH5 and the Gαi α4β6 loop residue, Lys-317. To investigate the dynamics and nature of the conformational changes involved in CB2·Gi complex formation, we carried out microsecond-time scale molecular dynamics simulations of the CB2 R*·Gαi1β1γ2 complex embedded in a 1-palmitoyl-2-oleoyl-phosphatidylcholine bilayer, using cross-linking information as validation. Our results show that although molecular dynamics simulations started with the G protein orientation in the β2-AR*·Gαsβ1γ2 complex crystal structure, the Gαi1β1γ2 protein reoriented itself within 300 ns. Two major changes occurred as follows. 1) The Gαi1 α5 helix tilt changed due to the outward movement of TMH5 in CB2 R*. 2) A 25° clockwise rotation of Gαi1β1γ2 underneath CB2 R* occurred, with rotation ceasing when Pro-139 (IC-2 loop) anchors in a hydrophobic pocket on Gαi1 (Val-34, Leu-194, Phe-196, Phe-336, Thr-340, Ile-343, and Ile-344). In this complex, all three experimentally identified cross-links can occur. These findings should be relevant for other class A G protein-coupled receptors that couple to Gi proteins.
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Affiliation(s)
- Jagjeet S Mnpotra
- From the Department of Chemistry and Biochemistry, University of North Carolina, Greensboro, North Carolina 27402
| | - Zhuanhong Qiao
- the Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky 40292
| | - Jian Cai
- the Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky 40292
| | - Diane L Lynch
- From the Department of Chemistry and Biochemistry, University of North Carolina, Greensboro, North Carolina 27402
| | - Alan Grossfield
- the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Nicholas Leioatts
- the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Dow P Hurst
- From the Department of Chemistry and Biochemistry, University of North Carolina, Greensboro, North Carolina 27402
| | - Michael C Pitman
- From the Department of Chemistry and Biochemistry, University of North Carolina, Greensboro, North Carolina 27402, the Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598
| | - Zhao-Hui Song
- the Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky 40292,
| | - Patricia H Reggio
- From the Department of Chemistry and Biochemistry, University of North Carolina, Greensboro, North Carolina 27402,
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74
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Abstract
Allostery is the most direct and efficient way for regulation of biological macromolecule function, ranging from the control of metabolic mechanisms to signal transduction pathways. Allosteric modulators target to allosteric sites, offering distinct advantages compared to orthosteric ligands that target to active sites, such as greater specificity, reduced side effects, and lower toxicity. Allosteric modulators have therefore drawn increasing attention as potential therapeutic drugs in the design and development of new drugs. In recent years, advancements in our understanding of the fundamental principles underlying allostery, coupled with the exploitation of powerful techniques and methods in the field of allostery, provide unprecedented opportunities to discover allosteric proteins, detect and characterize allosteric sites, design and develop novel efficient allosteric drugs, and recapitulate the universal features of allosteric proteins and allosteric modulators. In the present review, we summarize the recent advances in the repertoire of allostery, with a particular focus on the aforementioned allosteric compounds.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai, China
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75
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Ksenofontova OI. Investigation of conformational mobility of insulin superfamily peptides: Use of SPC/E and TIP4P water models. Mol Biol 2014. [DOI: 10.1134/s0026893314030121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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76
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Bias in chemokine receptor signalling. Trends Immunol 2014; 35:243-52. [PMID: 24679437 DOI: 10.1016/j.it.2014.02.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 01/14/2023]
Abstract
Chemokine receptors are widely expressed on a variety of immune cells and play a crucial role in normal physiology as well as in inflammatory and infectious diseases. The existence of 23 chemokine receptors and 48 chemokine ligands guarantees a tight control and fine-tuning of the immune system. Here, we discuss the multiple regulatory mechanisms of chemokine signalling at a systemic, cellular, and molecular level. In particular, we focus on the impact of biased signalling at the receptor level; an emerging concept in molecular pharmacology. An improved understanding of these mechanisms may provide a framework for more effective drug discovery and development at a target class that is so relevant for immune function.
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77
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Thaker TM, Sarwar M, Preininger AM, Hamm HE, Iverson TM. A transient interaction between the phosphate binding loop and switch I contributes to the allosteric network between receptor and nucleotide in Gαi1. J Biol Chem 2014; 289:11331-11341. [PMID: 24596087 DOI: 10.1074/jbc.m113.539064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Receptor-mediated activation of the Gα subunit of heterotrimeric G proteins requires allosteric communication between the receptor binding site and the guanine nucleotide binding site, which are separated by >30 Å. Structural changes in the allosteric network connecting these sites are predicted to be transient in the wild-type Gα subunit, making studies of these connections challenging. In the current work, site-directed mutants that alter the energy barriers between the activation states are used as tools to better understand the transient features of allosteric signaling in the Gα subunit. The observed differences in relative receptor affinity for intact Gαi1 subunits versus C-terminal Gαi1 peptides harboring the K345L mutation are consistent with this mutation modulating the allosteric network in the protein subunit. Measurement of nucleotide exchange rates, affinity for metarhodopsin II, and thermostability suggest that the K345L Gαi1 variant has reduced stability in both the GDP-bound and nucleotide-free states as compared with wild type but similar stability in the GTPγS-bound state. High resolution x-ray crystal structures reveal conformational changes accompanying the destabilization of the GDP-bound state. Of these, the conformation for Switch I was stabilized by an ionic interaction with the phosphate binding loop. Further site-directed mutagenesis suggests that this interaction between Switch I and the phosphate binding loop is important for receptor-mediated nucleotide exchange in the wild-type Gαi1 subunit.
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Affiliation(s)
- Tarjani M Thaker
- Department of Biochemistry and Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Maruf Sarwar
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Anita M Preininger
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Heidi E Hamm
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232.
| | - T M Iverson
- Department of Biochemistry and Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee 37232.
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78
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Alexander NS, Preininger AM, Kaya AI, Stein RA, Hamm HE, Meiler J. Energetic analysis of the rhodopsin-G-protein complex links the α5 helix to GDP release. Nat Struct Mol Biol 2014; 21:56-63. [PMID: 24292645 PMCID: PMC3947367 DOI: 10.1038/nsmb.2705] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 10/02/2013] [Indexed: 01/19/2023]
Abstract
We present a model of interaction of Gi protein with the activated receptor (R*) rhodopsin, which pinpoints energetic contributions to activation and reconciles the β2 adrenergic receptor-Gs crystal structure with new and previously published experimental data. In silico analysis demonstrated energetic changes when the Gα C-terminal helix (α5) interacts with the R* cytoplasmic pocket, thus leading to displacement of the helical domain and GDP release. The model features a less dramatic domain opening compared with the crystal structure. The α5 helix undergoes a 63° rotation, accompanied by a 5.7-Å translation, that reorganizes interfaces between α5 and α1 helices and between α5 and β6-α5. Changes in the β6-α5 loop displace αG. All of these movements lead to opening of the GDP-binding pocket. The model creates a roadmap for experimental studies of receptor-mediated G-protein activation.
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Affiliation(s)
- Nathan S Alexander
- 1] Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA. [2]
| | - Anita M Preininger
- 1] Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA. [2]
| | - Ali I Kaya
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Heidi E Hamm
- Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
| | - Jens Meiler
- 1] Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA. [2] Department of Pharmacology, Vanderbilt University, Nashville, Tennessee, USA
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79
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Orban T, Jastrzebska B, Palczewski K. Structural approaches to understanding retinal proteins needed for vision. Curr Opin Cell Biol 2013; 27:32-43. [PMID: 24680428 DOI: 10.1016/j.ceb.2013.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/31/2013] [Accepted: 11/01/2013] [Indexed: 12/21/2022]
Abstract
The past decade has witnessed an impressive expansion of our knowledge of retinal photoreceptor signal transduction and the regulation of the visual cycle required for normal eyesight. Progress in human genetics and next generation sequencing technologies have revealed the complexity behind many inherited retinal diseases. Structural studies have markedly increased our understanding of the visual process. Moreover, technical innovations and improved methodologies in proteomics, macromolecular crystallization and high resolution imaging at different levels set the scene for even greater advances. Pharmacology combined with structural biology of membrane proteins holds great promise for developing innovative accessible therapies for millions robbed of their sight or progressing toward blindness.
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Affiliation(s)
- Tivadar Orban
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Beata Jastrzebska
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Krzysztof Palczewski
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA.
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80
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Moreira IS. Structural features of the G-protein/GPCR interactions. Biochim Biophys Acta Gen Subj 2013; 1840:16-33. [PMID: 24016604 DOI: 10.1016/j.bbagen.2013.08.027] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/27/2013] [Accepted: 08/28/2013] [Indexed: 01/07/2023]
Abstract
BACKGROUND The details of the functional interaction between G proteins and the G protein coupled receptors (GPCRs) have long been subjected to extensive investigations with structural and functional assays and a large number of computational studies. SCOPE OF REVIEW The nature and sites of interaction in the G-protein/GPCR complexes, and the specificities of these interactions selecting coupling partners among the large number of families of GPCRs and G protein forms, are still poorly defined. MAJOR CONCLUSIONS Many of the contact sites between the two proteins in specific complexes have been identified, but the three dimensional molecular architecture of a receptor-Gα interface is only known for one pair. Consequently, many fundamental questions regarding this macromolecular assembly and its mechanism remain unanswered. GENERAL SIGNIFICANCE In the context of current structural data we review the structural details of the interfaces and recognition sites in complexes of sub-family A GPCRs with cognate G-proteins, with special emphasis on the consequences of activation on GPCR structure, the prevalence of preassembled GPCR/G-protein complexes, the key structural determinants for selective coupling and the possible involvement of GPCR oligomerization in this process.
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Affiliation(s)
- Irina S Moreira
- REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal.
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81
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Elgeti M, Rose AS, Bartl FJ, Hildebrand PW, Hofmann KP, Heck M. Precision vs flexibility in GPCR signaling. J Am Chem Soc 2013; 135:12305-12. [PMID: 23883288 DOI: 10.1021/ja405133k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The G protein coupled receptor (GPCR) rhodopsin activates the heterotrimeric G protein transducin (Gt) to transmit the light signal into retinal rod cells. The rhodopsin activity is virtually zero in the dark and jumps by more than one billion fold after photon capture. Such perfect switching implies both high fidelity and speed of rhodopsin/Gt coupling. We employed Fourier transform infrared (FTIR) spectroscopy and supporting all-atom molecular dynamics (MD) simulations to study the conformational diversity of rhodopsin in membrane environment and extend the static picture provided by the available crystal structures. The FTIR results show how the equilibria of inactive and active protein states of the receptor (so-called metarhodopsin states) are regulated by the highly conserved E(D)RY and Yx7K(R) motives. The MD data identify an intrinsically unstructured cytoplasmic loop region connecting transmembrane helices 5 and 6 (CL3) and show how each protein state is split into conformational substates. The C-termini of the Gtγ- and Gtα-subunits (GαCT and GγCT), prepared as synthetic peptides, are likely to bind sequentially and at different sites of the active receptor. The peptides have different effects on the receptor conformation. While GγCT stabilizes the active states but preserves CL3 flexibility, GαCT selectively stabilizes a single conformational substate with largely helical CL3, as it is found in crystal structures. Based on these results we propose a mechanism for the fast and precise signal transfer from rhodopsin to Gt, which assumes a stepwise and mutual reduction of their conformational space. The mechanism relies on conserved amino acids and may therefore underlie GPCR/G protein coupling in general.
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Affiliation(s)
- Matthias Elgeti
- Institut für Medizinische Physik und Biophysik (CC2), Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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82
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Kalodimos C. Regulation of Biological Function by Allosteric Interactions. J Mol Biol 2013; 425:2277-8. [DOI: 10.1016/j.jmb.2013.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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