1
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Noh S, Tombola F, Burke P. Nanowire biosensors with olfactory proteins: towards a genuine electronic nose with single molecule sensitivity and high selectivity. NANOTECHNOLOGY 2023; 34:465502. [PMID: 37524056 DOI: 10.1088/1361-6528/acebf3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023]
Abstract
We describe the concept and roadmap of an engineered electronic nose with specificity towards analytes that differ by as little as one carbon atom, and sensitivity of being able to electrically register a single molecule of analyte. The analyte could be anything that natural noses can detect, e.g. trinitrotoluene (TNT), cocaine, aromatics, volatile organic compounds etc. The strategy envisioned is to genetically engineer a fused olfactory odorant receptor (odorant receptor (OR), a membrane-bound G-protein coupled receptor (GPCR) with high selectivity) to an ion channel protein, which opens in response to binding of the ligand to the OR. The lipid bilayer supporting the fused sensing protein would be intimately attached to a nanowire or nanotube network (either via a covalent tether or a non-covalent physisorption process), which would electrically detect the opening of the ion channel, and hence the binding of a single ligand to a single OR protein domain. Three man-made technological advances: (1) fused GPCR to ion channel protein, (2) nanowire sensing of single ion channel activity, and (3) lipid bilayer to nanotube/nanowire tethering chemistry and on natural technology (sensitivity and selectivity of OR domains to specific analytes) each have been demonstrated and/or studied independently. The combination of these three technological advances and the result of millions of years of evolution of OR proteins would enable the goal of single molecule sensing with specificity towards analytes that differ by as little as one carbon atom. This is both a review of the past and a vision of the future.
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Affiliation(s)
- Sangjun Noh
- EECS, UC Irvine, Irvine, CA, United States of America
| | - Francesco Tombola
- Dept. of Physiology and Biophysics, UC Irvine, Irvine, CA, United States of America
| | - Peter Burke
- EECS, UC Irvine, Irvine, CA, United States of America
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2
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García-Fernández MD, Chatelain FC, Nury H, Moroni A, Moreau CJ. Distinct classes of potassium channels fused to GPCRs as electrical signaling biosensors. CELL REPORTS METHODS 2021; 1:None. [PMID: 34977850 PMCID: PMC8688152 DOI: 10.1016/j.crmeth.2021.100119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/05/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022]
Abstract
Ligand-gated ion channels (LGICs) are natural biosensors generating electrical signals in response to the binding of specific ligands. Creating de novo LGICs for biosensing applications is technically challenging. We have previously designed modified LGICs by linking G protein-coupled receptors (GPCRs) to the Kir6.2 channel. In this article, we extrapolate these design concepts to other channels with different structures and oligomeric states, namely a tetrameric viral Kcv channel and the dimeric mouse TREK-1 channel. After precise engineering of the linker regions, the two ion channels were successfully regulated by a GPCR fused to their N-terminal domain. Two-electrode voltage-clamp recordings showed that Kcv and mTREK-1 fusions were inhibited and activated by GPCR agonists, respectively, and antagonists abolished both effects. Thus, dissimilar ion channels can be allosterically regulated through their N-terminal domains, suggesting that this is a generalizable approach for ion channel engineering.
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Affiliation(s)
| | - Franck C. Chatelain
- Université Côte d’Azur, IPMC CNRS UMR7275, Laboratory of Excellence ICST, 660 route des Lucioles, 06650 Valbonne, France
| | - Hugues Nury
- Université Grenoble Alpes, CNRS, CEA, IBS, 71, av. Martyrs, CS10090, 38044 Grenoble Cedex9, France
| | - Anna Moroni
- University of Milan, Department of Biosciences, Via Celoria 26, 20133 Milano, Italy
| | - Christophe J. Moreau
- Université Grenoble Alpes, CNRS, CEA, IBS, 71, av. Martyrs, CS10090, 38044 Grenoble Cedex9, France
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3
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Lemel L, Nieścierowicz K, García-Fernández MD, Darré L, Durroux T, Busnelli M, Pezet M, Rébeillé F, Jouhet J, Mouillac B, Domene C, Chini B, Cherezov V, Moreau CJ. The ligand-bound state of a G protein-coupled receptor stabilizes the interaction of functional cholesterol molecules. J Lipid Res 2021; 62:100059. [PMID: 33647276 PMCID: PMC8050779 DOI: 10.1016/j.jlr.2021.100059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/11/2021] [Indexed: 12/30/2022] Open
Abstract
Cholesterol is a major component of mammalian plasma membranes that not only affects the physical properties of the lipid bilayer but also is the function of many membrane proteins including G protein-coupled receptors. The oxytocin receptor (OXTR) is involved in parturition and lactation of mammals and in their emotional and social behaviors. Cholesterol acts on OXTR as an allosteric modulator inducing a high-affinity state for orthosteric ligands through a molecular mechanism that has yet to be determined. Using the ion channel-coupled receptor technology, we developed a functional assay of cholesterol modulation of G protein-coupled receptors that is independent of intracellular signaling pathways and operational in living cells. Using this assay, we discovered a stable binding of cholesterol molecules to the receptor when it adopts an orthosteric ligand-bound state. This stable interaction preserves the cholesterol-dependent activity of the receptor in cholesterol-depleted membranes. This mechanism was confirmed using time-resolved FRET experiments on WT OXTR expressed in CHO cells. Consequently, a positive cross-regulation sequentially occurs in OXTR between cholesterol and orthosteric ligands.
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Affiliation(s)
- Laura Lemel
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | | | - Leonardo Darré
- Functional Genomics Laboratory and Biomolecular Simulations Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Thierry Durroux
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Marta Busnelli
- CNR, Institute of Neuroscience, U28 and NeuroMI Center for Neuroscience, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Mylène Pezet
- Institute for Advanced Biosciences, Inserm U 1209, CNRS UMR 5309, Grenoble Alpes University, Grenoble, France
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
| | - Juliette Jouhet
- Laboratoire de Physiologie Cellulaire Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, Grenoble, France
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Carmen Domene
- Department of Chemistry, University of Bath, Bath, United Kingdom; Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Bice Chini
- CNR, Institute of Neuroscience, U28 and NeuroMI Center for Neuroscience, University of Milano-Bicocca, Vedano al Lambro (MB), Italy
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA
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Adamski W, Salvi N, Maurin D, Magnat J, Milles S, Jensen MR, Abyzov A, Moreau CJ, Blackledge M. A Unified Description of Intrinsically Disordered Protein Dynamics under Physiological Conditions Using NMR Spectroscopy. J Am Chem Soc 2019; 141:17817-17829. [PMID: 31591893 DOI: 10.1021/jacs.9b09002] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Intrinsically disordered proteins (IDPs) are flexible biomolecules whose essential functions are defined by their dynamic nature. Nuclear magnetic resonance (NMR) spectroscopy is ideally suited to the investigation of this behavior at atomic resolution. NMR relaxation is increasingly used to detect conformational dynamics in free and bound forms of IDPs under conditions approaching physiological, although a general framework providing a quantitative interpretation of these exquisitely sensitive probes as a function of experimental conditions is still lacking. Here, measuring an extensive set of relaxation rates sampling multiple-time-scale dynamics over a broad range of crowding conditions, we develop and test an integrated analytical description that accurately portrays the motion of IDPs as a function of the intrinsic properties of the crowded molecular environment. In particular we observe a strong dependence of both short-range and long-range motional time scales of the protein on the friction of the solvent. This tight coupling between the dynamic behavior of the IDP and its environment allows us to develop analytical expressions for protein motions and NMR relaxation properties that can be accurately applied over a vast range of experimental conditions. This unified dynamic description provides new insight into the physical behavior of IDPs, extending our ability to quantitatively investigate their conformational dynamics under complex environmental conditions, and accurately predicting relaxation rates reporting on motions on time scales up to tens of nanoseconds, both in vitro and in cellulo.
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Affiliation(s)
- Wiktor Adamski
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Nicola Salvi
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Damien Maurin
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Justine Magnat
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Sigrid Milles
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Anton Abyzov
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Christophe J Moreau
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Martin Blackledge
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
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Polovinkin L, Hassaine G, Perot J, Neumann E, Jensen AA, Lefebvre SN, Corringer PJ, Neyton J, Chipot C, Dehez F, Schoehn G, Nury H. Conformational transitions of the serotonin 5-HT 3 receptor. Nature 2018; 563:275-279. [PMID: 30401839 DOI: 10.1038/s41586-018-0672-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 09/07/2018] [Indexed: 01/03/2023]
Abstract
The serotonin 5-HT3 receptor is a pentameric ligand-gated ion channel (pLGIC). It belongs to a large family of receptors that function as allosteric signal transducers across the plasma membrane1,2; upon binding of neurotransmitter molecules to extracellular sites, the receptors undergo complex conformational transitions that result in transient opening of a pore permeable to ions. 5-HT3 receptors are therapeutic targets for emesis and nausea, irritable bowel syndrome and depression3. In spite of several reported pLGIC structures4-8, no clear unifying view has emerged on the conformational transitions involved in channel gating. Here we report four cryo-electron microscopy structures of the full-length mouse 5-HT3 receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator, at resolutions ranging from 3.2 Å to 4.5 Å. The tropisetron-bound structure resembles those obtained with an inhibitory nanobody5 or without ligand9. The other structures include an 'open' state and two ligand-bound states. We present computational insights into the dynamics of the structures, their pore hydration and free-energy profiles, and characterize movements at the gate level and cation accessibility in the pore. Together, these data deepen our understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.
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Affiliation(s)
| | | | - Jonathan Perot
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France
| | | | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Solène N Lefebvre
- Channel Receptors Unit, CNRS UMR 3571, Institut Pasteur, Paris, France
| | | | - Jacques Neyton
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France.
| | - Christophe Chipot
- Université de Lorraine, CNRS, LPCT, Nancy, France.,Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Francois Dehez
- Université de Lorraine, CNRS, LPCT, Nancy, France.,Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France
| | - Guy Schoehn
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France
| | - Hugues Nury
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France.
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6
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Principalli MA, Lemel L, Rongier A, Godet AC, Langer K, Revilloud J, Darré L, Domene C, Vivaudou M, Moreau CJ. Functional mapping of the N-terminal arginine cluster and C-terminal acidic residues of Kir6.2 channel fused to a G protein-coupled receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2144-2153. [PMID: 28757124 DOI: 10.1016/j.bbamem.2017.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/06/2017] [Accepted: 07/26/2017] [Indexed: 10/19/2022]
Abstract
Ion channel-coupled receptors (ICCRs) are original man-made ligand-gated ion channels created by fusion of G protein-coupled receptors (GPCRs) to the inward-rectifier potassium channel Kir6.2. GPCR conformational changes induced by ligand binding are transduced into electrical current by the ion channel. This functional coupling is closely related to the length of the linker region formed by the GPCR C-terminus (C-ter) and Kir6.2N-terminus (N-ter). Manipulating the GPCR C-ter length allows to finely tune the channel regulation, both in amplitude and sign (opening or closing Kir6.2). In this work, we demonstrate that the primary sequence of the channel N-terminal domain is an additional parameter for the functional coupling with GPCRs. As for all Kir channels, a cluster of basic residues is present in the N-terminal domain of Kir6.2 and is composed of 5 arginines which are proximal to the GPCR C-ter in the fusion proteins. Using a functional mapping approach, we demonstrate the role of specific arginines (R27 and R32) for the function of ICCRs, indicating that the position and not the cluster of positively-charged arginines is critical for the channel regulation by the GPCR. Following observations provided by molecular dynamics simulation, we explore the hypothesis of interaction of these arginines with acidic residues, and using site-directed mutagenesis, we identified aspartate D307 and glutamate E308 residues as critical for the function of ICCRs. These results demonstrate the critical role of the N-terminal and C-terminal charged residues of Kir6.2 for its allosteric regulation by the fused GPCR.
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Affiliation(s)
- Maria A Principalli
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Laura Lemel
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Anaëlle Rongier
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Anne-Claire Godet
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Karla Langer
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Jean Revilloud
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Leonardo Darré
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Carmen Domene
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Michel Vivaudou
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France
| | - Christophe J Moreau
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, LabEx ICST, 71, avenue des Martyrs, CS10090, F-38044 Grenoble, France.
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Tuning the allosteric regulation of artificial muscarinic and dopaminergic ligand-gated potassium channels by protein engineering of G protein-coupled receptors. Sci Rep 2017; 7:41154. [PMID: 28145461 PMCID: PMC5286527 DOI: 10.1038/srep41154] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/14/2016] [Indexed: 12/15/2022] Open
Abstract
Ligand-gated ion channels enable intercellular transmission of action potential through synapses by transducing biochemical messengers into electrical signal. We designed artificial ligand-gated ion channels by coupling G protein-coupled receptors to the Kir6.2 potassium channel. These artificial channels called ion channel-coupled receptors offer complementary properties to natural channels by extending the repertoire of ligands to those recognized by the fused receptors, by generating more sustained signals and by conferring potassium selectivity. The first artificial channels based on the muscarinic M2 and the dopaminergic D2L receptors were opened and closed by acetylcholine and dopamine, respectively. We find here that this opposite regulation of the gating is linked to the length of the receptor C-termini, and that C-terminus engineering can precisely control the extent and direction of ligand gating. These findings establish the design rules to produce customized ligand-gated channels for synthetic biology applications.
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Ion Channels as Reporters of Membrane Receptor Function: Automated Analysis in Xenopus Oocytes. Methods Mol Biol 2017; 1635:283-301. [PMID: 28755375 DOI: 10.1007/978-1-4939-7151-0_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G-protein-coupled receptors (GPCR) are the most widely used system of communication used by cells. They sense external signals and translate them into intracellular signals. The information is carried mechanically across the cell membrane, without perturbing its integrity. Agonist binding on the extracellular side causes a change in receptor conformation which propagates to the intracellular side and causes release of activated G-proteins, the first messengers of a variety of signaling cascades.Permitting access to powerful electrophysiological techniques, ion channels can be employed to monitor precisely the most proximal steps of GPCR signaling, receptor conformational changes, and G-protein release. The former is achieved by physical attachment of a potassium channel to the GPCR to create an Ion-Channel Coupled Receptor (ICCR). The latter is based on the use of G-protein-regulated potassium channels (GIRK). We describe here how these two systems may be used in the Xenopus oocyte heterologous system with a robotic system for increased throughput.
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Abstract
G protein-coupled receptors (GPCRs) remain a major domain of pharmaceutical discovery. The identification of GPCR lead compounds and their optimization are now structure-based, thanks to advances in X-ray crystallography, molecular modeling, protein engineering and biophysical techniques. In silico screening provides useful hit molecules. New pharmacological approaches to tuning the pleotropic action of GPCRs include: allosteric modulators, biased ligands, GPCR heterodimer-targeted compounds, manipulation of polypharmacology, receptor antibodies and tailoring of drug molecules to fit GPCR pharmacogenomics. Measurements of kinetics and drug efficacy are factors influencing clinical success. With the exception of inhibitors of GPCR kinases, targeting of intracellular GPCR signaling or receptor cycling for therapeutic purposes remains a futuristic concept. New assay approaches are more efficient and multidimensional: cell-based, label-free, fluorescence-based assays, and biosensors. Tailoring GPCR drugs to a patient's genetic background is now being considered. Chemoinformatic tools can predict ADME-tox properties. New imaging technology visualizes drug action in vivo. Thus, there is reason to be optimistic that new technology for GPCR ligand discovery will help reverse the current narrowing of the pharmaceutical pipeline.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892, USA.
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