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Menon I, Sych T, Son Y, Morizumi T, Lee J, Ernst OP, Khelashvili G, Sezgin E, Levitz J, Menon AK. A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors. J Biol Chem 2024; 300:105649. [PMID: 38237683 PMCID: PMC10874734 DOI: 10.1016/j.jbc.2024.105649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/04/2024] [Accepted: 01/07/2024] [Indexed: 01/30/2024] Open
Abstract
Class A G protein-coupled receptors (GPCRs), a superfamily of cell membrane signaling receptors, moonlight as constitutively active phospholipid scramblases. The plasma membrane of metazoan cells is replete with GPCRs yet has a strong resting trans-bilayer phospholipid asymmetry, with the signaling lipid phosphatidylserine confined to the cytoplasmic leaflet. To account for the persistence of this lipid asymmetry in the presence of GPCR scramblases, we hypothesized that GPCR-mediated lipid scrambling is regulated by cholesterol, a major constituent of the plasma membrane. We now present a technique whereby synthetic vesicles reconstituted with GPCRs can be supplemented with cholesterol to a level similar to that of the plasma membrane and show that the scramblase activity of two prototypical GPCRs, opsin and the β1-adrenergic receptor, is impaired upon cholesterol loading. Our data suggest that cholesterol acts as a switch, inhibiting scrambling above a receptor-specific threshold concentration to disable GPCR scramblases at the plasma membrane.
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Affiliation(s)
- Indu Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA
| | - Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Yeeun Son
- Graduate program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School, New York, New York, USA; Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Joon Lee
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA; Institute of Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Erdinc Sezgin
- Graduate program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School, New York, New York, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York, USA.
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2
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Menon I, Sych T, Son Y, Morizumi T, Lee J, Ernst OP, Khelashvili G, Sezgin E, Levitz J, Menon AK. A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors. bioRxiv 2024:2023.11.24.568580. [PMID: 38045315 PMCID: PMC10690279 DOI: 10.1101/2023.11.24.568580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Class A G protein-coupled receptors (GPCRs), a superfamily of cell membrane signaling receptors, moonlight as constitutively active phospholipid scramblases. The plasma membrane of metazoan cells is replete with GPCRs, yet has a strong resting trans-bilayer phospholipid asymmetry, with the signaling lipid phosphatidylserine confined to the cytoplasmic leaflet. To account for the persistence of this lipid asymmetry in the presence of GPCR scramblases, we hypothesized that GPCR-mediated lipid scrambling is regulated by cholesterol, a major constituent of the plasma membrane. We now present a technique whereby synthetic vesicles reconstituted with GPCRs can be supplemented with cholesterol to a level similar to that of the plasma membrane and show that the scramblase activity of two prototypical GPCRs, opsin and the β1-adrenergic receptor, is impaired upon cholesterol loading. Our data suggest that cholesterol acts as a switch, inhibiting scrambling above a receptor-specific threshold concentration to disable GPCR scramblases at the plasma membrane.
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Affiliation(s)
- Indu Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Taras Sych
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, 17165 Solna, Sweden
| | - Yeeun Son
- Graduate program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School, New York, NY 10065, USA
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Joon Lee
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Oliver P. Ernst
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada M5S 1A8
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - George Khelashvili
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
- Institute of Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Erdinc Sezgin
- Graduate program in Biochemistry, Cell and Molecular Biology, Weill Cornell Graduate School, New York, NY 10065, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
| | - Anant K. Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, NY 10065, USA
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3
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Hermet P, Delache B, Herate C, Wolf E, Kivi G, Juronen E, Mumm K, Žusinaite E, Kainov D, Sankovski E, Virumäe K, Planken A, Merits A, Besaw JE, Yee AW, Morizumi T, Kim K, Kuo A, Berriche A, Dereuddre-Bosquet N, Sconosciuti Q, Naninck T, Relouzat F, Cavarelli M, Ustav M, Wilson D, Ernst OP, Männik A, LeGrand R, Ustav M. Broadly neutralizing humanized SARS-CoV-2 antibody binds to a conserved epitope on Spike and provides antiviral protection through inhalation-based delivery in non-human primates. PLoS Pathog 2023; 19:e1011532. [PMID: 37531329 PMCID: PMC10395824 DOI: 10.1371/journal.ppat.1011532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 07/03/2023] [Indexed: 08/04/2023] Open
Abstract
The COVID-19 pandemic represents a global challenge that has impacted and is expected to continue to impact the lives and health of people across the world for the foreseeable future. The rollout of vaccines has provided highly anticipated relief, but effective therapeutics are required to further reduce the risk and severity of infections. Monoclonal antibodies have been shown to be effective as therapeutics for SARS-CoV-2, but as new variants of concern (VoC) continue to emerge, their utility and use have waned due to limited or no efficacy against these variants. Furthermore, cumbersome systemic administration limits easy and broad access to such drugs. As well, concentrations of systemically administered antibodies in the mucosal epithelium, a primary site of initial infection, are dependent on neonatal Fc receptor mediated transport and require high drug concentrations. To reduce the viral load more effectively in the lung, we developed an inhalable formulation of a SARS-CoV-2 neutralizing antibody binding to a conserved epitope on the Spike protein, ensuring pan-neutralizing properties. Administration of this antibody via a vibrating mesh nebulization device retained antibody integrity and resulted in effective distribution of the antibody in the upper and lower respiratory tract of non-human primates (NHP). In comparison with intravenous administration, significantly higher antibody concentrations can be obtained in the lung, resulting in highly effective reduction in viral load post SARS-CoV-2 challenge. This approach may reduce the barriers of access and uptake of antibody therapeutics in real-world clinical settings and provide a more effective blueprint for targeting existing and potentially emerging respiratory tract viruses.
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Affiliation(s)
| | - Benoît Delache
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT); Fontenay-aux-Roses, France
| | - Cecile Herate
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT); Fontenay-aux-Roses, France
| | | | - Gaily Kivi
- Icosagen Cell Factory OÜ; Tartu, Estonia
| | | | - Karl Mumm
- Icosagen Cell Factory OÜ; Tartu, Estonia
| | | | | | | | | | | | | | - Jessica E Besaw
- Department of Biochemistry, University of Toronto; Toronto, Canada
| | - Ai Woon Yee
- Department of Biochemistry, University of Toronto; Toronto, Canada
| | | | - Kyumhyuk Kim
- Department of Biochemistry, University of Toronto; Toronto, Canada
| | - Anling Kuo
- Department of Biochemistry, University of Toronto; Toronto, Canada
| | - Asma Berriche
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT); Fontenay-aux-Roses, France
| | - Nathalie Dereuddre-Bosquet
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT); Fontenay-aux-Roses, France
| | - Quentin Sconosciuti
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT); Fontenay-aux-Roses, France
| | - Thibaut Naninck
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT); Fontenay-aux-Roses, France
| | - Francis Relouzat
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT); Fontenay-aux-Roses, France
| | - Mariangela Cavarelli
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT); Fontenay-aux-Roses, France
| | - Mart Ustav
- Icosagen Cell Factory OÜ; Tartu, Estonia
| | | | - Oliver P Ernst
- Department of Biochemistry, University of Toronto; Toronto, Canada
- Department of Molecular Genetics, University of Toronto; Toronto, Canada
| | | | - Roger LeGrand
- Université Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT); Fontenay-aux-Roses, France
| | - Mart Ustav
- Icosagen Cell Factory OÜ; Tartu, Estonia
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4
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Morizumi T, Kim K, Li H, Govorunova EG, Sineshchekov OA, Wang Y, Zheng L, Bertalan É, Bondar AN, Askari A, Brown LS, Spudich JL, Ernst OP. Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K + and Na + selectivities. Nat Commun 2023; 14:4365. [PMID: 37474513 PMCID: PMC10359266 DOI: 10.1038/s41467-023-40041-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is a light-gated channel used for optogenetic silencing of mammalian neurons. It selects K+ over Na+ in the absence of the canonical tetrameric K+ selectivity filter found universally in voltage- and ligand-gated channels. The genome of H. catenoides also encodes a highly homologous cation channelrhodopsin (HcCCR), a Na+ channel with >100-fold larger Na+ to K+ permeability ratio. Here, we use cryo-electron microscopy to determine atomic structures of these two channels embedded in peptidiscs to elucidate structural foundations of their dramatically different cation selectivity. Together with structure-guided mutagenesis, we show that K+ versus Na+ selectivity is determined at two distinct sites on the putative ion conduction pathway: in a patch of critical residues in the intracellular segment (Leu69/Phe69, Ile73/Ser73 and Asp116) and within a cluster of aromatic residues in the extracellular segment (primarily, Trp102 and Tyr222). The two filters are on the opposite sides of the photoactive site involved in channel gating.
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Affiliation(s)
- Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Kyumhyuk Kim
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Hai Li
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Elena G Govorunova
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Oleg A Sineshchekov
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Yumei Wang
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Lei Zheng
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Éva Bertalan
- Physikzentrum, RWTH-Aachen University, Aachen, Germany
| | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Măgurele, Romania
- Institute of Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich, Germany
| | - Azam Askari
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - John L Spudich
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA.
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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5
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Mehrabi P, Bücker R, Bourenkov G, Ginn HM, von Stetten D, Müller-Werkmeister HM, Kuo A, Morizumi T, Eger BT, Ou WL, Oghbaey S, Sarracini A, Besaw JE, Pare-Labrosse O, Meier S, Schikora H, Tellkamp F, Marx A, Sherrell DA, Axford D, Owen RL, Ernst OP, Pai EF, Schulz EC, Miller RJD. Serial femtosecond and serial synchrotron crystallography can yield data of equivalent quality: A systematic comparison. Sci Adv 2021; 7:7/12/eabf1380. [PMID: 33731353 PMCID: PMC7968842 DOI: 10.1126/sciadv.abf1380] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/28/2021] [Indexed: 05/09/2023]
Abstract
For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.
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Affiliation(s)
- P Mehrabi
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R Bücker
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Centre for Structural Systems Biology, Department of Chemistry, University of Hamburg, Notkestraße 85, 22607 Hamburg, Germany
| | - G Bourenkov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, D-22603 Hamburg, Germany
| | - H M Ginn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - D von Stetten
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, D-22603 Hamburg, Germany
| | - H M Müller-Werkmeister
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - A Kuo
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - T Morizumi
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - B T Eger
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - W-L Ou
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - S Oghbaey
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - A Sarracini
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - J E Besaw
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - O Pare-Labrosse
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - S Meier
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
| | - H Schikora
- Scientific Support Unit Machine Physics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - F Tellkamp
- Scientific Support Unit Machine Physics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - A Marx
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - D A Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - D Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - R L Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - O P Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - E F Pai
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, 101 College Street, Toronto, Ontario M5G 1L7, Canada
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - E C Schulz
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - R J D Miller
- Department for Atomically Resolved Dynamics, Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
- Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, Universität Hamburg, Jungiusstrasse 9, 20355 Hamburg, Germany
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6
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Liu J, Cheng R, Van Eps N, Wang N, Morizumi T, Ou WL, Klauser PC, Rozovsky S, Ernst OP, Wang L. Genetically Encoded Quinone Methides Enabling Rapid, Site-Specific, and Photocontrolled Protein Modification with Amine Reagents. J Am Chem Soc 2020; 142:17057-17068. [PMID: 32915556 DOI: 10.1021/jacs.0c06820] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Site-specific modification of proteins with functional molecules provides powerful tools for researching and engineering proteins. Here we report a new chemical conjugation method which photocages highly reactive but chemically selective moieties, enabling the use of protein-inert amines for selective protein modification. New amino acids FnbY and FmnbY, bearing photocaged quinone methides (QMs), were genetically incorporated into proteins. Upon light activation, they generated highly reactive QM, which rapidly reacted with amine derivatives. This method features a rare combination of desired properties including fast kinetics, small and stable linkage, compatibility with low temperature, photocontrollability, and widely available reagents. Moreover, labeling via FnbY occurs on the β-carbon, affording the shortest linkage to protein backbone which is essential for advanced studies involving orientation and distance. We installed various functionalities onto proteins and attached a spin label as close as possible to the protein backbone, achieving high resolution in double electron-electron paramagnetic resonance distance measurements.
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Affiliation(s)
- Jun Liu
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Rujin Cheng
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nanxi Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Wei-Lin Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Paul C Klauser
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lei Wang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, 555 Mission Bay Blvd. South, San Francisco, California 94158, United States
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7
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Besaw JE, Ou WL, Morizumi T, Eger BT, Sanchez Vasquez JD, Chu JHY, Harris A, Brown LS, Miller RJD, Ernst OP. The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants. J Biol Chem 2020; 295:14793-14804. [PMID: 32703899 DOI: 10.1074/jbc.ra120.014118] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/14/2020] [Indexed: 01/25/2023] Open
Abstract
Microbial rhodopsins are versatile and ubiquitous retinal-binding proteins that function as light-driven ion pumps, light-gated ion channels, and photosensors, with potential utility as optogenetic tools for altering membrane potential in target cells. Insights from crystal structures have been central for understanding proton, sodium, and chloride transport mechanisms of microbial rhodopsins. Two of three known groups of anion pumps, the archaeal halorhodopsins (HRs) and bacterial chloride-pumping rhodopsins, have been structurally characterized. Here we report the structure of a representative of a recently discovered third group consisting of cyanobacterial chloride and sulfate ion-pumping rhodopsins, the Mastigocladopsis repens rhodopsin (MastR). Chloride-pumping MastR contains in its ion transport pathway a unique Thr-Ser-Asp (TSD) motif, which is involved in the binding of a chloride ion. The structure reveals that the chloride-binding mode is more similar to HRs than chloride-pumping rhodopsins, but the overall structure most closely resembles bacteriorhodopsin (BR), an archaeal proton pump. The MastR structure shows a trimer arrangement reminiscent of BR-like proton pumps and shows features at the extracellular side more similar to BR than the other chloride pumps. We further solved the structure of the MastR-T74D mutant, which contains a single amino acid replacement in the TSD motif. We provide insights into why this point mutation can convert the MastR chloride pump into a proton pump but cannot in HRs. Our study points at the importance of precise coordination and exact location of the water molecule in the active center of proton pumps, which serves as a bridge for the key proton transfer.
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Affiliation(s)
- Jessica E Besaw
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Wei-Lin Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Juan D Sanchez Vasquez
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jessica H Y Chu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Harris
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - R J Dwayne Miller
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada; Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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8
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Gozem S, Johnson PJM, Halpin A, Luk HL, Morizumi T, Prokhorenko VI, Ernst OP, Olivucci M, Miller RJD. Excited-State Vibronic Dynamics of Bacteriorhodopsin from Two-Dimensional Electronic Photon Echo Spectroscopy and Multiconfigurational Quantum Chemistry. J Phys Chem Lett 2020; 11:3889-3896. [PMID: 32330041 PMCID: PMC9198827 DOI: 10.1021/acs.jpclett.0c01063] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Owing to the ultrafast time scale of the photoinduced reaction and high degree of spectral overlap among the reactant, product, and excited electronic states in bacteriorhodopsin (bR), it has been a challenge for traditional spectroscopies to resolve the interplay between vibrational dynamics and electronic processes occurring in the retinal chromophore of bR. Here, we employ ultrafast two-dimensional electronic photon echo spectroscopy to follow the early excited-state dynamics of bR preceding the isomerization. We detect an early periodic photoinduced absorptive signal that, employing a hybrid multiconfigurational quantum/molecular mechanical model of bR, we attribute to periodic mixing of the first and second electronic excited states (S1 and S2, respectively). This recurrent interaction between S1 and S2, induced by a bond length alternation of the retinal chromohore, supports the hypothesis that the ultrafast photoisomerization in bR is initiated by a process involving coupled nuclear and electronic motion on three different electronic states.
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Affiliation(s)
- Samer Gozem
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Philip J M Johnson
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Alexei Halpin
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - Hoi Ling Luk
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Valentyn I Prokhorenko
- Max Planck Institute for the Structure and Dynamics of Matter, Atomically Resolved Dynamics Division, Building 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Department of Biotechnology, Chemistry and Pharmacology, Universitá di Siena, via De Gasperi 2, I-53100Siena, Italy
| | - R J Dwayne Miller
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
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9
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Zhao DY, Pöge M, Morizumi T, Gulati S, Van Eps N, Zhang J, Miszta P, Filipek S, Mahamid J, Plitzko JM, Baumeister W, Ernst OP, Palczewski K. Cryo-EM structure of the native rhodopsin dimer in nanodiscs. J Biol Chem 2019; 294:14215-14230. [PMID: 31399513 DOI: 10.1074/jbc.ra119.010089] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 08/02/2019] [Indexed: 02/03/2023] Open
Abstract
Imaging of rod photoreceptor outer-segment disc membranes by atomic force microscopy and cryo-electron tomography has revealed that the visual pigment rhodopsin, a prototypical class A G protein-coupled receptor (GPCR), can organize as rows of dimers. GPCR dimerization and oligomerization offer possibilities for allosteric regulation of GPCR activity, but the detailed structures and mechanism remain elusive. In this investigation, we made use of the high rhodopsin density in the native disc membranes and of a bifunctional cross-linker that preserves the native rhodopsin arrangement by covalently tethering rhodopsins via Lys residue side chains. We purified cross-linked rhodopsin dimers and reconstituted them into nanodiscs for cryo-EM analysis. We present cryo-EM structures of the cross-linked rhodopsin dimer as well as a rhodopsin dimer reconstituted into nanodiscs from purified monomers. We demonstrate the presence of a preferential 2-fold symmetrical dimerization interface mediated by transmembrane helix 1 and the cytoplasmic helix 8 of rhodopsin. We confirmed this dimer interface by double electron-electron resonance measurements of spin-labeled rhodopsin. We propose that this interface and the arrangement of two protomers is a prerequisite for the formation of the observed rows of dimers. We anticipate that the approach outlined here could be extended to other GPCRs or membrane receptors to better understand specific receptor dimerization mechanisms.
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Affiliation(s)
- Dorothy Yanling Zhao
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Matthias Pöge
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697.,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jianye Zhang
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697.,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Przemyslaw Miszta
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland
| | - Slawomir Filipek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw 02-093, Poland
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697 .,Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106
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10
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Morizumi T, Ou WL, Van Eps N, Inoue K, Kandori H, Brown LS, Ernst OP. X-ray Crystallographic Structure and Oligomerization of Gloeobacter Rhodopsin. Sci Rep 2019; 9:11283. [PMID: 31375689 PMCID: PMC6677831 DOI: 10.1038/s41598-019-47445-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/24/2019] [Indexed: 01/27/2023] Open
Abstract
Gloeobacter rhodopsin (GR) is a cyanobacterial proton pump which can be potentially applied to optogenetics. We solved the crystal structure of GR and found that it has overall similarity to the homologous proton pump from Salinibacter ruber, xanthorhodopsin (XR). We identified distinct structural characteristics of GR’s hydrogen bonding network in the transmembrane domain as well as the displacement of extracellular sides of the transmembrane helices relative to those of XR. Employing Raman spectroscopy and flash-photolysis, we found that GR in the crystals exists in a state which displays retinal conformation and photochemical cycle similar to the functional form observed in lipids. Based on the crystal structure of GR, we selected a site for spin labeling to determine GR’s oligomerization state using double electron–electron resonance (DEER) spectroscopy and demonstrated the pH-dependent pentamer formation of GR. Determination of the structure of GR as well as its pentamerizing propensity enabled us to reveal the role of structural motifs (extended helices, 3-omega motif and flipped B-C loop) commonly found among light-driven bacterial pumps in oligomer formation. Here we propose a new concept to classify these pumps based on the relationship between their oligomerization propensities and these structural determinants.
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Affiliation(s)
- Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Wei-Lin Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Keiichi Inoue
- The Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 464-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 464-8555, Japan
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. .,Department of Molecular Genetics, University of Toronto, Ontario, M5S 1A8, Canada.
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11
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Verchère A, Ou WL, Ploier B, Morizumi T, Goren MA, Bütikofer P, Ernst OP, Khelashvili G, Menon AK. Light-independent phospholipid scramblase activity of bacteriorhodopsin from Halobacterium salinarum. Sci Rep 2017; 7:9522. [PMID: 28842688 PMCID: PMC5572738 DOI: 10.1038/s41598-017-09835-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/31/2017] [Indexed: 12/11/2022] Open
Abstract
The retinylidene protein bacteriorhodopsin (BR) is a heptahelical light-dependent proton pump found in the purple membrane of the archaeon Halobacterium salinarum. We now show that when reconstituted into large unilamellar vesicles, purified BR trimers exhibit light-independent lipid scramblase activity, thereby facilitating transbilayer exchange of phospholipids between the leaflets of the vesicle membrane at a rate >10,000 per trimer per second. This activity is comparable to that of recently described scramblases including bovine rhodopsin and fungal TMEM16 proteins. Specificity tests reveal that BR scrambles fluorescent analogues of common phospholipids but does not transport a glycosylated diphosphate isoprenoid lipid. In silico analyses suggest that membrane-exposed polar residues in transmembrane helices 1 and 2 of BR may provide the molecular basis for lipid translocation by coordinating the polar head-groups of transiting phospholipids. Consistent with this possibility, extensive coarse-grained molecular dynamics simulations of a BR trimer in an explicit phospholipid membrane revealed water penetration along transmembrane helix 1 with the cooperation of a polar residue (Y147 in transmembrane helix 5) in the adjacent protomer. These results suggest that the lipid translocation pathway may lie at or near the interface of the protomers of a BR trimer.
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Affiliation(s)
- Alice Verchère
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York, 10065, USA
| | - Wei-Lin Ou
- Department of Biochemistry, University of Toronto, 1 Kings College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Birgit Ploier
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York, 10065, USA
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, 1 Kings College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Michael A Goren
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York, 10065, USA
| | - Peter Bütikofer
- Institute of Biochemistry and Molecular Medicine, University of Bern, 3012, Bern, Switzerland
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, 1 Kings College Circle, Toronto, Ontario, Canada, M5S 1A8.,Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - George Khelashvili
- Department of Physiology and Biophysics, and Institute for Computational Biomedicine, Weill Cornell Medical College, 1300 York Avenue, New York, New York, 10065, USA
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York, 10065, USA.
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12
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Johnson PJM, Farag MH, Halpin A, Morizumi T, Prokhorenko VI, Knoester J, Jansen TLC, Ernst OP, Miller RJD. The Primary Photochemistry of Vision Occurs at the Molecular Speed Limit. J Phys Chem B 2017; 121:4040-4047. [PMID: 28358485 DOI: 10.1021/acs.jpcb.7b02329] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultrafast photochemical reactions are initiated by vibronic transitions from the reactant ground state to the excited potential energy surface, directly populating excited-state vibrational modes. The primary photochemical reaction of vision, the isomerization of retinal in the protein rhodopsin, is known to be a vibrationally coherent reaction, but the Franck-Condon factors responsible for initiating the process have been difficult to resolve with conventional time-resolved spectroscopies. Here we employ experimental and theoretical 2D photon echo spectroscopy to directly resolve for the first time the Franck-Condon factors that initiate isomerization on the excited potential energy surface and track the reaction dynamics. The spectral dynamics reveal vibrationally coherent isomerization occurring on the fastest possible time scale, that of a single period of the local torsional reaction coordinate. We successfully model this process as coherent wavepacket motion through a conical intersection on a ∼30 fs time scale, confirming the reaction coordinate as a local torsional coordinate with a frequency of ∼570 cm-1. As a result of spectral features being spread out along two frequency coordinates, we unambiguously assign reactant and product states following passage through the conical intersection, which reveal the key vibronic transitions that initiate the vibrationally coherent photochemistry of vision.
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Affiliation(s)
- Philip J M Johnson
- Departments of Chemistry & Physics, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Marwa H Farag
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Alexei Halpin
- Departments of Chemistry & Physics, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - Valentyn I Prokhorenko
- Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Luruper Chaussee 149, Hamburg 22761, Germany
| | - Jasper Knoester
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.,Department of Molecular Genetics, University of Toronto , 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
| | - R J Dwayne Miller
- Departments of Chemistry & Physics, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada.,Max Planck Institute for the Structure and Dynamics of Matter , Atomically Resolved Dynamics Division, Luruper Chaussee 149, Hamburg 22761, Germany
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13
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Ou WL, Van Eps N, Morizumi T, Balo AR, Ernst OP. Interdomain Conformational Changes in Visual Arrestin upon Binding to Different Forms of Rhodopsin. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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14
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Ploier B, Caro LN, Morizumi T, Pandey K, Pearring JN, Goren MA, Finnemann SC, Graumann J, Arshavsky VY, Dittman JS, Ernst OP, Menon AK. Dimerization deficiency of enigmatic retinitis pigmentosa-linked rhodopsin mutants. Nat Commun 2016; 7:12832. [PMID: 27694816 PMCID: PMC5059438 DOI: 10.1038/ncomms12832] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 08/03/2016] [Indexed: 02/05/2023] Open
Abstract
Retinitis pigmentosa (RP) is a blinding disease often associated with mutations in rhodopsin, a light-sensing G protein-coupled receptor and phospholipid scramblase. Most RP-associated mutations affect rhodopsin's activity or transport to disc membranes. Intriguingly, some mutations produce apparently normal rhodopsins that nevertheless cause disease. Here we show that three such enigmatic mutations—F45L, V209M and F220C—yield fully functional visual pigments that bind the 11-cis retinal chromophore, activate the G protein transducin, traffic to the light-sensitive photoreceptor compartment and scramble phospholipids. However, tests of scramblase activity show that unlike wild-type rhodopsin that functionally reconstitutes into liposomes as dimers or multimers, F45L, V209M and F220C rhodopsins behave as monomers. This result was confirmed in pull-down experiments. Our data suggest that the photoreceptor pathology associated with expression of these enigmatic RP-associated pigments arises from their unexpected inability to dimerize via transmembrane helices 1 and 5. Retinitis pigmentosa is often caused by mutations that affect the activity or transport of rhodopsin, but some mutations cause disease even though an apparently functional protein is produced. Here the authors show that three such enigmatic mutants retain scramblase activity but are unable to dimerize.
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Affiliation(s)
- Birgit Ploier
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Lydia N Caro
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Kalpana Pandey
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Jillian N Pearring
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Michael A Goren
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Silvia C Finnemann
- Department of Biological Sciences, Center for Cancer, Genetic Diseases and Gene Regulation, Fordham University, Bronx, New York 10458, USA
| | - Johannes Graumann
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA.,Weill Cornell Medicine-Qatar, Qatar Foundation, Education City P.O.Box 24144, Doha, State of Qatar
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jeremy S Dittman
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
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15
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Johnson PJM, Halpin A, Morizumi T, Prokhorenko VI, Ernst OP, Miller RJD. Local vibrational coherences drive the primary photochemistry of vision. Nat Chem 2015; 7:980-6. [DOI: 10.1038/nchem.2398] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 10/15/2015] [Indexed: 01/06/2023]
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16
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Van Eps N, Caro LN, Morizumi T, Ernst OP. Characterizing rhodopsin signaling by EPR spectroscopy: from structure to dynamics. Photochem Photobiol Sci 2015; 14:1586-97. [PMID: 26140679 DOI: 10.1039/c5pp00191a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy, together with spin labeling techniques, has played a major role in the characterization of rhodopsin, the photoreceptor protein and G protein-coupled receptor (GPCR) in rod cells. Two decades ago, these biophysical tools were the first to identify transmembrane helical movements in rhodopsin upon photo-activation, a critical step in the study of GPCR signaling. EPR methods were employed to identify functional loop dynamics within rhodopsin, to measure light-induced millisecond timescale changes in rhodopsin conformation, to characterize the effects of partial agonists on the apoprotein opsin, and to study lipid interactions with rhodopsin. With the emergence of advanced pulsed EPR techniques, the stage was set to determine the amplitude of structural changes in rhodopsin and the dynamics in the rhodopsin signaling complexes. Work in this area has yielded invaluable information about mechanistic properties of GPCRs. Using EPR techniques, receptors are studied in native-like membrane environments and the effects of lipids on conformational equilibria can be explored. This perspective addresses the impact of EPR methods on rhodopsin and GPCR structural biology, highlighting historical discoveries made with spin labeling techniques, and outlining exciting new directions in the field.
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Affiliation(s)
- Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
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17
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Goren MA, Morizumi T, Menon I, Joseph JS, Dittman JS, Cherezov V, Stevens RC, Ernst OP, Menon AK. Constitutive phospholipid scramblase activity of a G protein-coupled receptor. Nat Commun 2014; 5:5115. [PMID: 25296113 PMCID: PMC4198942 DOI: 10.1038/ncomms6115] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 09/01/2014] [Indexed: 12/26/2022] Open
Abstract
Opsin, the rhodopsin apoprotein, was recently shown to be an ATP-independent flippase (or scramblase) that equilibrates phospholipids across photoreceptor disc membranes in mammalian retina, a process required for disc homeostasis. Here we show that scrambling is a constitutive activity of rhodopsin, distinct from its light-sensing function. Upon reconstitution into vesicles, discrete conformational states of the protein (rhodopsin, a metarhodopsin II-mimic, and two forms of opsin) facilitated rapid (>10,000 phospholipids per protein per second) scrambling of phospholipid probes. Our results indicate that the large conformational changes involved in converting rhodopsin to metarhodopsin II are not required for scrambling, and that the lipid translocation pathway either lies near the protein surface or involves membrane packing defects in the vicinity of the protein. Additionally, we demonstrate that β2-adrenergic and adenosine A2A receptors scramble lipids, suggesting that rhodopsin-like G protein-coupled receptors may play an unexpected moonlighting role in re-modeling cell membranes.
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Affiliation(s)
- Michael A Goren
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, USA
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Indu Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, USA
| | - Jeremiah S Joseph
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jeremy S Dittman
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, USA
| | - Vadim Cherezov
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Raymond C Stevens
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Oliver P Ernst
- 1] Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8 [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, New York, New York 10065, USA
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18
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Johnson PJM, Halpin A, Morizumi T, Brown LS, Prokhorenko VI, Ernst OP, Dwayne Miller RJ. The photocycle and ultrafast vibrational dynamics of bacteriorhodopsin in lipid nanodiscs. Phys Chem Chem Phys 2014; 16:21310-20. [PMID: 25178090 DOI: 10.1039/c4cp01826e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photocycle and vibrational dynamics of bacteriorhodopsin in a lipid nanodisc microenvironment have been studied by steady-state and time-resolved spectroscopies. Linear absorption and circular dichroism indicate that the nanodiscs do not perturb the structure of the retinal binding pocket, while transient absorption and flash photolysis measurements show that the photocycle which underlies proton pumping is unchanged from that in the native purple membranes. Vibrational dynamics during the initial photointermediate formation are subsequently studied by ultrafast broadband transient absorption spectroscopy, where the low scattering afforded by the lipid nanodisc microenvironment allows for unambiguous assignment of ground and excited state nuclear dynamics through Fourier filtering of frequency regions of interest and subsequent time domain analysis of the retrieved vibrational dynamics. Canonical ground state oscillations corresponding to high frequency ethylenic and C-C stretches, methyl rocks, and hydrogen out-of-plane wags are retrieved, while large amplitude, short dephasing time vibrations are recovered predominantly in the frequency region associated with out-of-plane dynamics and low frequency torsional modes implicated in isomerization.
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Affiliation(s)
- Philip J M Johnson
- Institute for Optical Sciences & Departments of Chemistry & Physics, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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19
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Redka DS, Morizumi T, Elmslie G, Paranthaman P, Shivnaraine RV, Ellis J, Ernst OP, Wells JW. Coupling of g proteins to reconstituted monomers and tetramers of the M2 muscarinic receptor. J Biol Chem 2014; 289:24347-65. [PMID: 25023280 DOI: 10.1074/jbc.m114.559294] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
G protein-coupled receptors can be reconstituted as monomers in nanodiscs and as tetramers in liposomes. When reconstituted with G proteins, both forms enable an allosteric interaction between agonists and guanylyl nucleotides. Both forms, therefore, are candidates for the complex that controls signaling at the level of the receptor. To identify the biologically relevant form, reconstituted monomers and tetramers of the purified M2 muscarinic receptor were compared with muscarinic receptors in sarcolemmal membranes for the effect of guanosine 5'-[β,γ-imido]triphosphate (GMP-PNP) on the inhibition of N-[(3)H]methylscopolamine by the agonist oxotremorine-M. With monomers, a stepwise increase in the concentration of GMP-PNP effected a lateral, rightward shift in the semilogarithmic binding profile (i.e. a progressive decrease in the apparent affinity of oxotremorine-M). With tetramers and receptors in sarcolemmal membranes, GMP-PNP effected a vertical, upward shift (i.e. an apparent redistribution of sites from a state of high affinity to one of low affinity with no change in affinity per se). The data were analyzed in terms of a mechanistic scheme based on a ligand-regulated equilibrium between uncoupled and G protein-coupled receptors (the "ternary complex model"). The model predicts a rightward shift in the presence of GMP-PNP and could not account for the effects at tetramers in vesicles or receptors in sarcolemmal membranes. Monomers present a special case of the model in which agonists and guanylyl nucleotides interact within a complex that is both constitutive and stable. The results favor oligomers of the M2 receptor over monomers as the biologically relevant state for coupling to G proteins.
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Affiliation(s)
- Dar'ya S Redka
- From the Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Takefumi Morizumi
- the Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Gwendolynne Elmslie
- the Departments of Psychiatry and Pharmacology, Hershey Medical Center, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania 17033, and
| | - Pranavan Paranthaman
- From the Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Rabindra V Shivnaraine
- From the Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - John Ellis
- the Departments of Psychiatry and Pharmacology, Hershey Medical Center, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania 17033, and
| | - Oliver P Ernst
- the Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada, the Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - James W Wells
- From the Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada,
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Park JH, Morizumi T, Li Y, Hong JE, Pai EF, Hofmann KP, Choe HW, Ernst OP. Opsin, a structural model for olfactory receptors? Angew Chem Int Ed Engl 2013; 52:11021-4. [PMID: 24038729 DOI: 10.1002/anie.201302374] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 07/30/2013] [Indexed: 11/11/2022]
Abstract
Receptor-ligand interaction: Olfactory receptors (ORs) are G-protein-coupled receptors (GPCRs), which detect signaling molecules such as hormones and odorants. The structure of opsin, the GPCR employed in vision, with a detergent molecule bound deep in its orthosteric ligand-binding pocket provides a template for OR homology modeling, thus enabling investigation of the structural basis of the mechanism of odorant-receptor recognition.
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Affiliation(s)
- Jung Hee Park
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Chonbuk National University, 570-752 Iksan (Republic of Korea).
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21
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Park JH, Morizumi T, Li Y, Hong JE, Pai EF, Hofmann KP, Choe HW, Ernst OP. Opsin, a Structural Model for Olfactory Receptors? Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302374] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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22
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Gurevich V, Kim M, Vishnivetskiy SA, Van Eps N, Alexander NS, Cleghorn WM, Zhan X, Hanson SM, Morizumi T, Ernst OP, Meiler J, Hubbell WL. The conformation of active receptor‐bound arrestin. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.1031.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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23
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Johnson PJM, Halpin A, Morizumi T, Prokhorenko VI, Ernst OP, Dwayne Miller RJ. Mixed Potential Energy Surfaces of the Ultrafast Isomerization of Retinal in Bacteriorhodopsin. EPJ Web of Conferences 2013. [DOI: 10.1051/epjconf/20134107020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Yamashita T, Nakamura S, Tsutsui K, Morizumi T, Shichida Y. Chloride-Dependent Spectral Tuning Mechanism of L-Group Cone Visual Pigments. Biochemistry 2013; 52:1192-7. [DOI: 10.1021/bi3016058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takahiro Yamashita
- Department of Biophysics,
Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shuhei Nakamura
- Department of Biophysics,
Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kei Tsutsui
- Department of Biophysics,
Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Takefumi Morizumi
- Department of Biophysics,
Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshinori Shichida
- Department of Biophysics,
Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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25
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Redka DS, Morizumi T, Paranthaman P, Heerklotz H, Ernst OP, Wells JW. Functional Comparison of Monomers and Tetramers of the M2 Muscarinic Receptor. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Morizumi T, Sato K, Shichida Y. Spectroscopic Analysis of the Effect of Chloride on the Active Intermediates of the Primate L Group Cone Visual Pigment. Biochemistry 2012; 51:10017-23. [DOI: 10.1021/bi300995s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takefumi Morizumi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Keita Sato
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Elgeti M, Kazmin R, Heck M, Morizumi T, Ritter E, Scheerer P, Ernst OP, Siebert F, Hofmann KP, Bartl FJ. Conserved Tyr223(5.58) plays different roles in the activation and G-protein interaction of rhodopsin. J Am Chem Soc 2011; 133:7159-65. [PMID: 21506561 DOI: 10.1021/ja200545n] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rhodopsin, a seven transmembrane helix (TM) receptor, binds its ligand 11-cis-retinal via a protonated Schiff base. Coupling to the G-protein transducin (G(t)) occurs after light-induced cis/trans-retinal isomerization, which leads through photoproducts into a sequence of metarhodopsin (Meta) states: Meta I ⇌ Meta IIa ⇌ Meta IIb ⇌ Meta IIbH(+). The structural changes behind this three-step activation scheme are mediated by microswitch domains consisting of conserved amino acids. Here we focus on Tyr223(5.58) as part of the Y(5.58)X(7)K(R)(5.66) motif. Mutation to Ala, Phe, or Glu results in specific impairments of G(t)-activation measured by intrinsic G(t) fluorescence. UV-vis/FTIR spectroscopy of rhodopsin and its complex with a C-terminal G(t)α peptide allows the assignment of these deficiencies to specific steps in the activation path. Effects of mutation occur already in Meta I but do not directly influence deprotonation of the Schiff base during formation of Meta IIa. Absence of the whole phenol ring (Y223A) allows the activating motion of TM6 in Meta IIb but impairs the coupling to G(t). When only the hydroxyl group is lacking (Y223F), Meta IIb does not accumulate, but the activity toward G(t) remains substantial. From the FTIR features of Meta IIbH(+) we conclude that proton uptake to Glu134(3.49) is mandatory for Tyr223(5.58) to engage in the interaction with the key player Arg135(3.50) predicted by X-ray analysis. This polar interaction is partially recovered in Y223E, explaining its relatively high activity. Only the phenol side chain of tyrosine provides all characteristics for accumulation of the active state and G-protein activation.
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Affiliation(s)
- Matthias Elgeti
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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Bayburt TH, Vishnivetskiy SA, McLean MA, Morizumi T, Huang CC, Tesmer JJG, Ernst OP, Sligar SG, Gurevich VV. Monomeric rhodopsin is sufficient for normal rhodopsin kinase (GRK1) phosphorylation and arrestin-1 binding. J Biol Chem 2010; 286:1420-8. [PMID: 20966068 DOI: 10.1074/jbc.m110.151043] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
G-protein-coupled receptor (GPCR) oligomerization has been observed in a wide variety of experimental contexts, but the functional significance of this phenomenon at different stages of the life cycle of class A GPCRs remains to be elucidated. Rhodopsin (Rh), a prototypical class A GPCR of visual transduction, is also capable of forming dimers and higher order oligomers. The recent demonstration that Rh monomer is sufficient to activate its cognate G protein, transducin, prompted us to test whether the same monomeric state is sufficient for rhodopsin phosphorylation and arrestin-1 binding. Here we show that monomeric active rhodopsin is phosphorylated by rhodopsin kinase (GRK1) as efficiently as rhodopsin in the native disc membrane. Monomeric phosphorylated light-activated Rh (P-Rh*) in nanodiscs binds arrestin-1 essentially as well as P-Rh* in native disc membranes. We also measured the affinity of arrestin-1 for P-Rh* in nanodiscs using a fluorescence-based assay and found that arrestin-1 interacts with monomeric P-Rh* with low nanomolar affinity and 1:1 stoichiometry, as previously determined in native disc membranes. Thus, similar to transducin activation, rhodopsin phosphorylation by GRK1 and high affinity arrestin-1 binding only requires a rhodopsin monomer.
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Affiliation(s)
- Timothy H Bayburt
- Department of Biochemistry, University of Illinois, Urbana, Illinois 61801, USA
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29
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Vishnivetskiy SA, Bayburt TH, Morizumi T, Huang C, Tesmer JJ, Ernst OP, Sligar SG, Gurevich VV. Monomeric rhodopsin in nanodiscs is phosphorylated by rhodopsin kinase and binds arrestin with high affinity in the presence of negatively charged lipids. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.707.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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30
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Sato K, Morizumi T, Yamashita T, Shichida Y. Direct observation of the pH-dependent equilibrium between metarhodopsins I and II and the pH-independent interaction of metarhodopsin II with transducin C-terminal peptide. Biochemistry 2010; 49:736-41. [PMID: 20030396 DOI: 10.1021/bi9018412] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bovine rhodopsin contains 11-cis-retinal as a light-absorbing chromophore that binds to a lysine residue of the apoprotein opsin via a protonated Schiff base linkage. Light isomerizes 11-cis-retinal into the all-trans form, which eventually leads to the formation of an enzymatically active state, metarhodopsin II (MII). It is widely believed that MII forms a pH-dependent equilibrium with metarhodopsin I (MI), but direct evidence for this equilibrium has not been reported. Here, we confirmed this equilibrium by direct observation of the mutual conversions of MI and MII upon changing the pH of the MI/MII mixture. We also observed a reversible binding of the synthetic peptide constituting the C-terminal 11 amino acids of the transducin alpha-subunit to MII, which resulted in change of the amounts of MI and MII in the equilibrium. Interestingly, addition of the peptide did not induce a simple pK(a) shift but rather induced an increase of the MII fraction at high pH. These results indicate that in addition to the MII that is formed from MI in a pH-dependent manner there also exists another MII, which is in equilibrium with MI in a pH-independent manner and can bind to the peptide. Therefore, there is no need for proton uptake by the protein moiety of opsin for the binding to the peptide.
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Affiliation(s)
- Keita Sato
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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31
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Morizumi T, Kimata N, Terakita A, Imamoto Y, Yamashita T, Shichida Y. G Protein Subtype Specificity of Rhodopsin Intermediates Metarhodopsin Ib and Metarhodopsin II. Photochem Photobiol 2009; 85:57-62. [DOI: 10.1111/j.1751-1097.2008.00396.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Abstract
Rhodopsin is a member of the family of G-protein-coupled receptors (GPCRs), and is an excellent molecular switch for converting light signals into electrical response of the rod photoreceptor cells. Light initiates cis-trans isomerization of the retinal chromophore of rhodopsin and leads to the formation of several thermolabile intermediates during the bleaching process. Recent investigations have identified spectrally distinguishable two intermediate states that can interact with the retinal G-protein, transducin, and have elucidated the functional sharing of these intermediates. The initial contact with GDP-bound G-protein occurs in the meta-Ib intermediate state, which has a protonated Schiff base as its chromophore. The meta-Ib intermediate in the complex with the G-protein converts to the meta-II intermediate with releasing GDP from the alpha-subunit of the G protein. Meta-II has a de-protonated Schiff base chromophore and induces binding of GTP to the alpha-subunit of the G-protein. Thus, the GDP-GTP exchange reaction, namely G-protein activation, by rhodopsin proceeds through at least two steps, with conformational changes in both rhodopsin and the G-protein.
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Affiliation(s)
- Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, CREST, Japan Science and Technology Agency, Japan.
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Imai H, Kefalov V, Sakurai K, Chisaka O, Ueda Y, Onishi A, Morizumi T, Fu Y, Ichikawa K, Nakatani K, Honda Y, Chen J, Yau KW, Shichida Y. Molecular properties of rhodopsin and rod function. J Biol Chem 2007; 282:6677-84. [PMID: 17194706 PMCID: PMC2885910 DOI: 10.1074/jbc.m610086200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Signal transduction in rod cells begins with photon absorption by rhodopsin and leads to the generation of an electrical response. The response profile is determined by the molecular properties of the phototransduction components. To examine how the molecular properties of rhodopsin correlate with the rod-response profile, we have generated a knock-in mouse with rhodopsin replaced by its E122Q mutant, which exhibits properties different from those of wild-type (WT) rhodopsin. Knock-in mouse rods with E122Q rhodopsin exhibited a photosensitivity about 70% of WT. Correspondingly, their single-photon response had an amplitude about 80% of WT, and a rate of decline from peak about 1.3 times of WT. The overall 30% lower photosensitivity of mutant rods can be explained by a lower pigment photosensitivity (0.9) and the smaller single-photon response (0.8). The slower decline of the response, however, did not correlate with the 10-fold shorter lifetime of the meta-II state of E122Q rhodopsin. This shorter lifetime became evident in the recovery phase of rod cells only when arrestin was absent. Simulation analysis of the photoresponse profile indicated that the slower decline and the smaller amplitude of the single-photon response can both be explained by the shift in the meta-I/meta-II equilibrium of E122Q rhodopsin toward meta-I. The difference in meta-III lifetime between WT and E122Q mutant became obvious in the recovery phase of the dark current after moderate photobleaching of rod cells. Thus, the present study clearly reveals how the molecular properties of rhodopsin affect the amplitude, shape, and kinetics of the rod response.
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Affiliation(s)
- Hiroo Imai
- Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto 606-8502, Japan
| | - Vladimir Kefalov
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Keisuke Sakurai
- Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto 606-8502, Japan
| | - Osamu Chisaka
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshiki Ueda
- Department of Ophthalmology and Visual Science, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Akishi Onishi
- Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto 606-8502, Japan
| | - Takefumi Morizumi
- Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto 606-8502, Japan
| | - Yingbin Fu
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Kazuhisa Ichikawa
- Department of Brain and Bioinformation Science, Kanazawa Institute of Technology, Ishikawa 924-0838, Japan
| | - Kei Nakatani
- Graduate School of Life and Environmental Sciences, University of Tsukuba and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Ibaraki 305-8572, Japan
| | - Yoshihito Honda
- Department of Ophthalmology and Visual Science, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Jeannie Chen
- The Mary D. Allen Laboratory for Vision Research, Doheny Eye Institute, Keck School of Medicine, University of Southern California, Los Angeles, California 90033
| | - King-Wai Yau
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto 606-8502, Japan
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Morizumi T, Imai H, Shichida Y. Direct observation of the complex formation of GDP-bound transducin with the rhodopsin intermediate having a visible absorption maximum in rod outer segment membranes. Biochemistry 2005; 44:9936-43. [PMID: 16026166 DOI: 10.1021/bi0504512] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rhodopsin is a photoreceptive protein that is present in rod photoreceptor cells, inducing a GDP-GTP exchange reaction on the retinal G-protein transducin (Gt) upon light absorption. This exchange reaction proceeds through at least three steps, which include the binding of photoactivated rhodopsin to GDP-bound Gt, the dissociation of GDP from the rhodopsin-Gt complex, and the binding of GTP to the nucleotide-unbound Gt. These steps have been thought to occur after the formation of the rhodopsin intermediate, meta-II; however, the extra formation of meta-II, which reflects the formation of a complex with Gt, was inhibited in the presence of excess GDP. Here, we use a newly developed CCD spectrophotometer to show that a meta-II precursor, meta-Ib, which has an absorption maximum at visible region, can bind to Gt in its GDP-bound form in urea-washed bovine rod outer segment membranes. The affinity of meta-Ib for GDP-bound Gt is about two times less than that of meta-II for GDP-unbound Gt, indicating that the extra formation of meta-II is observed at equilibrium even in the presence of the meta-Ib-Gt complex. This is the first identification of a complex that includes the GDP-bound form of G protein. Our results strongly suggest that the protein conformational change of the rhodopsin intermediate after binding to Gt is important for the induction of the nucleotide release from the alpha-subunit of Gt.
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Affiliation(s)
- Takefumi Morizumi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan, and CREST, Japan Science and Technology Agency, Japan
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Imai H, Morizumi T, Shichida Y. [Interaction between rhodopsin intermediates and G-protein transducin on the outer segment membrane of photoreceptor cells]. Tanpakushitsu Kakusan Koso 2005; 50:1220-5. [PMID: 16104588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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36
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Imai H, Kuwayama S, Onishi A, Morizumi T, Chisaka O, Shichida Y. Molecular properties of rod and cone visual pigments from purified chicken cone pigments to mouse rhodopsin in situ. Photochem Photobiol Sci 2005; 4:667-74. [PMID: 16121275 DOI: 10.1039/b416731g] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the molecular properties of rod and cone visual pigments to elucidate the differences in the molecular mechanism(s) of the photoresponses between rod and cone photoreceptor cells. We have found that the cone pigments exhibit a faster pigment regeneration and faster decay of meta-II and meta-III intermediates than the rod pigment, rhodopsin. Mutagenesis experiments have revealed that the amino acid residues at positions 122 and 189 in the opsins are the determinants for these differences. In order to study the relationship between the molecular properties of visual pigments and the physiology of rod photoreceptors, we used mouse rhodopsin as a model pigment because, by gene-targeting, the spectral properties of the pigment can be directly correlated to the physiology of the cells. In the present paper, we summarize the spectroscopic properties of cone pigments and describe our studies with mouse rhodopsin utilizing a high performance charge coupled device (CCD) spectrophotometer.
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Affiliation(s)
- Hiroo Imai
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
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Abstract
Vertebrate retinas have two types of photoreceptor cells, rods and cones, which contain visual pigments with different molecular properties. These pigments diverged from a common ancestor, and their difference in molecular properties originates from the difference in their amino acid residues. We previously reported that the difference in decay times of G protein-activating meta-II intermediates between the chicken rhodopsin and green-sensitive cone (chicken green) pigments is about 50 times. This difference only originates from the differences of two residues at positions 122 and 189 (Kuwayama, S., Imai, H., Hirano, T., Terakita, A., and Shichida, Y. (2002) Biochemistry 41, 15245-15252). Here we show that the meta-III intermediates exhibit about 700 times difference in decay times between the two pigments, and the faster decay in chicken green can be converted to the slower decay in rhodopsin by replacing the residues in chicken green with the corresponding rhodopsin residues. However, the inverse directional conversion did not occur when the two residues in rhodopsin were replaced by those of chicken green. Analysis using chimerical mutants derived from these pigments has demonstrated that amino acid residues responsible for the slow rhodopsin meta-III decay are situated at several positions throughout the C-terminal half of rhodopsin. Considering that rhodopsins evolved from cone pigments, it has been suggested that the molecular properties of rhodopsin have been optimized by mutations at several positions, and the chicken green mutants at two positions could be rhodopsin-like pigments transiently produced in the course of molecular evolution.
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Affiliation(s)
- Shigeki Kuwayama
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, and CREST, Japan Science and Technology Agency, Kyoto, Japan
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Morizumi T, Imai H, Shichida Y. Two-step mechanism of interaction of rhodopsin intermediates with the C-terminal region of the transducin alpha-subunit. J Biochem 2003; 134:259-67. [PMID: 12966076 DOI: 10.1093/jb/mvg139] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Rhodopsin is a prototypical G-protein-coupled receptor that contains 11-cis-retinal as a light-absorbing chromophore. Light causes conformational changes in the protein moiety through cis-trans isomerization of the chromophore, which leads to the formation of G-protein-interacting states. Our previous studies indicated that there are two intermediate states of rhodopsin, Meta Ib and Meta II, which interact differently with retinal G-protein transducin (Gt) [S. Tachibanaki, H. Imai, T. Mizukami, T. Okada, Y. Imamoto, T. Matsuda, Y. Fukada, A. Terakita, and Y. Shichida (1997) Biochemistry 36, 14173-14180]. Here we demonstrate that the interactions of Gt with these intermediates in the absence of GTPgammaS can be mimicked by the C-terminus 11-amino acid peptide (340-350) of the alpha-subunit of Gt (Gt(alpha)), suggesting that the C-terminal region of Gt(alpha) plays important roles in the interaction with rhodopsin intermediates. Replacement of either of the two leucine residues (Leu344 and Leu349) in the peptide with alanine caused the loss of the interaction with Meta II. However, the interaction with Meta Ib was abolished only when both residues were replaced. These results indicate that rearrangement of the C-terminal region of Gt(alpha) after the binding of a rhodopsin intermediate is necessary for the GDP-GTP exchange reaction on Gt(alpha).
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Affiliation(s)
- Takefumi Morizumi
- Department of Biophysics, Graduate School of Science, Kyoto University, and Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Kyoto 606-8502
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