1
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Podoliak E, Lamm GHU, Marin E, Schellbach AV, Fedotov DA, Stetsenko A, Asido M, Maliar N, Bourenkov G, Balandin T, Baeken C, Astashkin R, Schneider TR, Bateman A, Wachtveitl J, Schapiro I, Busskamp V, Guskov A, Gordeliy V, Alekseev A, Kovalev K. A subgroup of light-driven sodium pumps with an additional Schiff base counterion. Nat Commun 2024; 15:3119. [PMID: 38600129 PMCID: PMC11006869 DOI: 10.1038/s41467-024-47469-0] [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: 10/12/2023] [Accepted: 04/01/2024] [Indexed: 04/12/2024] Open
Abstract
Light-driven sodium pumps (NaRs) are unique ion-transporting microbial rhodopsins. The major group of NaRs is characterized by an NDQ motif and has two aspartic acid residues in the central region essential for sodium transport. Here we identify a subgroup of the NDQ rhodopsins bearing an additional glutamic acid residue in the close vicinity to the retinal Schiff base. We thoroughly characterize a member of this subgroup, namely the protein ErNaR from Erythrobacter sp. HL-111 and show that the additional glutamic acid results in almost complete loss of pH sensitivity for sodium-pumping activity, which is in contrast to previously studied NaRs. ErNaR is capable of transporting sodium efficiently even at acidic pH levels. X-ray crystallography and single particle cryo-electron microscopy reveal that the additional glutamic acid residue mediates the connection between the other two Schiff base counterions and strongly interacts with the aspartic acid of the characteristic NDQ motif. Hence, it reduces its pKa. Our findings shed light on a subgroup of NaRs and might serve as a basis for their rational optimization for optogenetics.
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Affiliation(s)
- E Podoliak
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - G H U Lamm
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - E Marin
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - A V Schellbach
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - D A Fedotov
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - A Stetsenko
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - M Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - N Maliar
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - G Bourenkov
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany
| | - T Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - C Baeken
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - R Astashkin
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - T R Schneider
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany
| | - A Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - J Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - I Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - V Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - A Guskov
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - V Gordeliy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - A Alekseev
- University Medical Center Göttingen, Institute for Auditory Neuroscience and InnerEarLab, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - K Kovalev
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany.
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2
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Rokitskaya TI, Maliar N, Kovalev KV, Volkov O, Gordeliy VI, Antonenko YN. Rhodopsin Channel Activity Can Be Evaluated by Measuring the Photocurrent Voltage Dependence in Planar Bilayer Lipid Membranes. Biochemistry (Mosc) 2021; 86:409-419. [PMID: 33941063 DOI: 10.1134/s0006297921040039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The studies of the functional properties of retinal-containing proteins often include experiments in model membrane systems, e.g., measurements of electric current through planar bilayer lipid membranes (BLMs) with proteoliposomes adsorbed on one of the membrane surfaces. However, the possibilities of this method have not been fully explored yet. We demonstrated that the voltage dependence of stationary photocurrents for two light-sensitive proteins, bacteriorhodopsin (bR) and channelrhodopsin 2 (ChR2), in the presence of protonophore had very different characteristics. In the case of the bR (proton pump), the photocurrent through the BLM did not change direction when the polarity of the applied voltage was switched. In the case of the photosensitive channel protein ChR2, the photocurrent increased with the increase in voltage and the current polarity changed with the change in the voltage polarity. The protonophore 4,5,6,7-tetrachloro-2-trifluoromethyl benzimidazole (TTFB) was more efficient in the maximizing stationary photocurrents. In the presence of carbonyl cyanide-m-chlorophenylhydrazone (CCCP), the amplitude of the measured photocurrents for bR significantly decreased, while in the case of ChR2, the photocurrents virtually disappeared. The difference between the effects of TTFB and CCCP was apparently due to the fact that, in contrast to TTFB, CCCP transfers protons across the liposome membranes with a higher rate than through the decane-containing BLM used as a surface for the proteoliposome adsorption.
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Affiliation(s)
- Tatyana I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Nina Maliar
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Kirill V Kovalev
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, 38044, France
| | - Oleksandr Volkov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Juelich, 52425, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Juelich, 52425, Germany
| | - Valentin I Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, 38044, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Juelich, 52425, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Juelich, 52425, Germany
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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3
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Bogorodskiy A, Okhrimenko I, Maslov I, Maliar N, Burkatovskii D, von Ameln F, Schulga A, Jakobs P, Altschmied J, Haendeler J, Katranidis A, Sorokin I, Mishin A, Gordeliy V, Büldt G, Voos W, Gensch T, Borshchevskiy V. Accessing Mitochondrial Protein Import in Living Cells by Protein Microinjection. Front Cell Dev Biol 2021; 9:698658. [PMID: 34307376 PMCID: PMC8292824 DOI: 10.3389/fcell.2021.698658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/15/2021] [Indexed: 01/06/2023] Open
Abstract
Mitochondrial protein biogenesis relies almost exclusively on the expression of nuclear-encoded polypeptides. The current model postulates that most of these proteins have to be delivered to their final mitochondrial destination after their synthesis in the cytoplasm. However, the knowledge of this process remains limited due to the absence of proper experimental real-time approaches to study mitochondria in their native cellular environment. We developed a gentle microinjection procedure for fluorescent reporter proteins allowing a direct non-invasive study of protein transport in living cells. As a proof of principle, we visualized potential-dependent protein import into mitochondria inside intact cells in real-time. We validated that our approach does not distort mitochondrial morphology and preserves the endogenous expression system as well as mitochondrial protein translocation machinery. We observed that a release of nascent polypeptides chains from actively translating cellular ribosomes by puromycin strongly increased the import rate of the microinjected pre-protein. This suggests that a substantial amount of mitochondrial translocase complexes was involved in co-translational protein import of endogenously expressed pre-proteins. Our protein microinjection method opens new possibilities to study the role of mitochondrial protein import in cell models of various pathological conditions as well as aging processes.
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Affiliation(s)
- Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nina Maliar
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmitrii Burkatovskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Florian von Ameln
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- IUF–Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Alexey Schulga
- Molecular Immunology Laboratory, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Philipp Jakobs
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Joachim Altschmied
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- IUF–Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Judith Haendeler
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexandros Katranidis
- Institute of Biological Information Processing (IBI-6: Cellular Structural Biology), Forschungszentrum Jülich, Jülich, Germany
| | - Ivan Sorokin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Georg Büldt
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Wolfgang Voos
- Institute of Biochemistry and Molecular Biology (IBMB), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Thomas Gensch
- Institute of Biological Information Processing (IBI-1: Molecular and Cellular Physiology), Forschungszentrum Jülich, Jülich, Germany
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
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4
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Maliar N, Okhrimenko IS, Petrovskaya LE, Alekseev AA, Kovalev KV, Soloviov DV, Popov PA, Rokitskaya TI, Antonenko YN, Zabelskii DV, Dolgikh DA, Kirpichnikov MP, Gordeliy VI. Erratum to: Novel pH-Sensitive Microbial Rhodopsin from Sphingomonas paucimobilis. DOKL BIOCHEM BIOPHYS 2021; 497:158. [PMID: 33895933 DOI: 10.1134/s1607672921020198] [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] [Received: 01/28/2021] [Revised: 01/28/2021] [Accepted: 01/28/2021] [Indexed: 11/23/2022]
Affiliation(s)
- N Maliar
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia
| | - I S Okhrimenko
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia
| | - L E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - A A Alekseev
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - K V Kovalev
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institut de Biologie Structurale (IBS), University Grenoble Alpes,CEA, CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - D V Soloviov
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institute for Safety Problems of Nuclear Power Plants, National Academy of Sciences of Ukraine, Kyiv, Ukraine.,Joint Institute for Nuclear Research, Dubna, Russia
| | - P A Popov
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - T I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Y N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - D V Zabelskii
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - D A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Biological Faculty, Moscow State University, Moscow, Russia
| | - M P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Biological Faculty, Moscow State University, Moscow, Russia
| | - V I Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia. .,Institut de Biologie Structurale (IBS), University Grenoble Alpes,CEA, CNRS, Grenoble, France. .,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany. .,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.
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5
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Maliar N, Okhrimenko IS, Petrovskaya LE, Alekseev AA, Kovalev KV, Soloviov DV, Popov PA, Rokitskaya TI, Antonenko YN, Zabelskii DV, Dolgikh DA, Kirpichnikov MP, Gordeliy VI. Novel pH-Sensitive Microbial Rhodopsin from Sphingomonas paucimobilis. DOKL BIOCHEM BIOPHYS 2020; 495:342-346. [PMID: 33368048 DOI: 10.1134/s1607672920060162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 09/03/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 11/23/2022]
Abstract
This work provides the first characteristics of the rhodopsin SpaR from Sphingomonas paucimobilis, aerobic bacteria associated with opportunistic infections. The sequence analysis of SpaR has shown that this protein has unusual DTS motif which has never reported in rhodopsins from Proteobacteria. We report that SpaR operates as an outward proton pump at low pH; however, proton pumping is almost absent at neutral and alkaline pH. The photocycle of this rhodopsin in detergent micelles slows down with an increase in pH because of longer Schiff base reprotonation. Our results show that the novel microbial ion transporter SpaR of interest both as an object for basic research of membrane proteins and as a promising optogenetic tool.
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Affiliation(s)
- N Maliar
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia
| | - I S Okhrimenko
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia
| | - L E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - A A Alekseev
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - K V Kovalev
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - D V Soloviov
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institute for Safety Problems of Nuclear Power Plants, National Academy of Sciences of Ukraine, Kyiv, Ukraine.,Joint Institute for Nuclear Research, Dubna, Russia
| | - P A Popov
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - T I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - Y N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
| | - D V Zabelskii
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - D A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Biological Faculty, Moscow State University, Moscow, Russia
| | - M P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Biological Faculty, Moscow State University, Moscow, Russia
| | - V I Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Moscow oblast, Russia. .,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France. .,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany. .,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.
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6
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Kovalev K, Astashkin R, Gushchin I, Orekhov P, Volkov D, Zinovev E, Marin E, Rulev M, Alekseev A, Royant A, Carpentier P, Vaganova S, Zabelskii D, Baeken C, Sergeev I, Balandin T, Bourenkov G, Carpena X, Boer R, Maliar N, Borshchevskiy V, Büldt G, Bamberg E, Gordeliy V. Molecular mechanism of light-driven sodium pumping. Nat Commun 2020; 11:2137. [PMID: 32358514 PMCID: PMC7195465 DOI: 10.1038/s41467-020-16032-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/03/2020] [Indexed: 11/13/2022] Open
Abstract
The light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 Å, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools.
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Affiliation(s)
- Kirill Kovalev
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Roman Astashkin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmytro Volkov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Egor Zinovev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Maksim Rulev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- European Synchrotron Radiation Facility Grenoble, Grenoble, France
| | - Alexey Alekseev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Antoine Royant
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- European Synchrotron Radiation Facility Grenoble, Grenoble, France
| | - Philippe Carpentier
- European Synchrotron Radiation Facility Grenoble, Grenoble, France
- Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Svetlana Vaganova
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dmitrii Zabelskii
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Christian Baeken
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ilya Sergeev
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Xavier Carpena
- XALOC beamline, ALBA synchrotron (CELLS), Cerdanyola del Valles, Catalunya, Spain
| | - Roeland Boer
- XALOC beamline, ALBA synchrotron (CELLS), Cerdanyola del Valles, Catalunya, Spain
| | - Nina Maliar
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Georg Büldt
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ernst Bamberg
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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