1
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Nikolaev A, Kuzmin A, Markeeva E, Kuznetsova E, Ryzhykau YL, Semenov O, Anuchina A, Remeeva A, Gushchin I. Reengineering of a flavin-binding fluorescent protein using ProteinMPNN. Protein Sci 2024; 33:e4958. [PMID: 38501498 PMCID: PMC10949330 DOI: 10.1002/pro.4958] [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: 09/05/2023] [Revised: 01/12/2024] [Accepted: 02/18/2024] [Indexed: 03/20/2024]
Abstract
Recent advances in machine learning techniques have led to development of a number of protein design and engineering approaches. One of them, ProteinMPNN, predicts an amino acid sequence that would fold and match user-defined backbone structure. Its performance was previously tested for proteins composed of standard amino acids, as well as for peptide- and protein-binding proteins. In this short report, we test whether ProteinMPNN can be used to reengineer a non-proteinaceous ligand-binding protein, flavin-based fluorescent protein CagFbFP. We fixed the native backbone conformation and the identity of 20 amino acids interacting with the chromophore (flavin mononucleotide, FMN) while letting ProteinMPNN predict the rest of the sequence. The software package suggested replacing 36-48 out of the remaining 86 amino acids so that the resulting sequences are 55%-66% identical to the original one. The three designs that we tested experimentally displayed different expression levels, yet all were able to bind FMN and displayed fluorescence, thermal stability, and other properties similar to those of CagFbFP. Our results demonstrate that ProteinMPNN can be used to generate diverging unnatural variants of fluorescent proteins, and, more generally, to reengineer proteins without losing their ligand-binding capabilities.
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Affiliation(s)
- Andrey Nikolaev
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alexander Kuzmin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elena Markeeva
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elizaveta Kuznetsova
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
- Frank Laboratory of Neutron PhysicsJoint Institute for Nuclear ResearchDubnaRussia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Arina Anuchina
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
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2
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Kiirikki AM, Antila HS, Bort LS, Buslaev P, Favela-Rosales F, Ferreira TM, Fuchs PFJ, Garcia-Fandino R, Gushchin I, Kav B, Kučerka N, Kula P, Kurki M, Kuzmin A, Lalitha A, Lolicato F, Madsen JJ, Miettinen MS, Mingham C, Monticelli L, Nencini R, Nesterenko AM, Piggot TJ, Piñeiro Á, Reuter N, Samantray S, Suárez-Lestón F, Talandashti R, Ollila OHS. Overlay databank unlocks data-driven analyses of biomolecules for all. Nat Commun 2024; 15:1136. [PMID: 38326316 PMCID: PMC10850068 DOI: 10.1038/s41467-024-45189-z] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024] Open
Abstract
Tools based on artificial intelligence (AI) are currently revolutionising many fields, yet their applications are often limited by the lack of suitable training data in programmatically accessible format. Here we propose an effective solution to make data scattered in various locations and formats accessible for data-driven and machine learning applications using the overlay databank format. To demonstrate the practical relevance of such approach, we present the NMRlipids Databank-a community-driven, open-for-all database featuring programmatic access to quality-evaluated atom-resolution molecular dynamics simulations of cellular membranes. Cellular membrane lipid composition is implicated in diseases and controls major biological functions, but membranes are difficult to study experimentally due to their intrinsic disorder and complex phase behaviour. While MD simulations have been useful in understanding membrane systems, they require significant computational resources and often suffer from inaccuracies in model parameters. Here, we demonstrate how programmable interface for flexible implementation of data-driven and machine learning applications, and rapid access to simulation data through a graphical user interface, unlock possibilities beyond current MD simulation and experimental studies to understand cellular membranes. The proposed overlay databank concept can be further applied to other biomolecules, as well as in other fields where similar barriers hinder the AI revolution.
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Affiliation(s)
- Anne M Kiirikki
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
| | - Hanne S Antila
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Department of Biomedicine, University of Bergen, 5020, Bergen, Norway
| | - Lara S Bort
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- University of Potsdam, Institute of Physics and Astronomy, 14476, Potsdam-Golm, Germany
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Fernando Favela-Rosales
- Departamento de Ciencias Básicas, Tecnológico Nacional de México - ITS Zacatecas Occidente, Sombrerete, 99102, Zacatecas, Mexico
| | - Tiago Mendes Ferreira
- NMR group - Institute for Physics, Martin Luther University Halle-Wittenberg, 06120, Halle (Saale), Germany
| | - Patrick F J Fuchs
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), F-75005, Paris, France
- Université Paris Cité, F-75006, Paris, France
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | | | - Batuhan Kav
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428, Jülich, Germany
- ariadne.ai GmbH (Germany), Häusserstraße 3, 69115, Heidelberg, Germany
| | - Norbert Kučerka
- Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, 832 32, Bratislava, Slovakia
| | - Patrik Kula
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610, Prague, Czech Republic
| | - Milla Kurki
- School of Pharmacy, University of Eastern Finland, 70211, Kuopio, Finland
| | | | - Anusha Lalitha
- Institut Charles Gerhardt Montpellier (UMR CNRS 5253), Université Montpellier, Place Eugène Bataillon, 34095, Montpellier, Cedex 05, France
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany
- Department of Physics, University of Helsinki, FI-00014, Helsinki, Finland
| | - Jesper J Madsen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 33612, Tampa, FL, USA
- Center for Global Health and Infectious Diseases Research, Global and Planetary Health, College of Public Health, University of South Florida, 33612, Tampa, FL, USA
| | - Markus S Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - Cedric Mingham
- Hochschule Mannheim, University of Applied Sciences, 68163, Mannheim, Germany
| | - Luca Monticelli
- University of Lyon, CNRS, Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), F-69007, Lyon, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), Lyon, France
| | - Ricky Nencini
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, 00014, Helsinki, Finland
| | - Alexey M Nesterenko
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - Thomas J Piggot
- Chemistry, University of Southampton, Highfield, SO17 1BJ, Southampton, UK
| | - Ángel Piñeiro
- Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - Suman Samantray
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Fabián Suárez-Lestón
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, E-15782, Santiago de Compostela, Spain
- Department of Applied Physics, Faculty of Physics, University of Santiago de Compostela, E-15782, Santiago de Compostela, Spain
- MD.USE Innovations S.L., Edificio Emprendia, 15782, Santiago de Compostela, Spain
| | - Reza Talandashti
- Department of Chemistry, University of Bergen, 5007, Bergen, Norway
- Department of Informatics, Computational Biology Unit, University of Bergen, 5008, Bergen, Norway
| | - O H Samuli Ollila
- University of Helsinki, Institute of Biotechnology, Helsinki, Finland.
- VTT Technical Research Centre of Finland, Espoo, Finland.
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3
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Nikolaev A, Tropina EV, Boldyrev KN, Maksimov EG, Borshchevskiy V, Mishin A, Yudenko A, Kuzmin A, Kuznetsova E, Semenov O, Remeeva A, Gushchin I. Two distinct mechanisms of flavoprotein spectral tuning revealed by low-temperature and time-dependent spectroscopy. Protein Sci 2024; 33:e4851. [PMID: 38038877 PMCID: PMC10731561 DOI: 10.1002/pro.4851] [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: 07/22/2023] [Revised: 10/22/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Flavins such as flavin mononucleotide or flavin adenine dinucleotide are bound by diverse proteins, yet have very similar spectra when in the oxidized state. Recently, we developed new variants of flavin-binding protein CagFbFP exhibiting notable blue (Q148V) or red (I52V A85Q) shifts of fluorescence emission maxima. Here, we use time-resolved and low-temperature spectroscopy to show that whereas the chromophore environment is static in Q148V, an additional protein-flavin hydrogen bond is formed upon photoexcitation in the I52V A85Q variant. Consequently, in Q148V, excitation, emission, and phosphorescence spectra are shifted, whereas in I52V A85Q, excitation and low-temperature phosphorescence spectra are relatively unchanged, while emission spectrum is altered. We also determine the x-ray structures of the two variants to reveal the flavin environment and complement the spectroscopy data. Our findings illustrate two distinct color-tuning mechanisms of flavin-binding proteins and could be helpful for the engineering of new variants with improved optical properties.
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Affiliation(s)
- Andrey Nikolaev
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elena V. Tropina
- Institute of Spectroscopy RASTroitskMoscowRussia
- National Research University Higher School of EconomicsMoscowRussia
| | | | | | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alexander Kuzmin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elizaveta Kuznetsova
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
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4
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Kovalev K, Tsybrov F, Alekseev A, Shevchenko V, Soloviov D, Siletsky S, Bourenkov G, Agthe M, Nikolova M, von Stetten D, Astashkin R, Bukhdruker S, Chizhov I, Royant A, Kuzmin A, Gushchin I, Rosselli R, Rodriguez-Valera F, Ilyinskiy N, Rogachev A, Borshchevskiy V, Schneider TR, Bamberg E, Gordeliy V. Mechanisms of inward transmembrane proton translocation. Nat Struct Mol Biol 2023:10.1038/s41594-023-01020-9. [PMID: 37386213 DOI: 10.1038/s41594-023-01020-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 05/15/2023] [Indexed: 07/01/2023]
Abstract
Proton transport is indispensable for cell life. It is believed that molecular mechanisms of proton movement through different types of proton-conducting molecules have general universal features. However, elucidation of such mechanisms is a challenge. It requires true-atomic-resolution structures of all key proton-conducting states. Here we present a comprehensive function-structure study of a light-driven bacterial inward proton pump, xenorhodopsin, from Bacillus coahuilensis in all major proton-conducting states. The structures reveal that proton translocation is based on proton wires regulated by internal gates. The wires serve as both selectivity filters and translocation pathways for protons. The cumulative results suggest a general concept of proton translocation. We demonstrate the use of serial time-resolved crystallography at a synchrotron source with sub-millisecond resolution for rhodopsin studies, opening the door for principally new applications. The results might also be of interest for optogenetics since xenorhodopsins are the only alternative tools to fire neurons.
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Affiliation(s)
- Kirill Kovalev
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Fedor Tsybrov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany
| | - Vitaly Shevchenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmytro Soloviov
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Sergey Siletsky
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Michael Agthe
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Marina Nikolova
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - David von Stetten
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Roman Astashkin
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Antoine Royant
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Alexander Kuzmin
- 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
| | - Riccardo Rosselli
- Dpto. Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Francisco Rodriguez-Valera
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Evolutionary Genomics Group, Departamento de Produccion Vegetal y Microbiologıa, Universidad Miguel Hernandez, San Juan de Alicante, Alicante, Spain
| | - Nikolay Ilyinskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Rogachev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, Dubna, Russian Federation
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, Dubna, Russian Federation
| | - Thomas R Schneider
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin Gordeliy
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France.
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5
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Remeeva A, Yudenko A, Nazarenko VV, Semenov O, Smolentseva A, Bogorodskiy A, Maslov I, Borshchevskiy V, Gushchin I. Development and Characterization of Flavin-Binding Fluorescent Proteins, Part I: Basic Characterization. Methods Mol Biol 2023; 2564:121-141. [PMID: 36107340 DOI: 10.1007/978-1-0716-2667-2_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Flavin-based fluorescent proteins (FbFPs) are small fluorescent proteins derived from light-oxygen-voltage (LOV) domains. The proteins bind ubiquitous endogenous flavins as chromophores and can be used as versatile in vivo reporter proteins under aerobic and anaerobic conditions. This chapter presents the methodology to identify LOV domain sequences in genomic databases; design new FbFPs; characterize their biochemical, spectroscopic, photophysical, and photochemical properties; and conduct basic fluorescence microscopy experiments.
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Affiliation(s)
- Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Bogorodskiy
- 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
| | - Valentin Borshchevskiy
- 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.
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6
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Astashkin R, Kovalev K, Bukhdruker S, Vaganova S, Kuzmin A, Alekseev A, Balandin T, Zabelskii D, Gushchin I, Royant A, Volkov D, Bourenkov G, Koonin E, Engelhard M, Bamberg E, Gordeliy V. Structural insights into light-driven anion pumping in cyanobacteria. Nat Commun 2022; 13:6460. [PMID: 36309497 PMCID: PMC9617919 DOI: 10.1038/s41467-022-34019-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 10/11/2022] [Indexed: 12/25/2022] Open
Abstract
Transmembrane ion transport is a key process in living cells. Active transport of ions is carried out by various ion transporters including microbial rhodopsins (MRs). MRs perform diverse functions such as active and passive ion transport, photo-sensing, and others. In particular, MRs can pump various monovalent ions like Na+, K+, Cl-, I-, NO3-. The only characterized MR proposed to pump sulfate in addition to halides belongs to the cyanobacterium Synechocystis sp. PCC 7509 and is named Synechocystis halorhodopsin (SyHR). The structural study of SyHR may help to understand what makes an MR pump divalent ions. Here we present the crystal structure of SyHR in the ground state, the structure of its sulfate-bound form as well as two photoreaction intermediates, the K and O states. These data reveal the molecular origin of the unique properties of the protein (exceptionally strong chloride binding and proposed pumping of divalent anions) and sheds light on the mechanism of anion release and uptake in cyanobacterial halorhodopsins. The unique properties of SyHR highlight its potential as an optogenetics tool and may help engineer different types of anion pumps with applications in optogenetics.
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Affiliation(s)
- R. Astashkin
- grid.450307.50000 0001 0944 2786Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - K. Kovalev
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - S. Bukhdruker
- grid.5398.70000 0004 0641 6373European Synchrotron Radiation Facility Grenoble, Grenoble, France ,grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - S. Vaganova
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - A. Kuzmin
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - A. Alekseev
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - T. Balandin
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - D. Zabelskii
- grid.434729.f0000 0004 0590 2900European XFEL GmbH, Schenefeld, Germany
| | - I. Gushchin
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - A. Royant
- grid.450307.50000 0001 0944 2786Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France ,grid.5398.70000 0004 0641 6373European Synchrotron Radiation Facility Grenoble, Grenoble, France
| | - D. Volkov
- grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - G. Bourenkov
- grid.475756.20000 0004 0444 5410European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - E. Koonin
- grid.419234.90000 0004 0604 5429National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD USA
| | - M. Engelhard
- grid.418441.c0000 0004 0491 3333Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - E. Bamberg
- grid.419494.50000 0001 1018 9466Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - V. Gordeliy
- grid.450307.50000 0001 0944 2786Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France ,grid.8385.60000 0001 2297 375XInstitute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany ,grid.8385.60000 0001 2297 375XJuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
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7
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Lyapina E, Marin E, Gusach A, Orekhov P, Gerasimov A, Luginina A, Vakhrameev D, Ergasheva M, Kovaleva M, Khusainov G, Khorn P, Shevtsov M, Kovalev K, Bukhdruker S, Okhrimenko I, Popov P, Hu H, Weierstall U, Liu W, Cho Y, Gushchin I, Rogachev A, Bourenkov G, Park S, Park G, Hyun HJ, Park J, Gordeliy V, Borshchevskiy V, Mishin A, Cherezov V. Structural basis for receptor selectivity and inverse agonism in S1P 5 receptors. Nat Commun 2022; 13:4736. [PMID: 35961984 PMCID: PMC9374744 DOI: 10.1038/s41467-022-32447-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 03/01/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
The bioactive lysophospholipid sphingosine-1-phosphate (S1P) acts via five different subtypes of S1P receptors (S1PRs) - S1P1-5. S1P5 is predominantly expressed in nervous and immune systems, regulating the egress of natural killer cells from lymph nodes and playing a role in immune and neurodegenerative disorders, as well as carcinogenesis. Several S1PR therapeutic drugs have been developed to treat these diseases; however, they lack receptor subtype selectivity, which leads to side effects. In this article, we describe a 2.2 Å resolution room temperature crystal structure of the human S1P5 receptor in complex with a selective inverse agonist determined by serial femtosecond crystallography (SFX) at the Pohang Accelerator Laboratory X-Ray Free Electron Laser (PAL-XFEL) and analyze its structure-activity relationship data. The structure demonstrates a unique ligand-binding mode, involving an allosteric sub-pocket, which clarifies the receptor subtype selectivity and provides a template for structure-based drug design. Together with previously published S1PR structures in complex with antagonists and agonists, our structure with S1P5-inverse agonist sheds light on the activation mechanism and reveals structural determinants of the inverse agonism in the S1PR family. S1P5 is a sphingosine-1-phosphate (S1P) receptor implicated in immune and neurodegenerative disorders. Here, authors report a crystal structure of the S1P5 receptor in complex with a selective inverse agonist, revealing an allosteric subpocket and shedding light on inverse agonism in S1P receptors.
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Affiliation(s)
- Elizaveta Lyapina
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Egor Marin
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Anastasiia Gusach
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.,MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Philipp Orekhov
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, 518172, China
| | | | - Aleksandra Luginina
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Daniil Vakhrameev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Margarita Ergasheva
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Margarita Kovaleva
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Georgii Khusainov
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.,Division of Biology and Chemistry, Paul Scherrer Institute, Forschungsstrasse 111, 5232, Villigen, PSI, Switzerland
| | - Polina Khorn
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Mikhail Shevtsov
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Kirill Kovalev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.,European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Sergey Bukhdruker
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Ivan Okhrimenko
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Petr Popov
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.,iMolecule, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Hao Hu
- Department of Physics, Arizona State University, Tempe, AZ, 85281, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ, 85281, USA
| | - Wei Liu
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Yunje Cho
- Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Ivan Gushchin
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Andrey Rogachev
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.,Joint Institute for Nuclear Research, Dubna, 141980, Russia
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Sehan Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
| | - Gisu Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
| | - Hyo Jung Hyun
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea
| | - Jaehyun Park
- Pohang Accelerator Laboratory, POSTECH, Pohang, 37673, Republic of Korea.,Department of Chemical Engineering, POSTECH, Pohang, 37673, Republic of Korea
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, 38400, France
| | - Valentin Borshchevskiy
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia. .,Joint Institute for Nuclear Research, Dubna, 141980, Russia.
| | - Alexey Mishin
- Research Сenter for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.
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8
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Kuzmin A, Orekhov P, Astashkin R, Gordeliy V, Gushchin I. Structure and dynamics of the SARS-CoV-2 envelope protein monomer. Proteins 2022; 90:1102-1114. [PMID: 35119706 DOI: 10.1002/prot.26317] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [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: 11/05/2021] [Revised: 01/09/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022]
Abstract
Coronaviruses, especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), present an ongoing threat to human wellbeing. Consequently, elucidation of molecular determinants of their function and interaction with the host is an important task. Whereas some of the coronaviral proteins are extensively characterized, others remain understudied. Here, we use molecular dynamics simulations to analyze the structure and dynamics of the SARS-CoV-2 envelope (E) protein (a viroporin) in the monomeric form. The protein consists of the hydrophobic α-helical transmembrane domain (TMD) and amphiphilic α-helices H2 and H3, connected by flexible linkers. We show that TMD has a preferable orientation in the membrane, while H2 and H3 reside at the membrane surface. Orientation of H2 is strongly influenced by palmitoylation of cysteines Cys40, Cys43, and Cys44. Glycosylation of Asn66 affects the orientation of H3. We also observe that the monomeric E protein both generates and senses the membrane curvature, preferably localizing with the C-terminus at the convex regions of the membrane; the protein in the pentameric form displays these properties as well. Localization to curved regions may be favorable for assembly of the E protein oligomers, whereas induction of curvature may facilitate the budding of the viral particles. The presented results may be helpful for a better understanding of the function of the coronaviral E protein and viroporins in general, and for overcoming the ongoing SARS-CoV-2 pandemic.
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Affiliation(s)
- Alexander Kuzmin
- 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.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Roman Astashkin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 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
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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9
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Orekhov PS, Bozdaganyan ME, Voskoboynikova N, Mulkidjanian AY, Karlova MG, Yudenko A, Remeeva A, Ryzhykau YL, Gushchin I, Gordeliy VI, Sokolova OS, Steinhoff HJ, Kirpichnikov MP, Shaitan KV. Mechanisms of Formation, Structure, and Dynamics of Lipoprotein Discs Stabilized by Amphiphilic Copolymers: A Comprehensive Review. Nanomaterials 2022; 12:nano12030361. [PMID: 35159706 PMCID: PMC8838559 DOI: 10.3390/nano12030361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/16/2022]
Abstract
Amphiphilic copolymers consisting of alternating hydrophilic and hydrophobic units account for a major recent methodical breakthrough in the investigations of membrane proteins. Styrene–maleic acid (SMA), diisobutylene–maleic acid (DIBMA), and related copolymers have been shown to extract membrane proteins directly from lipid membranes without the need for classical detergents. Within the particular experimental setup, they form disc-shaped nanoparticles with a narrow size distribution, which serve as a suitable platform for diverse kinds of spectroscopy and other biophysical techniques that require relatively small, homogeneous, water-soluble particles of separate membrane proteins in their native lipid environment. In recent years, copolymer-encased nanolipoparticles have been proven as suitable protein carriers for various structural biology applications, including cryo-electron microscopy (cryo-EM), small-angle scattering, and conventional and single-molecule X-ray diffraction experiments. Here, we review the current understanding of how such nanolipoparticles are formed and organized at the molecular level with an emphasis on their chemical diversity and factors affecting their size and solubilization efficiency.
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Affiliation(s)
- Philipp S. Orekhov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
- Correspondence: (P.S.O.); (K.V.S.)
| | - Marine E. Bozdaganyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Natalia Voskoboynikova
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria G. Karlova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Yury L. Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
| | - Valentin I. Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (A.Y.); (A.R.); (Y.L.R.); (I.G.); (V.I.G.)
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
| | - Heinz-Jürgen Steinhoff
- Department of Physics, University of Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany; (N.V.); (A.Y.M.); (H.-J.S.)
| | - Mikhail P. Kirpichnikov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Konstantin V. Shaitan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.E.B.); (M.G.K.); (O.S.S.); (M.P.K.)
- Correspondence: (P.S.O.); (K.V.S.)
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10
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Abstract
The first microbial rhodopsin, a light-driven proton pump bacteriorhodopsin from Halobacterium salinarum (HsBR), was discovered in 1971. Since then, this seven-α-helical protein, comprising a retinal molecule as a cofactor, became a major driver of groundbreaking developments in membrane protein research. However, until 1999 only a few archaeal rhodopsins, acting as light-driven proton and chloride pumps and also photosensors, were known. A new microbial rhodopsin era started in 2000 when the first bacterial rhodopsin, a proton pump, was discovered. Later it became clear that there are unexpectedly many rhodopsins, and they are present in all the domains of life and even in viruses. It turned out that they execute such a diversity of functions while being "nearly the same." The incredible evolution of the research area of rhodopsins and the scientific and technological potential of the proteins is described in the review with a focus on their function-structure relationships.
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Affiliation(s)
- Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - 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 (National Research University), Dolgoprudny, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Francisco Rodriguez-Valera
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Egor Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Dmitrii Zabelskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Riccardo Rosselli
- Departamento de Fisiología, Genetica y Microbiología. Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
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11
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Smolentseva A, Goncharov IM, Yudenko A, Bogorodskiy A, Semenov O, Nazarenko VV, Borshchevskiy V, Fonin AV, Remeeva A, Jaeger KE, Krauss U, Gordeliy V, Gushchin I. Extreme dependence of Chloroflexus aggregans LOV domain thermo- and photostability on the bound flavin species. Photochem Photobiol Sci 2021; 20:1645-1656. [PMID: 34796467 DOI: 10.1007/s43630-021-00138-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/08/2021] [Indexed: 01/10/2023]
Abstract
Light-oxygen-voltage (LOV) domains are common photosensory modules that found many applications in fluorescence microscopy and optogenetics. Here, we show that the Chloroflexus aggregans LOV domain can bind different flavin species (lumichrome, LC; riboflavin, RF; flavin mononucleotide, FMN; flavin adenine dinucleotide, FAD) during heterologous expression and that its physicochemical properties depend strongly on the nature of the bound flavin. We show that whereas the dissociation constants for different chromophores are similar, the melting temperature of the protein reconstituted with single flavin species varies from ~ 60 °C for LC to ~ 81 °C for FMN, and photobleaching half-times vary almost 100-fold. These observations serve as a caution for future studies of LOV domains in non-native conditions yet raise the possibility of fine-tuning various properties of LOV-based fluorescent probes and optogenetic tools by manipulating the chromophore composition.
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Affiliation(s)
- Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - 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, 52428, Jülich, Germany
| | - Alexander V Fonin
- Institute of Cytology, Russian Academy of Sciences, 194064, Saint Petersburg, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000, Grenoble, France.,Institute of Biological Information Processing IBI-7: Structural Biochemistry, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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12
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Sluchanko NN, Tugaeva KV, Gushchin I, Remeeva A, Kovalev K, Cooley RB. Crystal structure of human 14-3-3ζ complexed with the noncanonical phosphopeptide from proapoptotic BAD. Biochem Biophys Res Commun 2021; 583:100-105. [PMID: 34735870 DOI: 10.1016/j.bbrc.2021.10.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
Several signaling pathways control phosphorylation of the proapoptotic protein BAD and its phosphorylation-dependent association with 14-3-3 proteins in the cytoplasm. The stability of the 14-3-3/BAD complex determines the cell fate: unphosphorylated BAD escapes from 14-3-3, migrates to the mitochondria and initiates apoptosis. While the 14-3-3/BAD interaction represents a promising drug target, it lacks structural characterization. Among several phosphosites identified in vivo, Ser75 and Ser99 of human BAD match the consensus sequence RXXpSXP recognized by 14-3-3 and, therefore, represent canonical 14-3-3-binding sites. Yet, BAD contains other serines phosphorylatable in vivo, whose role is less understood. Here, we report a 2.36 Å crystal structure of 14-3-3ζ complexed with a BAD fragment which includes residues Ser74 and Ser75, both being substrates for protein kinases. While the BAD peptide is anchored to 14-3-3 by phosphoserine as expected, the BAD peptide was unexpectedly phosphorylated at Ser74 instead of Ser75, revealing noncanonical binding within the amphipathic groove and leading to a one-step positional shift and reorganization of the interface. This observation exemplifies plasticity of the amphipathic 14-3-3 groove in accommodating various peptides and suggests the redundancy of Ser74 and Ser75 phosphosites with respect to binding of BAD to 14-3-3.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Russia; European Molecular Biology Laboratory, 22607, Hamburg, Germany
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
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13
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Bacle A, Buslaev P, Garcia-Fandino R, Favela-Rosales F, Mendes Ferreira T, Fuchs PFJ, Gushchin I, Javanainen M, Kiirikki AM, Madsen JJ, Melcr J, Milán Rodríguez P, Miettinen MS, Ollila OHS, Papadopoulos CG, Peón A, Piggot TJ, Piñeiro Á, Virtanen SI. Inverse Conformational Selection in Lipid-Protein Binding. J Am Chem Soc 2021; 143:13701-13709. [PMID: 34465095 DOI: 10.1021/jacs.1c05549] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Interest in lipid interactions with proteins and other biomolecules is emerging not only in fundamental biochemistry but also in the field of nanobiotechnology where lipids are commonly used, for example, in carriers of mRNA vaccines. The outward-facing components of cellular membranes and lipid nanoparticles, the lipid headgroups, regulate membrane interactions with approaching substances, such as proteins, drugs, RNA, or viruses. Because lipid headgroup conformational ensembles have not been experimentally determined in physiologically relevant conditions, an essential question about their interactions with other biomolecules remains unanswered: Do headgroups exchange between a few rigid structures, or fluctuate freely across a practically continuous spectrum of conformations? Here, we combine solid-state NMR experiments and molecular dynamics simulations from the NMRlipids Project to resolve the conformational ensembles of headgroups of four key lipid types in various biologically relevant conditions. We find that lipid headgroups sample a wide range of overlapping conformations in both neutral and charged cellular membranes, and that differences in the headgroup chemistry manifest only in probability distributions of conformations. Furthermore, the analysis of 894 protein-bound lipid structures from the Protein Data Bank suggests that lipids can bind to proteins in a wide range of conformations, which are not limited by the headgroup chemistry. We propose that lipids can select a suitable headgroup conformation from the wide range available to them to fit the various binding sites in proteins. The proposed inverse conformational selection model will extend also to lipid binding to targets other than proteins, such as drugs, RNA, and viruses.
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Affiliation(s)
- Amélie Bacle
- Laboratoire Coopératif "Lipotoxicity and Channelopathies - ConicMeds", Université de Poitiers, 1 rue Georges Bonnet, Poitiers 86000, France
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland.,Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials (CiQUS), Universidade de Santiago de Compostela, Santiago de Compostela E-15782, Spain.,CIQUP, Centro de Investigao em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Fernando Favela-Rosales
- Departamento de Ciencias Básicas, Tecnológico Nacional de México - ITS Zacatecas Occidente, Sombrerete, Zacatecas 99102, México
| | - Tiago Mendes Ferreira
- NMR group - Institute for Physics, Martin Luther University Halle-Wittenberg, Halle (Saale), 06120, Germany
| | - Patrick F J Fuchs
- Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), Sorbonne Université, Paris 75005, France.,UFR Sciences du Vivant, Université de Paris, Paris 75013, France
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, Prague CZ-16610, Czech Republic
| | - Anne M Kiirikki
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Jesper J Madsen
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States.,Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida 33612, United States
| | - Josef Melcr
- Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Materials, University of Groningen, Groningen9747 AG, The Netherlands
| | - Paula Milán Rodríguez
- Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), Sorbonne Université, Paris 75005, France
| | - Markus S Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam 14424, Germany
| | - O H Samuli Ollila
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Chris G Papadopoulos
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Antonio Peón
- CIQUP, Centro de Investigao em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Thomas J Piggot
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, Santiago de Compostela E-15782, Spain
| | - Salla I Virtanen
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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14
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Goncharov IM, Smolentseva A, Semenov O, Natarov I, Nazarenko VV, Yudenko A, Remeeva A, Gushchin I. High-resolution structure of a naturally red-shifted LOV domain. Biochem Biophys Res Commun 2021; 567:143-147. [PMID: 34153684 DOI: 10.1016/j.bbrc.2021.06.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/13/2021] [Indexed: 12/30/2022]
Abstract
LOV domains are widespread photosensory modules that have also found applications in fluorescence microscopy, optogenetics, and light-driven generation of reactive oxygen species. Many of these applications require stable proteins with altered spectra. Here, we report a flavin-based fluorescent protein CisFbFP derived from Chloroflexus islandicus LOV domain-containing protein. We show that CisFbFP is thermostable, and its absorption and fluorescence spectra are red-shifted for ∼6 nm, which has not been observed for other cysteine-substituted natural LOV domains. We also provide a crystallographic structure of CisFbFP at the resolution of 1.2 Å that reveals alterations in the active site due to replacement of conservative asparagine with a serine. Finally, we discuss the possible effects of presence of cis-proline in the Aβ-Bβ loop on the protein's structure and stability. The findings provide the basis for engineering and color tuning of LOV-based tools for molecular biology.
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Affiliation(s)
- Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Ilia Natarov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia.
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15
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Gushchin I, Aleksenko VA, Orekhov P, Goncharov IM, Nazarenko VV, Semenov O, Remeeva A, Gordeliy V. Nitrate- and Nitrite-Sensing Histidine Kinases: Function, Structure, and Natural Diversity. Int J Mol Sci 2021; 22:5933. [PMID: 34072989 PMCID: PMC8199190 DOI: 10.3390/ijms22115933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/12/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/18/2022] Open
Abstract
Under anaerobic conditions, bacteria may utilize nitrates and nitrites as electron acceptors. Sensitivity to nitrous compounds is achieved via several mechanisms, some of which rely on sensor histidine kinases (HKs). The best studied nitrate- and nitrite-sensing HKs (NSHKs) are NarQ and NarX from Escherichia coli. Here, we review the function of NSHKs, analyze their natural diversity, and describe the available structural information. In particular, we show that around 6000 different NSHK sequences forming several distinct clusters may now be found in genomic databases, comprising mostly the genes from Beta- and Gammaproteobacteria as well as from Bacteroidetes and Chloroflexi, including those from anaerobic ammonia oxidation (annamox) communities. We show that the architecture of NSHKs is mostly conserved, although proteins from Bacteroidetes lack the HAMP and GAF-like domains yet sometimes have PAS. We reconcile the variation of NSHK sequences with atomistic models and pinpoint the structural elements important for signal transduction from the sensor domain to the catalytic module over the transmembrane and cytoplasmic regions spanning more than 200 Å.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vladimir A. Aleksenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia; (V.A.A.); (P.O.); (I.M.G.); (V.V.N.); (O.S.); (A.R.)
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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16
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Yaroshevich IA, Maksimov EG, Sluchanko NN, Zlenko DV, Stepanov AV, Slutskaya EA, Slonimskiy YB, Botnarevskii VS, Remeeva A, Gushchin I, Kovalev K, Gordeliy VI, Shelaev IV, Gostev FE, Khakhulin D, Poddubnyy VV, Gostev TS, Cherepanov DA, Polívka T, Kloz M, Friedrich T, Paschenko VZ, Nadtochenko VA, Rubin AB, Kirpichnikov MP. Role of hydrogen bond alternation and charge transfer states in photoactivation of the Orange Carotenoid Protein. Commun Biol 2021; 4:539. [PMID: 33972665 PMCID: PMC8110590 DOI: 10.1038/s42003-021-02022-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 09/03/2020] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
Here, we propose a possible photoactivation mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP), suggesting that the reaction involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. Taking advantage of engineering an OCP variant carrying the Y201W mutation, which shows superior spectroscopic and structural properties, it is shown that the presence of Trp201 augments the impact of one critical H-bond between the ketocarotenoid and the protein. This confers an unprecedented homogeneity of the dark-adapted OCP state and substantially increases the yield of the excited photoproduct S*, which is important for the productive photocycle to proceed. A 1.37 Å crystal structure of OCP Y201W combined with femtosecond time-resolved absorption spectroscopy, kinetic analysis, and deconvolution of the spectral intermediates, as well as extensive quantum chemical calculations incorporating the effect of the local electric field, highlighted the role of charge-transfer states during OCP photoconversion. Yaroshevich et al. present a chemical reaction mechanism of a 35-kDa blue light-triggered photoreceptor, the Orange Carotenoid Protein (OCP). They find that photoactivation critically involves the transient formation of a protonated ketocarotenoid (oxocarbenium cation) state. This study suggests the role of charge-transfer states during OCP photoconversion.
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Affiliation(s)
- Igor A Yaroshevich
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Eugene G Maksimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia. .,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V Zlenko
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexey V Stepanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina A Slutskaya
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yury B Slonimskiy
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Viacheslav S Botnarevskii
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alina Remeeva
- 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
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.,Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Valentin I Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan V Shelaev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Fedor E Gostev
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Timofey S Gostev
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Moscow State University, Moscow, Russia
| | - Tomáš Polívka
- Institute of Physics, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Miroslav Kloz
- ELI-Beamlines, Institute of Physics, Praha, Czech Republic
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry PC14, Berlin, Germany
| | | | - Victor A Nadtochenko
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Andrew B Rubin
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P Kirpichnikov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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17
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Nazarenko V, Remeeva A, Ryzhykau Y, Orekhov P, Semenov O, Goncharov I, Yudenko A, Gushchin I. Small Angle X‐ray Scattering Study of a Histidine Kinase Embedded in Styrene‐Maleic Acid Copolymer Lipid Particles. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.05129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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]
Affiliation(s)
| | - Alina Remeeva
- Moscow Institute of Physics and TechnologyDolgoprudny
| | - Yury Ryzhykau
- Moscow Institute of Physics and TechnologyDolgoprudny
| | - Philipp Orekhov
- Moscow Institute of Physics and TechnologyDolgoprudny
- M.V. Lomonosov Moscow State UniversityMoscow
| | - Oleg Semenov
- Moscow Institute of Physics and TechnologyDolgoprudny
| | | | - Anna Yudenko
- Moscow Institute of Physics and TechnologyDolgoprudny
| | - Ivan Gushchin
- Moscow Institute of Physics and TechnologyDolgoprudny
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18
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Röllen K, Granzin J, Remeeva A, Davari MD, Gensch T, Nazarenko VV, Kovalev K, Bogorodskiy A, Borshchevskiy V, Hemmer S, Schwaneberg U, Gordeliy V, Jaeger KE, Batra-Safferling R, Gushchin I, Krauss U. The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins. J Biol Chem 2021; 296:100662. [PMID: 33862085 PMCID: PMC8131319 DOI: 10.1016/j.jbc.2021.100662] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 01/07/2021] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 01/09/2023] Open
Abstract
Photoactive biological systems modify the optical properties of their chromophores, known as spectral tuning. Determining the molecular origin of spectral tuning is instrumental for understanding the function and developing applications of these biomolecules. Spectral tuning in flavin-binding fluorescent proteins (FbFPs), an emerging class of fluorescent reporters, is limited by their dependency on protein-bound flavins, whose structure and hence electronic properties cannot be altered by mutation. A blue-shifted variant of the plant-derived improved light, oxygen, voltage FbFP has been created by introducing a lysine within the flavin-binding pocket, but the molecular basis of this shift remains unconfirmed. We here structurally characterize the blue-shifted improved light, oxygen, voltage variant and construct a new blue-shifted CagFbFP protein by introducing an analogous mutation. X-ray structures of both proteins reveal displacement of the lysine away from the chromophore and opening up of the structure as instrumental for the blue shift. Site saturation mutagenesis and high-throughput screening yielded a red-shifted variant, and structural analysis revealed that the lysine side chain of the blue-shifted variant is stabilized close to the flavin by a secondary mutation, accounting for the red shift. Thus, a single additional mutation in a blue-shifted variant is sufficient to generate a red-shifted FbFP. Using spectroscopy, X-ray crystallography, and quantum mechanics molecular mechanics calculations, we provide a firm structural and functional understanding of spectral tuning in FbFPs. We also show that the identified blue- and red-shifted variants allow for two-color microscopy based on spectral separation. In summary, the generated blue- and red-shifted variants represent promising new tools for application in life sciences.
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Affiliation(s)
- Katrin Röllen
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Joachim Granzin
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mehdi D Davari
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Thomas Gensch
- IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France; Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Stefanie Hemmer
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany; IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany; DWI-Leibniz Institute for Interactive Materials, Aachen, Germany
| | - Valentin Gordeliy
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany; Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, Grenoble, France
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany; IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Renu Batra-Safferling
- IBI-7: Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany; JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, Jülich, Germany; IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.
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19
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Remeeva A, Nazarenko VV, Kovalev K, Goncharov IM, Yudenko A, Astashkin R, Gordeliy V, Gushchin I. Insights into the mechanisms of light-oxygen-voltage domain color tuning from a set of high-resolution X-ray structures. Proteins 2021; 89:1005-1016. [PMID: 33774867 DOI: 10.1002/prot.26078] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/16/2021] [Indexed: 01/01/2023]
Abstract
Light-oxygen-voltage (LOV) domains are widespread photosensory modules that can be used in fluorescence microscopy, optogenetics and controlled production of reactive oxygen species. All of the currently known LOV domains have absorption maxima in the range of ~440 to ~450 nm, and it is not clear whether they can be shifted significantly using mutations. Here, we have generated a panel of LOV domain variants by mutating the key chromophore-proximal glutamine aminoacid of a thermostable flavin based fluorescent protein CagFbFP (Gln148) to asparagine, aspartate, glutamate, histidine, lysine and arginine. Absorption spectra of all of the mutants are blue-shifted, with the maximal shift of 8 nm observed for the Q148H variant. While CagFbFP and its Q148N/D/E variants are not sensitive to pH, Q148H/K/R reveal a moderate red shift induced byacidic pH. To gain further insight, we determined high resolution crystal structures of all of the mutants studied at the resolutions from 1.07 Å for Q148D to 1.63 Å for Q148R. Whereas in some of the variants, the aminoacid 148 remains in the vicinity of the flavin, in Q148K, Q148R and partially Q148D, the C-terminus of the protein unlatches and the side chain of the residue 148 is reoriented away from the chromophore. Our results explain the absence of color shifts from replacing Gln148 with charged aminoacids and pave the way for rational design of color-shifted flavin based fluorescent proteins.
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Affiliation(s)
- Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kirill Kovalev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Roman Astashkin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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Yudenko A, Smolentseva A, Maslov I, Semenov O, Goncharov IM, Nazarenko VV, Maliar NL, Borshchevskiy V, Gordeliy V, Remeeva A, Gushchin I. Rational Design of a Split Flavin-Based Fluorescent Reporter. ACS Synth Biol 2021; 10:72-83. [PMID: 33325704 DOI: 10.1021/acssynbio.0c00454] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein-fragment complementation assays are used ubiquitously for probing protein-protein interactions. Most commonly, the reporter protein is split in two parts, which are then fused to the proteins of interest and can reassemble and provide a readout if the proteins of interest interact with each other. The currently known split fluorescent proteins either can be used only in aerobic conditions and assemble irreversibly, or require addition of exogenous chromophores, which complicates the design of experiments. In recent years, light-oxygen-voltage (LOV) domains of several photoreceptor proteins have been developed into flavin-based fluorescent proteins (FbFPs) that, under some circumstances, can outperform commonly used fluorescent proteins such as GFP. Here, we show that CagFbFP, a small thermostable FbFP based on a LOV domain-containing protein from Chloroflexus aggregans, can serve as a split fluorescent reporter. We use the available genetic and structural information to identify three loops between the conserved secondary structure elements, Aβ-Bβ, Eα-Fα, and Hβ-Iβ, that tolerate insertion of flexible poly-Gly/Ser segments and eventually splitting. We demonstrate that the designed split pairs, when fused to interacting proteins, are fluorescent in vivo in E. coli and human cells and have low background fluorescence. Our results enable probing protein-protein interactions in anaerobic conditions without using exogenous fluorophores and provide a basis for further development of LOV and PAS (Per-Arnt-Sim) domain-based fluorescent reporters and optogenetic tools.
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Affiliation(s)
- Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan M. Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Vera V. Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nina L. Maliar
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38044 Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
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21
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Buslaev P, Mustafin K, Gushchin I. Principal component analysis highlights the influence of temperature, curvature and cholesterol on conformational dynamics of lipids. Biochim Biophys Acta Biomembr 2020; 1862:183253. [PMID: 32142820 DOI: 10.1016/j.bbamem.2020.183253] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/14/2020] [Accepted: 02/27/2020] [Indexed: 01/06/2023]
Abstract
Membrane lipids are inherently highly dynamic molecules. Currently, it is difficult to probe the structures of individual lipids experimentally at the timescales corresponding to atomic motions, and consequently molecular dynamics simulations are used widely. In our previous work, we have introduced the principal component analysis (PCA) as a convenient framework for comprehensive quantitative description of lipid motions. Here, we present a newly developed open source script, PCAlipids, which automates the analysis and allows us to refine the approach and test its limitations. We use PCAlipids to determine the influence of temperature, cholesterol and curvature on individual lipids, and show that the most prominent lipid tail scissoring motion is strongly affected by these factors and allows tracking of phase transition. Addition of cholesterol affects the conformations and selectively changes the dynamics of lipid molecules, impacting the large-amplitude motions. Introduction of curvature biases the conformational ensembles towards more extended structures. We hope that the developed approach will be useful for understanding the molecular basis of different processes occurring in lipid membrane systems and will stimulate development of complementary experimental techniques probing the conformations of individual lipid molecules.
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Affiliation(s)
- P Buslaev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
| | - K Mustafin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - I Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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22
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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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Gushchin I, Orekhov P, Melnikov I, Polovinkin V, Yuzhakova A, Gordeliy V. Sensor Histidine Kinase NarQ Activates via Helical Rotation, Diagonal Scissoring, and Eventually Piston-Like Shifts. Int J Mol Sci 2020; 21:E3110. [PMID: 32354084 PMCID: PMC7247690 DOI: 10.3390/ijms21093110] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 03/25/2020] [Revised: 04/19/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
Membrane-embedded sensor histidine kinases (HKs) and chemoreceptors are used ubiquitously by bacteria and archaea to percept the environment, and are often crucial for their survival and pathogenicity. The proteins can transmit the signal from the sensor domain to the catalytic kinase domain reliably over the span of several hundreds of angstroms, and regulate the activity of the cognate response regulator proteins, with which they form two-component signaling systems (TCSs). Several mechanisms of transmembrane signal transduction in TCS receptors have been proposed, dubbed (swinging) piston, helical rotation, and diagonal scissoring. Yet, despite decades of studies, there is no consensus on whether these mechanisms are common for all TCS receptors. Here, we extend our previous work on Escherichia coli nitrate/nitrite sensor kinase NarQ. We determined a crystallographic structure of the sensor-TM-HAMP fragment of the R50S mutant, which, unexpectedly, was found in a ligand-bound-like conformation, despite an inability to bind nitrate. Subsequently, we reanalyzed the structures of the ligand-free and ligand-bound NarQ and NarX sensor domains, and conducted extensive molecular dynamics simulations of ligand-free and ligand-bound wild type and mutated NarQ. Based on the data, we show that binding of nitrate to NarQ causes, first and foremost, helical rotation and diagonal scissoring of the α-helices at the core of the sensor domain. These conformational changes are accompanied by a subtle piston-like motion, which is amplified by a switch in the secondary structure of the linker between the sensor and TM domains. We conclude that helical rotation, diagonal scissoring, and piston are simply different degrees of freedom in coiled-coil proteins and are not mutually exclusive in NarQ, and likely in other nitrate sensors and TCS proteins as well.
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Affiliation(s)
- Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Personalized Medicine, Sechenov University, 119146 Moscow, Russia
| | - Igor Melnikov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - Vitaly Polovinkin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
| | - Anastasia Yuzhakova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000 Grenoble, France
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
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24
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Kovalev K, Volkov D, Astashkin R, Alekseev A, Gushchin I, Haro-Moreno JM, Chizhov I, Siletsky S, Mamedov M, Rogachev A, Balandin T, Borshchevskiy V, Popov A, Bourenkov G, Bamberg E, Rodriguez-Valera F, Büldt G, Gordeliy V. High-resolution structural insights into the heliorhodopsin family. Proc Natl Acad Sci U S A 2020; 117:4131-4141. [PMID: 32034096 PMCID: PMC7049168 DOI: 10.1073/pnas.1915888117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Rhodopsins are the most abundant light-harvesting proteins. A new family of rhodopsins, heliorhodopsins (HeRs), has recently been discovered. Unlike in the known rhodopsins, in HeRs the N termini face the cytoplasm. The function of HeRs remains unknown. We present the structures of the bacterial HeR-48C12 in two states at the resolution of 1.5 Å, which highlight its remarkable difference from all known rhodopsins. The interior of HeR's extracellular part is completely hydrophobic, while the cytoplasmic part comprises a cavity (Schiff base cavity [SBC]) surrounded by charged amino acids and containing a cluster of water molecules, presumably being a primary proton acceptor from the Schiff base. At acidic pH, a planar triangular molecule (acetate) is present in the SBC. Structure-based bioinformatic analysis identified 10 subfamilies of HeRs, suggesting their diverse biological functions. The structures and available data suggest an enzymatic activity of HeR-48C12 subfamily and their possible involvement in fundamental redox biological processes.
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Affiliation(s)
- K Kovalev
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-Commission for Atomic Energy (CEA)-CNRS, 38000 Grenoble, France
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Institute of Crystallography, University of Aachen (Rheinisch-Westfälische Technische Hochschule Aachen [RWTH]), 52062 Aachen, Germany
| | - D Volkov
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - R Astashkin
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-Commission for Atomic Energy (CEA)-CNRS, 38000 Grenoble, France
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - A Alekseev
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Institute of Crystallography, University of Aachen (Rheinisch-Westfälische Technische Hochschule Aachen [RWTH]), 52062 Aachen, Germany
| | - I Gushchin
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - J M Haro-Moreno
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, 03202 San Juan de Alicante, Spain
| | - I Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, 30625 Hannover, Germany
| | - S Siletsky
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - M Mamedov
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - A Rogachev
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna 141980, Russia
| | - T Balandin
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - V Borshchevskiy
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - A Popov
- Structural Biology Group, European Synchrotron Radiation Facility, 38000 Grenoble, France
| | - G Bourenkov
- Hamburg Unit care of Deutsches Elektronen-Synchrotron (DESY), European Molecular Biology Laboratory, 22607 Hamburg, Germany
| | - E Bamberg
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Biophysical Chemistry, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - F Rodriguez-Valera
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, 03202 San Juan de Alicante, Spain
| | - G Büldt
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
| | - V Gordeliy
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-Commission for Atomic Energy (CEA)-CNRS, 38000 Grenoble, France;
- Institute of Biological Information Processing (Institute of Biological Information Processing: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- Research Center for Mechanisms of Aging and Age Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny 141701, Russia
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25
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Novitskaia O, Buslaev P, Gushchin I. Assembly of Spinach Chloroplast ATP Synthase Rotor Ring Protein-Lipid Complex. Front Mol Biosci 2019; 6:135. [PMID: 31850368 PMCID: PMC6896225 DOI: 10.3389/fmolb.2019.00135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 07/10/2019] [Accepted: 11/13/2019] [Indexed: 11/19/2022] Open
Abstract
Rotor ATPases are large multisubunit membrane protein complexes found in all kingdoms of life. The membrane parts of these ATPases include a ring-like assembly, so-called c-ring, consisting of several subunits c, plugged by a patch of phospholipids. In this report, we use a nature-inspired approach to model the assembly of the spinach (Spinacia oleracea) c14 ring protein-lipid complex, where partially assembled oligomers are pulled toward each other using a biasing potential. The resulting assemblies contain 23 to 26 encapsulated plug lipids, general position of which corresponds well to experimental maps. However, best fit to experimental data is achieved with 15 to 17 lipids inside the c-ring. In all of the simulations, the lipids from one leaflet (loop side of the c subunit) are ordered and static, whereas the lipids from the other leaflet are disordered and dynamic. Spontaneous permeation of water molecules toward Glu61 at the active site is also observed. The presented assembly approach is expected to be generalizable to other protein complexes with encapsulated lipid patches.
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Affiliation(s)
- Olga Novitskaia
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Pavel Buslaev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Nanoscience Center, Department of Chemistry, University of Jyväskylä, Jyväskylä, Finland
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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26
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Antila H, Buslaev P, Favela-Rosales F, Ferreira TM, Gushchin I, Javanainen M, Kav B, Madsen JJ, Melcr J, Miettinen MS, Määttä J, Nencini R, Ollila OHS, Piggot TJ. Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers. J Phys Chem B 2019; 123:9066-9079. [DOI: 10.1021/acs.jpcb.9b06091] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hanne Antila
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Pavel Buslaev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Russia
| | - Fernando Favela-Rosales
- Departamento de Investigación, Tecnológico Nacional de México, Campus Zacatecas Occidente, C. P. 99102 Zacatecas, México
| | - Tiago M. Ferreira
- NMR Group - Institute for Physics, Martin-Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Russia
| | - Matti Javanainen
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
| | - Batuhan Kav
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Jesper J. Madsen
- Department of Chemistry, The University of Chicago, 60637 Chicago, Illinois, United States of America
- Department of Global Health, College of Public Health, University of South Florida, 33612 Tampa, Florida, United States of America
| | - Josef Melcr
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
- Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Markus S. Miettinen
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany
| | - Jukka Määttä
- Department of Chemistry and Materials Science, Aalto University, 00076 Espoo, Finland
| | - Ricky Nencini
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
| | - O. H. Samuli Ollila
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 542/2, CZ-16610 Prague 6, Czech Republic
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Thomas J. Piggot
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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27
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Kovalev K, Polovinkin V, Gushchin I, Alekseev A, Shevchenko V, Borshchevskiy V, Astashkin R, Balandin T, Bratanov D, Vaganova S, Popov A, Chupin V, Büldt G, Bamberg E, Gordeliy V. Structure and mechanisms of sodium-pumping KR2 rhodopsin. Sci Adv 2019; 5:eaav2671. [PMID: 30989112 PMCID: PMC6457933 DOI: 10.1126/sciadv.aav2671] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/21/2019] [Indexed: 05/20/2023]
Abstract
Rhodopsins are the most universal biological light-energy transducers and abundant phototrophic mechanisms that evolved on Earth and have a remarkable diversity and potential for biotechnological applications. Recently, the first sodium-pumping rhodopsin KR2 from Krokinobacter eikastus was discovered and characterized. However, the existing structures of KR2 are contradictory, and the mechanism of Na+ pumping is not yet understood. Here, we present a structure of the cationic (non H+) light-driven pump at physiological pH in its pentameric form. We also present 13 atomic structures and functional data on the KR2 and its mutants, including potassium pumps, which show that oligomerization of the microbial rhodopsin is obligatory for its biological function. The studies reveal the structure of KR2 at nonphysiological low pH where it acts as a proton pump. The structure provides new insights into the mechanisms of microbial rhodopsins and opens the way to a rational design of novel cation pumps for optogenetics.
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Affiliation(s)
- Kirill Kovalev
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Vitaly Polovinkin
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Alexey Alekseev
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Vitaly Shevchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | | | - Roman Astashkin
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Dmitry Bratanov
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Svetlana Vaganova
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Alexander Popov
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Vladimir Chupin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Georg Büldt
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Ernst Bamberg
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Corresponding author. (V.G.); (E.B.)
| | - Valentin Gordeliy
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Corresponding author. (V.G.); (E.B.)
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28
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Nazarenko VV, Remeeva A, Yudenko A, Kovalev K, Dubenko A, Goncharov IM, Kuzmichev P, Rogachev AV, Buslaev P, Borshchevskiy V, Mishin A, Dhoke GV, Schwaneberg U, Davari MD, Jaeger KE, Krauss U, Gordeliy V, Gushchin I. A thermostable flavin-based fluorescent protein from Chloroflexus aggregans: a framework for ultra-high resolution structural studies. Photochem Photobiol Sci 2019; 18:1793-1805. [DOI: 10.1039/c9pp00067d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A new thermostable fluorescent protein is shown to be a promising model for ultra-high resolution structural studies of LOV domains and for application as a fluorescent reporter.
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29
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Maslov I, Bogorodskiy A, Mishin A, Okhrimenko I, Gushchin I, Kalenov S, Dencher NA, Fahlke C, Büldt G, Gordeliy V, Gensch T, Borshchevskiy V. Efficient non-cytotoxic fluorescent staining of halophiles. Sci Rep 2018; 8:2549. [PMID: 29416075 PMCID: PMC5803262 DOI: 10.1038/s41598-018-20839-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 01/19/2018] [Indexed: 11/09/2022] Open
Abstract
Research on halophilic microorganisms is important due to their relation to fundamental questions of survival of living organisms in a hostile environment. Here we introduce a novel method to stain halophiles with MitoTracker fluorescent dyes in their growth medium. The method is based on membrane-potential sensitive dyes, which were originally used to label mitochondria in eukaryotic cells. We demonstrate that these fluorescent dyes provide high staining efficiency and are beneficial for multi-staining purposes due to the spectral range covered (from orange to deep red). In contrast with other fluorescent dyes used so far, MitoTracker does not affect growth rate, and remains in cells after several washing steps and several generations in cell culture. The suggested dyes were tested on three archaeal (Hbt. salinarum, Haloferax sp., Halorubrum sp.) and two bacterial (Salicola sp., Halomonas sp.) strains of halophilic microorganisms. The new staining approach provides new insights into biology of Hbt. salinarum. We demonstrated the interconversion of rod-shaped cells of Hbt. salinarium to spheroplasts and submicron-sized spheres, as well as the cytoplasmic integrity of giant rod Hbt. salinarum species. By expanding the variety of tools available for halophile detection, MitoTracker dyes overcome long-standing limitations in fluorescence microscopy studies of halophiles.
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Affiliation(s)
- Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Sergei Kalenov
- Mendeleyev University of Chemical Technology of Russia, 125047, Moscow, Russia
| | - Norbert A Dencher
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
- CSI Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287, Darmstadt, Germany
| | - Christoph Fahlke
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
- Institute of Complex Systems (ICS), ICS-4: Cellular Biophysics, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Georg Büldt
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Thomas Gensch
- Institute of Complex Systems (ICS), ICS-4: Cellular Biophysics, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia.
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30
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Abstract
Microbial rhodopsins (MRs) are a large family of photoactive membrane proteins, found in microorganisms belonging to all kingdoms of life, with new members being constantly discovered. Among the MRs are light-driven proton, cation and anion pumps, light-gated cation and anion channels, and various photoreceptors. Due to their abundance and amenability to studies, MRs served as model systems for a great variety of biophysical techniques, and recently found a great application as optogenetic tools. While the basic aspects of microbial rhodopsins functioning have been known for some time, there is still a plenty of unanswered questions. This chapter presents and summarizes the available knowledge, focusing on the functional and structural studies.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany.
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31
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Gushchin I, Gordeliy V. Transmembrane Signal Transduction in Two-Component Systems: Piston, Scissoring, or Helical Rotation? Bioessays 2017; 40. [PMID: 29280502 DOI: 10.1002/bies.201700197] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 10/15/2017] [Revised: 11/30/2017] [Indexed: 11/10/2022]
Abstract
Allosteric and transmembrane (TM) signaling are among the major questions of structural biology. Here, we review and discuss signal transduction in four-helical TM bundles, focusing on histidine kinases and chemoreceptors found in two-component systems. Previously, piston, scissors, and helical rotation have been proposed as the mechanisms of TM signaling. We discuss theoretically possible conformational changes and examine the available experimental data, including the recent crystallographic structures of nitrate/nitrite sensor histidine kinase NarQ and phototaxis system NpSRII:NpHtrII. We show that TM helices can flex at multiple points and argue that the various conformational changes are not mutually exclusive, and often are observed concomitantly, throughout the TM domain or in its part. The piston and scissoring motions are the most prominent motions in the structures, but more research is needed for definitive conclusions.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, 141700, Dolgoprudniy, Russia.,Université Grenoble Alpes, CEA, CNRS, IBS, F-38000, Grenoble, France.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425, Jülich, Germany
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32
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Archer Frazao M, Nogly P, Gushchin I, Remeeva A, Esteves AM, Ma P, Borges N, Moraes I, Santos H, Gordeliy V. Membrane proteins involved in bacterial phospholipid biosynthesis as drug targets? Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s2053273317091768] [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: 11/10/2022] Open
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33
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Buslaev P, Gushchin I. Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules. Sci Rep 2017; 7:11476. [PMID: 28904383 PMCID: PMC5597592 DOI: 10.1038/s41598-017-11761-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 04/19/2017] [Accepted: 08/25/2017] [Indexed: 12/14/2022] Open
Abstract
Molecular dynamics simulations are used extensively to study the processes on biological membranes. The simulations can be conducted at different levels of resolution: all atom (AA), where all atomistic details are provided; united atom (UA), where hydrogen atoms are treated inseparably of corresponding heavy atoms; and coarse grained (CG), where atoms are grouped into larger particles. Here, we study the behavior of model bilayers consisting of saturated and unsaturated lipids DOPC, SOPC, OSPC and DSPC in simulations performed using all atom CHARMM36 and coarse grained Martini force fields. Using principal components analysis, we show that the structural and dynamical properties of the lipids are similar, both in AA and CG simulations, although the unsaturated molecules are more dynamic and favor more extended conformations. We find that CG simulations capture 75 to 100% of the major collective motions, overestimate short range ordering, result in more flexible molecules and 5–7 fold faster sampling. We expect that the results reported here will be useful for comprehensive quantitative comparisons of simulations conducted at different resolution levels and for further development and improvement of CG force fields.
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Affiliation(s)
- Pavel Buslaev
- Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia.
| | - Ivan Gushchin
- Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia. .,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425, Jülich, Germany.
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34
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Shevchenko V, Mager T, Kovalev K, Polovinkin V, Alekseev A, Juettner J, Chizhov I, Bamann C, Vavourakis C, Ghai R, Gushchin I, Borshchevskiy V, Rogachev A, Melnikov I, Popov A, Balandin T, Rodriguez-Valera F, Manstein DJ, Bueldt G, Bamberg E, Gordeliy V. Inward H + pump xenorhodopsin: Mechanism and alternative optogenetic approach. Sci Adv 2017; 3:e1603187. [PMID: 28948217 PMCID: PMC5609834 DOI: 10.1126/sciadv.1603187] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 09/05/2017] [Indexed: 05/20/2023]
Abstract
Generation of an electrochemical proton gradient is the first step of cell bioenergetics. In prokaryotes, the gradient is created by outward membrane protein proton pumps. Inward plasma membrane native proton pumps are yet unknown. We describe comprehensive functional studies of the representatives of the yet noncharacterized xenorhodopsins from Nanohaloarchaea family of microbial rhodopsins. They are inward proton pumps as we demonstrate in model membrane systems, Escherichia coli cells, human embryonic kidney cells, neuroblastoma cells, and rat hippocampal neuronal cells. We also solved the structure of a xenorhodopsin from the nanohalosarchaeon Nanosalina (NsXeR) and suggest a mechanism of inward proton pumping. We demonstrate that the NsXeR is a powerful pump, which is able to elicit action potentials in rat hippocampal neuronal cells up to their maximal intrinsic firing frequency. Hence, inwardly directed proton pumps are suitable for light-induced remote control of neurons, and they are an alternative to the well-known cation-selective channelrhodopsins.
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Affiliation(s)
- Vitaly Shevchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Thomas Mager
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Kirill Kovalev
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes–Commissariat à l’Energie Atomique et aux Energies Alternatives–CNRS, Grenoble, France
| | - Alexey Alekseev
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Josephine Juettner
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | | | - Charlotte Vavourakis
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Rohit Ghai
- Institute of Hydrobiology, Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Ivan Gushchin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Andrey Rogachev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Joint Institute for Nuclear Research, Dubna, Russia
| | - Igor Melnikov
- European Synchrotron Radiation Facility, 38027 Grenoble, France
| | - Alexander Popov
- European Synchrotron Radiation Facility, 38027 Grenoble, France
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Dietmar J. Manstein
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
- Division for Structural Biochemistry, Hannover Medical School, Hannover, Germany
| | - Georg Bueldt
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes–Commissariat à l’Energie Atomique et aux Energies Alternatives–CNRS, Grenoble, France
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35
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Gushchin I, Melnikov I, Polovinkin V, Ishchenko A, Yuzhakova A, Buslaev P, Bourenkov G, Grudinin S, Round E, Balandin T, Borshchevskiy V, Willbold D, Leonard G, Büldt G, Popov A, Gordeliy V. Mechanism of transmembrane signaling by sensor histidine kinases. Science 2017; 356:science.aah6345. [PMID: 28522691 DOI: 10.1126/science.aah6345] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 05/08/2017] [Indexed: 11/02/2022]
Abstract
One of the major and essential classes of transmembrane (TM) receptors, present in all domains of life, is sensor histidine kinases, parts of two-component signaling systems (TCSs). The structural mechanisms of TM signaling by these sensors are poorly understood. We present crystal structures of the periplasmic sensor domain, the TM domain, and the cytoplasmic HAMP domain of the Escherichia coli nitrate/nitrite sensor histidine kinase NarQ in the ligand-bound and mutated ligand-free states. The structures reveal that the ligand binding induces rearrangements and pistonlike shifts of TM helices. The HAMP domain protomers undergo leverlike motions and convert these pistonlike motions into helical rotations. Our findings provide the structural framework for complete understanding of TM TCS signaling and for development of antimicrobial treatments targeting TCSs.
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Affiliation(s)
- Ivan Gushchin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany. .,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Igor Melnikov
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Andrii Ishchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), 52056 Aachen, Germany
| | - Anastasia Yuzhakova
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Pavel Buslaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Outstation, 22607 Hamburg, Germany
| | - Sergei Grudinin
- Université Grenoble Alpes, LJK, F-38000 Grenoble, France.,CNRS, LJK, F-38000 Grenoble, France.,Inria, F-38000 Grenoble, France
| | - Ekaterina Round
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Dieter Willbold
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institute of Physical Biology, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Gordon Leonard
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Georg Büldt
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Alexander Popov
- European Synchrotron Radiation Facility, F-38043 Grenoble, France
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany. .,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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36
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Melnikov I, Polovinkin V, Kovalev K, Gushchin I, Shevtsov M, Shevchenko V, Mishin A, Alekseev A, Rodriguez-Valera F, Borshchevskiy V, Cherezov V, Leonard GA, Gordeliy V, Popov A. Fast iodide-SAD phasing for high-throughput membrane protein structure determination. Sci Adv 2017; 3:e1602952. [PMID: 28508075 PMCID: PMC5429034 DOI: 10.1126/sciadv.1602952] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/15/2017] [Indexed: 05/31/2023]
Abstract
We describe a fast, easy, and potentially universal method for the de novo solution of the crystal structures of membrane proteins via iodide-single-wavelength anomalous diffraction (I-SAD). The potential universality of the method is based on a common feature of membrane proteins-the availability at the hydrophobic-hydrophilic interface of positively charged amino acid residues with which iodide strongly interacts. We demonstrate the solution using I-SAD of four crystal structures representing different classes of membrane proteins, including a human G protein-coupled receptor (GPCR), and we show that I-SAD can be applied using data collection strategies based on either standard or serial x-ray crystallography techniques.
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Affiliation(s)
- Igor Melnikov
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Vitaly Polovinkin
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes–Commissariat à l'Energie Atomique et aux Energies Alternatives–CNRS, F-38000 Grenoble, France
- Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russia
| | - Kirill Kovalev
- Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russia
| | - Ivan Gushchin
- Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russia
| | - Mikhail Shevtsov
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russia
| | - Vitaly Shevchenko
- Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Alexey Mishin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russia
| | - Alexey Alekseev
- Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russia
| | - Francisco Rodriguez-Valera
- Department of Vegetal Production and Microbiology, Universidad Miguel Hernández de Elche, San Juan de Alicante, Valencia, Spain
| | | | - Vadim Cherezov
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russia
- Departments of Chemistry, Biological Sciences, and Physics & Astronomy, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Valentin Gordeliy
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes–Commissariat à l'Energie Atomique et aux Energies Alternatives–CNRS, F-38000 Grenoble, France
- Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Moscow Region, Russia
| | - Alexander Popov
- European Synchrotron Radiation Facility, 38043 Grenoble, France
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37
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Polovinkin V, Gushchin I, Sintsov M, Round E, Balandin T, Chervakov P, Shevchenko V, Utrobin P, Popov A, Borshchevskiy V, Mishin A, Kuklin A, Willbold D, Chupin V, Popot JL, Gordeliy V. Erratum to: High-Resolution Structure of a Membrane Protein Transferred from Amphipol to a Lipidic Mesophase. J Membr Biol 2017; 250:237. [PMID: 28229180 DOI: 10.1007/s00232-017-9949-y] [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: 11/28/2022]
Affiliation(s)
- V Polovinkin
- Univ. Grenoble Alpes, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Moscow Region, Russia
| | - I Gushchin
- Univ. Grenoble Alpes, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France.,Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Moscow Region, Russia
| | - M Sintsov
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Moscow Region, Russia
| | - E Round
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, 52425, Juelich, Germany
| | - T Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, 52425, Juelich, Germany
| | - P Chervakov
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, 52425, Juelich, Germany
| | - V Shevchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, 52425, Juelich, Germany
| | - P Utrobin
- Univ. Grenoble Alpes, IBS, 38044, Grenoble, France.,CNRS, IBS, 38044, Grenoble, France.,CEA, IBS, 38044, Grenoble, France
| | - A Popov
- European Synchrotron Radiation Facility, 38027, Grenoble, France
| | - V Borshchevskiy
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Moscow Region, Russia.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, 52425, Juelich, Germany
| | - A Mishin
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Moscow Region, Russia
| | - A Kuklin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, 141980, Dubna, Moscow Region, Russia
| | - D Willbold
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, 52425, Juelich, Germany.,Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - V Chupin
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Moscow Region, Russia
| | - J-L Popot
- Laboratoire de Physico-Chimie Moléculaire des Membranes Biologiques, UMR 7099, Institut de Biologie Physico-Chimique (CNRS FRC 550), Centre National de la Recherche Scientifique and Université Paris-7, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - V Gordeliy
- Univ. Grenoble Alpes, IBS, 38044, Grenoble, France. .,CNRS, IBS, 38044, Grenoble, France. .,CEA, IBS, 38044, Grenoble, France. .,Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Moscow Region, Russia. .,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, 52425, Juelich, Germany.
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38
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Ishchenko A, Round E, Borshchevskiy V, Grudinin S, Gushchin I, Klare JP, Remeeva A, Polovinkin V, Utrobin P, Balandin T, Engelhard M, Büldt G, Gordeliy V. New Insights on Signal Propagation by Sensory Rhodopsin II/Transducer Complex. Sci Rep 2017; 7:41811. [PMID: 28165484 PMCID: PMC5292967 DOI: 10.1038/srep41811] [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: 07/25/2016] [Accepted: 12/01/2016] [Indexed: 01/29/2023] Open
Abstract
The complex of two membrane proteins, sensory rhodopsin II (NpSRII) with its cognate transducer (NpHtrII), mediates negative phototaxis in halobacteria N. pharaonis. Upon light activation NpSRII triggers a signal transduction chain homologous to the two-component system in eubacterial chemotaxis. Here we report on crystal structures of the ground and active M-state of the complex in the space group I212121. We demonstrate that the relative orientation of symmetrical parts of the dimer is parallel (“U”-shaped) contrary to the gusset-like (“V”-shaped) form of the previously reported structures of the NpSRII/NpHtrII complex in the space group P21212, although the structures of the monomers taken individually are nearly the same. Computer modeling of the HAMP domain in the obtained “V”- and “U”-shaped structures revealed that only the “U”-shaped conformation allows for tight interactions of the receptor with the HAMP domain. This is in line with existing data and supports biological relevance of the “U” shape in the ground state. We suggest that the “V”-shaped structure may correspond to the active state of the complex and transition from the “U” to the “V”-shape of the receptor-transducer complex can be involved in signal transduction from the receptor to the signaling domain of NpHtrII.
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Affiliation(s)
- A Ishchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), Jägerstraße 17-19, 52056 Aachen, Germany
| | - E Round
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, F-38000 Grenoble, France
| | - V Borshchevskiy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - S Grudinin
- CNRS, Laboratoire Jean Kuntzmann, BP 53, Grenoble Cedex 9, France.,NANO-D, INRIA Grenoble-Rhone-Alpes Research Center, 38334 Saint Ismier Cedex, Montbonnot, France
| | - I Gushchin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, F-38000 Grenoble, France.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - J P Klare
- Max-Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.,Department of Physics, University of Osnabrück, Barbarastrasse 7, D-49069 Osnabrück, Germany
| | - A Remeeva
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - V Polovinkin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, F-38000 Grenoble, France
| | - P Utrobin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - T Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - M Engelhard
- Max-Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - G Büldt
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - V Gordeliy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany.,Institute of Crystallography, University of Aachen (RWTH), Jägerstraße 17-19, 52056 Aachen, Germany.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, F-38000 Grenoble, France.,Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
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39
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Buslaev P, Gordeliy V, Grudinin S, Gushchin I. Principal Component Analysis of Lipid Molecule Conformational Changes in Molecular Dynamics Simulations. J Chem Theory Comput 2016; 12:1019-28. [PMID: 26765212 DOI: 10.1021/acs.jctc.5b01106] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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
Molecular dynamics simulations of lipid bilayers are ubiquitous nowadays. Usually, either global properties of the bilayer or some particular characteristics of each lipid molecule are evaluated in such simulations, but the structural properties of the molecules as a whole are rarely studied. Here, we show how a comprehensive quantitative description of conformational space and dynamics of a single lipid molecule can be achieved via the principal component analysis (PCA). We illustrate the approach by analyzing and comparing simulations of DOPC bilayers obtained using eight different force fields: all-atom generalized AMBER, CHARMM27, CHARMM36, Lipid14, and Slipids and united-atom Berger, GROMOS43A1-S3, and GROMOS54A7. Similarly to proteins, most of the structural variance of a lipid molecule can be described by only a few principal components. These major components are similar in different simulations, although there are notable distinctions between the older and newer force fields and between the all-atom and united-atom force fields. The DOPC molecules in the simulations generally equilibrate on the time scales of tens to hundreds of nanoseconds. The equilibration is the slowest in the GAFF simulation and the fastest in the Slipids simulation. Somewhat unexpectedly, the equilibration in the united-atom force fields is generally slower than in the all-atom force fields. Overall, there is a clear separation between the more variable previous generation force fields and significantly more similar new generation force fields (CHARMM36, Lipid14, Slipids). We expect that the presented approaches will be useful for quantitative analysis of conformations and dynamics of individual lipid molecules in other simulations of lipid bilayers.
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Affiliation(s)
- Pavel Buslaev
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS , F-38000 Grenoble, France.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich , 52425 Jülich, Germany
| | - Sergei Grudinin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Université Grenoble Alpes, LJK, F-38000 Grenoble, France.,CNRS, LJK, F-38000 Grenoble, France.,Inria, F-38000 Grenoble, France
| | - Ivan Gushchin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudniy, Russia.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich , 52425 Jülich, Germany
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40
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Gushchin I, Shevchenko V, Polovinkin V, Borshchevskiy V, Buslaev P, Bamberg E, Gordeliy V. Structure of the light-driven sodium pump KR2 and its implications for optogenetics. FEBS J 2015; 283:1232-8. [DOI: 10.1111/febs.13585] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/22/2015] [Accepted: 10/30/2015] [Indexed: 01/27/2023]
Affiliation(s)
- Ivan Gushchin
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Vitaly Shevchenko
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
- Institut de Biologie Structurale; Université Grenoble Alpes; France
- Institut de Biologie Structurale; Centre National de la Recherche Scientifique; Grenoble France
- Institut de Biologie Structurale; Direction des Sciences du Vivant; Commissariat à l'Énergie Atomique; Grenoble France
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Pavel Buslaev
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics; Frankfurt am Main Germany
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
- Institut de Biologie Structurale; Université Grenoble Alpes; France
- Institut de Biologie Structurale; Centre National de la Recherche Scientifique; Grenoble France
- Institut de Biologie Structurale; Direction des Sciences du Vivant; Commissariat à l'Énergie Atomique; Grenoble France
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41
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Bratanov D, Balandin T, Round E, Shevchenko V, Gushchin I, Polovinkin V, Borshchevskiy V, Gordeliy V. An Approach to Heterologous Expression of Membrane Proteins. The Case of Bacteriorhodopsin. PLoS One 2015; 10:e0128390. [PMID: 26046789 PMCID: PMC4457421 DOI: 10.1371/journal.pone.0128390] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 04/24/2015] [Indexed: 12/02/2022] Open
Abstract
Heterologous overexpression of functional membrane proteins is a major bottleneck of structural biology. Bacteriorhodopsin from Halobium salinarum (bR) is a striking example of the difficulties in membrane protein overexpression. We suggest a general approach with a finite number of steps which allows one to localize the underlying problem of poor expression of a membrane protein using bR as an example. Our approach is based on constructing chimeric proteins comprising parts of a protein of interest and complementary parts of a homologous protein demonstrating advantageous expression. This complementary protein approach allowed us to increase bR expression by two orders of magnitude through the introduction of two silent mutations into bR coding DNA. For the first time the high quality crystals of bR expressed in E. Coli were obtained using the produced protein. The crystals obtained with in meso nanovolume crystallization diffracted to 1.67 Å.
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Affiliation(s)
- Dmitry Bratanov
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Institute of Crystallography, University of Aachen (RWTH), Jägerstrasse 17–19, Aachen, Germany
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
| | - Ekaterina Round
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Vitaly Shevchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Ivan Gushchin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- Research-Educational Centre “Bionanophysics”, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- * E-mail:
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42
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Gushchin I, Shevchenko V, Polovinkin V, Kovalev K, Alekseev A, Round E, Borshchevskiy V, Balandin T, Popov A, Gensch T, Fahlke C, Bamann C, Willbold D, Büldt G, Bamberg E, Gordeliy V. Crystal structure of a light-driven sodium pump. Nat Struct Mol Biol 2015; 22:390-5. [PMID: 25849142 DOI: 10.1038/nsmb.3002] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/09/2015] [Indexed: 11/09/2022]
Abstract
Recently, the first known light-driven sodium pumps, from the microbial rhodopsin family, were discovered. We have solved the structure of one of them, Krokinobacter eikastus rhodopsin 2 (KR2), in the monomeric blue state and in two pentameric red states, at resolutions of 1.45 Å and 2.2 and 2.8 Å, respectively. The structures reveal the ion-translocation pathway and show that the sodium ion is bound outside the protein at the oligomerization interface, that the ion-release cavity is capped by a unique N-terminal α-helix and that the ion-uptake cavity is unexpectedly large and open to the surface. Obstruction of the cavity with the mutation G263F imparts KR2 with the ability to pump potassium. These results pave the way for the understanding and rational design of cation pumps with new specific properties valuable for optogenetics.
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Affiliation(s)
- Ivan Gushchin
- 1] Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France. [2] Institut de Biologie Structurale, Centre National de la Recherche Scientifique, Grenoble, France. [3] Institut de Biologie Structurale, Commissariat à l'Énergie Atomique (CEA), Grenoble, France. [4] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [5] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Vitaly Shevchenko
- 1] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [2] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany. [3] Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Vitaly Polovinkin
- 1] Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France. [2] Institut de Biologie Structurale, Centre National de la Recherche Scientifique, Grenoble, France. [3] Institut de Biologie Structurale, Commissariat à l'Énergie Atomique (CEA), Grenoble, France. [4] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [5] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Kirill Kovalev
- 1] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [2] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Alexey Alekseev
- 1] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [2] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Ekaterina Round
- Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Valentin Borshchevskiy
- 1] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [2] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
| | | | - Thomas Gensch
- ICS, ICS-4, Cellular Biophysics, Research Center Jülich, Jülich, Germany
| | - Christoph Fahlke
- ICS, ICS-4, Cellular Biophysics, Research Center Jülich, Jülich, Germany
| | | | - Dieter Willbold
- 1] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany. [2] Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Georg Büldt
- 1] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [2] ICS, ICS-5, Molecular Biophysics, Research Center Jülich, Jülich, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin Gordeliy
- 1] Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France. [2] Institut de Biologie Structurale, Centre National de la Recherche Scientifique, Grenoble, France. [3] Institut de Biologie Structurale, Commissariat à l'Énergie Atomique (CEA), Grenoble, France. [4] Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy, Russia. [5] Institute of Complex Systems (ICS), ICS-6, Structural Biochemistry, Research Center Jülich, Jülich, Germany
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Borshchevskiy V, Round E, Bertsova Y, Polovinkin V, Gushchin I, Ishchenko A, Kovalev K, Mishin A, Kachalova G, Popov A, Bogachev A, Gordeliy V. Structural and functional investigation of flavin binding center of the NqrC subunit of sodium-translocating NADH:quinone oxidoreductase from Vibrio harveyi. PLoS One 2015; 10:e0118548. [PMID: 25734798 PMCID: PMC4348036 DOI: 10.1371/journal.pone.0118548] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 01/17/2015] [Indexed: 12/20/2022] Open
Abstract
Na+-translocating NADH:quinone oxidoreductase (NQR) is a redox-driven sodium pump operating in the respiratory chain of various bacteria, including pathogenic species. The enzyme has a unique set of redox active prosthetic groups, which includes two covalently bound flavin mononucleotide (FMN) residues attached to threonine residues in subunits NqrB and NqrC. The reason of FMN covalent bonding in the subunits has not been established yet. In the current work, binding of free FMN to the apo-form of NqrC from Vibrio harveyi was studied showing very low affinity of NqrC to FMN in the absence of its covalent bonding. To study structural aspects of flavin binding in NqrC, its holo-form was crystallized and its 3D structure was solved at 1.56 Å resolution. It was found that the isoalloxazine moiety of the FMN residue is buried in a hydrophobic cavity and that its pyrimidine ring is squeezed between hydrophobic amino acid residues while its benzene ring is extended from the protein surroundings. This structure of the flavin-binding pocket appears to provide flexibility of the benzene ring, which can help the FMN residue to take the bended conformation and thus to stabilize the one-electron reduced form of the prosthetic group. These properties may also lead to relatively weak noncovalent binding of the flavin. This fact along with periplasmic location of the FMN-binding domains in the vast majority of NqrC-like proteins may explain the necessity of the covalent bonding of this prosthetic group to prevent its loss to the external medium.
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Affiliation(s)
- Valentin Borshchevskiy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Ekaterina Round
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Yulia Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vitaly Polovinkin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Andrii Ishchenko
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Kirill Kovalev
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Alexey Mishin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Galina Kachalova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Alexander Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (AB); (VG)
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- * E-mail: (AB); (VG)
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Shevchenko V, Gushchin I, Polovinkin V, Round E, Borshchevskiy V, Utrobin P, Popov A, Balandin T, Büldt G, Gordeliy V. Crystal structure of Escherichia coli-expressed Haloarcula marismortui bacteriorhodopsin I in the trimeric form. PLoS One 2014; 9:e112873. [PMID: 25479443 PMCID: PMC4257550 DOI: 10.1371/journal.pone.0112873] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/17/2014] [Indexed: 12/02/2022] Open
Abstract
Bacteriorhodopsins are a large family of seven-helical transmembrane proteins that function as light-driven proton pumps. Here, we present the crystal structure of a new member of the family, Haloarcula marismortui bacteriorhodopsin I (HmBRI) D94N mutant, at the resolution of 2.5 Å. While the HmBRI retinal-binding pocket and proton donor site are similar to those of other archaeal proton pumps, its proton release region is extended and contains additional water molecules. The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins. Despite the expression in Escherichia coli and consequent absence of native lipids, the protein assembles as a trimer in crystals. The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface. Many lipidic hydrophobic tail groups are discernible in the membrane region, and their positions are similar to those of archaeal isoprenoid lipids in the crystals of other proton pumps, isolated from native or native-like sources. All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies.
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Affiliation(s)
- Vitaly Shevchenko
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
| | - Ivan Gushchin
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Vitaly Polovinkin
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Ekaterina Round
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
| | - Petr Utrobin
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | | | - Taras Balandin
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Georg Büldt
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- European Synchrotron Radiation Facility, Grenoble, France
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Borshchevskiy V, Round E, Erofeev I, Weik M, Ishchenko A, Gushchin I, Mishin A, Willbold D, Büldt G, Gordeliy V. Low-dose X-ray radiation induces structural alterations in proteins. ACTA ACUST UNITED AC 2014; 70:2675-85. [PMID: 25286851 DOI: 10.1107/s1399004714017295] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [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: 12/13/2013] [Accepted: 07/26/2014] [Indexed: 11/10/2022]
Abstract
X-ray-radiation-induced alterations to protein structures are still a severe problem in macromolecular crystallography. One way to avoid the influence of radiation damage is to reduce the X-ray dose absorbed by the crystal during data collection. However, here it is demonstrated using the example of the membrane protein bacteriorhodopsin (bR) that even a low dose of less than 0.06 MGy may induce structural alterations in proteins. This dose is about 500 times smaller than the experimental dose limit which should ideally not be exceeded per data set (i.e. 30 MGy) and 20 times smaller than previously detected specific radiation damage at the bR active site. To date, it is the lowest dose at which radiation modification of a protein structure has been described. Complementary use was made of high-resolution X-ray crystallography and online microspectrophotometry to quantitatively study low-dose X-ray-induced changes. It is shown that structural changes of the protein correlate with the spectroscopically observed formation of the so-called bR orange species. Evidence is provided for structural modifications taking place at the protein active site that should be taken into account in crystallographic studies which aim to elucidate the molecular mechanisms of bR function.
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Affiliation(s)
| | | | - Ivan Erofeev
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Martin Weik
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
| | - Andrii Ishchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Ivan Gushchin
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
| | - Alexey Mishin
- Laboratory for Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
| | - Dieter Willbold
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425 Jülich, Germany
| | - Georg Büldt
- Laboratory for Advanced Studies of Membrane Proteins, Moscow Institute of Physics and Technology, Dolgoprudniy 141700, Russian Federation
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Ishchenko A, Round E, Borshchevskiy V, Grudinin S, Gushchin I, Klare J, Balandin T, Remeeva A, Engelhard M, Büldt G, Gordeliy V. Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer. Journal of Photochemistry and Photobiology B: Biology 2013; 123:55-8. [DOI: 10.1016/j.jphotobiol.2013.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 02/27/2013] [Accepted: 03/19/2013] [Indexed: 11/15/2022]
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47
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Gushchin I, Reshetnyak A, Borshchevskiy V, Ishchenko A, Round E, Grudinin S, Engelhard M, Bldt G, Gordeliy V. Active State of Sensory Rhodopsin II: Structural Determinants for Signal Transfer and Proton Pumping. J Mol Biol 2011; 412:591-600. [DOI: 10.1016/j.jmb.2011.07.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 06/23/2011] [Accepted: 07/13/2011] [Indexed: 10/17/2022]
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48
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Gushchin I, Tishchenko AV. Fourier modal method for relief gratings with oblique boundary conditions. J Opt Soc Am A Opt Image Sci Vis 2010; 27:1575-1583. [PMID: 20596143 DOI: 10.1364/josaa.27.001575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Oblique boundary conditions are introduced in the Fourier modal method at each slice of the staircase decomposition of an arbitrary profile of a dielectric corrugation grating. The precision and convergence improvement are demonstrated by comparison with reference methods.
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Affiliation(s)
- Ivan Gushchin
- Hubert Curien Laboratory, University Jean Monnet, 18 rue B. Lauras, 42000 Saint-Etienne, France
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