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Nikolaev DM, Shtyrov AA, Vyazmin SY, Vasin AV, Panov MS, Ryazantsev MN. Fluorescence of the Retinal Chromophore in Microbial and Animal Rhodopsins. Int J Mol Sci 2023; 24:17269. [PMID: 38139098 PMCID: PMC10743670 DOI: 10.3390/ijms242417269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 11/30/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Fluorescence of the vast majority of natural opsin-based photoactive proteins is extremely low, in accordance with their functions that depend on efficient transduction of absorbed light energy. However, several recently proposed classes of engineered rhodopsins with enhanced fluorescence, along with the discovery of a new natural highly fluorescent rhodopsin, NeoR, opened a way to exploit these transmembrane proteins as fluorescent sensors and draw more attention to studies on this untypical rhodopsin property. Here, we review the available data on the fluorescence of the retinal chromophore in microbial and animal rhodopsins and their photocycle intermediates, as well as different isomers of the protonated retinal Schiff base in various solvents and the gas phase.
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Affiliation(s)
- Dmitrii M. Nikolaev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, 198504 St. Petersburg, Russia
| | - Andrey A. Shtyrov
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, 198504 St. Petersburg, Russia
| | - Sergey Yu. Vyazmin
- Nanotechnology Research and Education Centre RAS, Saint Petersburg Academic University, 8/3 Khlopina Street, 194021 St. Petersburg, Russia
| | - Andrey V. Vasin
- Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya Str., 195251 St. Petersburg, Russia
| | - Maxim S. Panov
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, 198504 St. Petersburg, Russia
- Center for Biophysical Studies, St. Petersburg State Chemical Pharmaceutical University, Professor Popov str. 14, lit. A, 197022 St. Petersburg, Russia
| | - Mikhail N. Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, 198504 St. Petersburg, Russia
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Broser M, Andruniów T, Kraskov A, Palombo R, Katz S, Kloz M, Dostál J, Bernardo C, Kennis JTM, Hegemann P, Olivucci M, Hildebrandt P. Experimental Assessment of the Electronic and Geometrical Structure of a Near-Infrared Absorbing and Highly Fluorescent Microbial Rhodopsin. J Phys Chem Lett 2023; 14:9291-9295. [PMID: 37815402 DOI: 10.1021/acs.jpclett.3c02167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The recently discovered Neorhodopsin (NeoR) exhibits absorption and emission maxima in the near-infrared spectral region, which together with the high fluorescence quantum yield makes it an attractive retinal protein for optogenetic applications. The unique optical properties can be rationalized by a theoretical model that predicts a high charge transfer character in the electronic ground state (S0) which is otherwise typical of the excited state S1 in canonical retinal proteins. The present study sets out to assess the electronic structure of the NeoR chromophore by resonance Raman (RR) spectroscopy since frequencies and relative intensities of RR bands are controlled by the ground and excited state's properties. The RR spectra of NeoR differ dramatically from those of canonical rhodopsins but can be reliably reproduced by the calculations carried out within two different structural models. The remarkable agreement between the experimental and calculated spectra confirms the consistency and robustness of the theoretical approach.
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Affiliation(s)
- Matthias Broser
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Tadeusz Andruniów
- Department of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Anastasia Kraskov
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Riccardo Palombo
- Dipartimento di Biotecnologie, Chimica e Farmacia, Universitâ di Siena, via A. Moro 2, 53100 Siena, Italy
| | - Sagie Katz
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Miroslav Kloz
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - Jakub Dostál
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - César Bernardo
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Universitâ di Siena, via A. Moro 2, 53100 Siena, Italy
- Department of Chemistry, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, United States
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623 Berlin, Germany
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Penzkofer A, Silapetere A, Hegemann P. Theoretical Investigation of the Photocycle Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor Archon2. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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QuasAr Odyssey: the origin of fluorescence and its voltage sensitivity in microbial rhodopsins. Nat Commun 2022; 13:5501. [PMID: 36127376 PMCID: PMC9489792 DOI: 10.1038/s41467-022-33084-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 08/26/2022] [Indexed: 11/29/2022] Open
Abstract
Rhodopsins had long been considered non-fluorescent until a peculiar voltage-sensitive fluorescence was reported for archaerhodopsin-3 (Arch3) derivatives. These proteins named QuasArs have been used for imaging membrane voltage changes in cell cultures and small animals. However due to the low fluorescence intensity, these constructs require use of much higher light intensity than other optogenetic tools. To develop the next generation of sensors, it is indispensable to first understand the molecular basis of the fluorescence and its modulation by the membrane voltage. Based on spectroscopic studies of fluorescent Arch3 derivatives, we propose a unique photo-reaction scheme with extended excited-state lifetimes and inefficient photoisomerization. Molecular dynamics simulations of Arch3, of the Arch3 fluorescent derivative Archon1, and of several its mutants have revealed different voltage-dependent changes of the hydrogen-bonding networks including the protonated retinal Schiff-base and adjacent residues. Experimental observations suggest that under negative voltage, these changes modulate retinal Schiff base deprotonation and promote a decrease in the populations of fluorescent species. Finally, we identified molecular constraints that further improve fluorescence quantum yield and voltage sensitivity. The authors present an in-depth investigation of excited state dynamics and molecular mechanism of the voltage sensing in microbial rhodopsins. Using a combination of spectroscopic investigations and molecular dynamics simulations, the study proposes the voltage-modulated deprotonation of the chromophore as the key event in the voltage sensing. Thus, molecular constraints that may further improve the fluorescence quantum yield and the voltage sensitivity are presented.
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Mikhailov OV. The Physical Chemistry and Chemical Physics (PCCP) Section of the International Journal of Molecular Sciences in Its Publications: The First 300 Thematic Articles in the First 3 Years. Int J Mol Sci 2021; 23:241. [PMID: 35008667 PMCID: PMC8745423 DOI: 10.3390/ijms23010241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The Physical Chemistry and Chemical Physics Section (PCCP Section) is one of the youngest among the sections of the International Journal of Molecular Sciences (IJMS)-the year 2021 will only mark three years since its inception [...].
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Affiliation(s)
- Oleg V Mikhailov
- Department of Analytical Chemistry, Certification and Quality Management, Kazan National Research Technological University, K. Marx Street 68, 420015 Kazan, Russia
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6
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Penzkofer A, Silapetere A, Hegemann P. Photocycle dynamics of the Archaerhodopsin 3 based fluorescent voltage sensor Archon2. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2021; 225:112331. [PMID: 34688164 DOI: 10.1016/j.jphotobiol.2021.112331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/21/2021] [Accepted: 10/05/2021] [Indexed: 11/28/2022]
Abstract
The retinal photocycle dynamics of the fluorescent voltage sensor Archon2 in pH 8 Tris buffer was studied. Archon2 is a mutant of Archaerhodopsin 3 (Arch) from Halorubrum sodomense obtained by a robotic multidimensional directed evolution approach (Archon2 = Arch T56P-P60S-T80P-D95H-T99S-T116I-F161V-T183I-L197I-A225C). The samples were photo-excited to the first absorption band of the protonated retinal Schiff base (PRSB) Ret_586 (absorption maximum at λmax = 586 nm, excitation wavelengths λexc = 590 nm and 632.8 nm). The photocycle dynamics were studied by recording absorption spectra during light exposure and after light exposure. Ret_586 photoisomerized to Ret_535 (main component) and Ret_485 (minor component). Ret_535 backward photoisomerized to Ret_586 in light-adapted state (named Ret_586la) and partly deprotonated to neutral retinal Schiff base (RSB) Ret_372 in light adapted state (named Ret_372la, same isomer form as Ret_535). After excitation light switch-off Ret_372la recovered to Ret_372 in dark-adapted state (Ret_372da) which slowly re-protonated to Ret_535, and Ret_535 slowly isomerized back to Ret_586 in dark-adapted state (Ret_586da). Photocycle schemes and reaction coordinate diagrams are developed and photocycle parameters are determined.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany.
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany
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Broser M, Spreen A, Konold PE, Schiewer E, Adam S, Borin V, Schapiro I, Seifert R, Kennis JTM, Bernal Sierra YA, Hegemann P. NeoR, a near-infrared absorbing rhodopsin. Nat Commun 2020; 11:5682. [PMID: 33173168 PMCID: PMC7655827 DOI: 10.1038/s41467-020-19375-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022] Open
Abstract
The Rhizoclosmatium globosum genome encodes three rhodopsin-guanylyl cyclases (RGCs), which are predicted to facilitate visual orientation of the fungal zoospores. Here, we show that RGC1 and RGC2 function as light-activated cyclases only upon heterodimerization with RGC3 (NeoR). RGC1/2 utilize conventional green or blue-light-sensitive rhodopsins (λmax = 550 and 480 nm, respectively), with short-lived signaling states, responsible for light-activation of the enzyme. The bistable NeoR is photoswitchable between a near-infrared-sensitive (NIR, λmax = 690 nm) highly fluorescent state (QF = 0.2) and a UV-sensitive non-fluorescent state, thereby modulating the activity by NIR pre-illumination. No other rhodopsin has been reported so far to be functional as a heterooligomer, or as having such a long wavelength absorption or high fluorescence yield. Site-specific mutagenesis and hybrid quantum mechanics/molecular mechanics simulations support the idea that the unusual photochemical properties result from the rigidity of the retinal chromophore and a unique counterion triad composed of two glutamic and one aspartic acids. These findings substantially expand our understanding of the natural potential and limitations of spectral tuning in rhodopsin photoreceptors.
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Affiliation(s)
- Matthias Broser
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Anika Spreen
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Patrick E Konold
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | - Enrico Schiewer
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Veniamin Borin
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Reinhard Seifert
- Molecular Sensory Systems, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - John T M Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
| | | | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
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Penzkofer A, Silapetere A, Hegemann P. Absorption and Emission Spectroscopic Investigation of the Thermal Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor Archon2. Int J Mol Sci 2020; 21:ijms21186576. [PMID: 32911811 PMCID: PMC7555599 DOI: 10.3390/ijms21186576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/12/2023] Open
Abstract
Archon2 is a fluorescent voltage sensor derived from Archaerhodopsin 3 (Arch) of Halorubrum sodomense using robotic multidimensional directed evolution approach. Here we report absorption and emission spectroscopic studies of Archon2 in Tris buffer at pH 8. Absorption cross-section spectra, fluorescence quantum distributions, fluorescence quantum yields, and fluorescence excitation spectra were determined. The thermal stability of Archon2 was studied by long-time attenuation coefficient measurements at room temperature (21 ± 1 °C) and at refrigerator temperature (3 ± 1 °C). The apparent melting temperature was determined by stepwise sample heating up and cooling down (obtained apparent melting temperature: 63 ± 3 °C). In the protein melting process protonated retinal Schiff base (PRSB) with absorption maximum at 586 nm converted to de-protonated retinal Schiff base (RSB) with absorption maximum at 380 nm. Storage of Archon2 at room temperature and refrigerator temperature caused absorption coefficient decrease because of partial protein clustering to aggregates at condensation nuclei and sedimentation. At room temperature an onset of light scattering was observed after two days because of the beginning of protein unfolding. During the period of observation (18 days at 21 °C, 22 days at 3 °C) no change of retinal isomer composition was observed indicating a high potential energy barrier of S0 ground-state isomerization.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
- Correspondence: ; Tel.: +49-941-943-2107
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany; (A.S.); (P.H.)
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany; (A.S.); (P.H.)
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Pal A, Tian L. Imaging voltage and brain chemistry with genetically encoded sensors and modulators. Curr Opin Chem Biol 2020; 57:166-176. [PMID: 32823064 DOI: 10.1016/j.cbpa.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 01/21/2023]
Abstract
Neurons and glia are functionally organized into circuits and higher-order structures that allow the precise information processing required for complex behaviors. To better understand the structure and function of the brain, we must understand synaptic connectivity, action potential generation and propagation, as well as well-orchestrated molecular signaling. Recently, dramatically improved sensors for voltage, intracellular calcium, and neurotransmitters/modulators, combined with advanced microscopy provide new opportunities for in vivo dissection of cellular and circuit activity in awake, behaving animals. This review focuses on the current trends in genetically encoded sensors for molecules and cellular events and their potential applicability to the study of nervous system in health and disease.
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Affiliation(s)
- Akash Pal
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Lin Tian
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA.
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Penzkofer A, Silapetere A, Hegemann P. Photocycle Dynamics of the Archaerhodopsin 3 Based Fluorescent Voltage Sensor QuasAr1. Int J Mol Sci 2019; 21:ijms21010160. [PMID: 31881701 PMCID: PMC6982170 DOI: 10.3390/ijms21010160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 11/16/2022] Open
Abstract
The retinal photocycle dynamics of the fluorescent voltage sensor QuasAr1 (Archaerhodopsin 3 P60S-T80S-D95H-D106H-F161V mutant from Halorubrum sodomense) in pH 8 Tris buffer was studied. The samples were photoexcited to the first absorption band of the protonated retinal Schiff base (PRSB) Ret_580 (absorption maximum at λmax ≈ 580 nm), and the retinal Schiff base photoisomerization and protonation state changes were followed by absorption spectra recordings during light exposure and after light exposure. Ret_580 turned out to be composed of two protonated retinal Schiff base isomers, namely Ret_580I and Ret_580II. Photoexcitation of Ret_580I resulted in barrier-involved isomerization to Ret_540 (quantum yield ≈ 0.056) and subsequent retinal proton release leading to Ret_410 deprotonated retinal Schiff base (RSB). In the dark, Ret_410 partially recovered to Ret_580I and partially stabilized to irreversible Ret_400 due to apoprotein restructuring (Ret_410 lifetime ≈ 2 h). Photoexcitation of Ret_580II resulted in barrier-involved isomerization to Ret_640 (quantum yield ≈ 0.00135) and subsequent deprotonation to Ret_370 (RSB). In the dark, Ret_370 partially recovered to Ret_580II and partially stabilized to irreversible Ret_350 due to apoprotein restructuring (Ret_370 lifetime ≈ 10 h). Photocycle schemes and reaction coordinate diagrams for Ret_580I and Ret_580II were developed and photocyle parameters were determined.
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Affiliation(s)
- Alfons Penzkofer
- Fakultät für Physik, Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
- Correspondence: ; Tel.: +49-941-943-2107
| | - Arita Silapetere
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany; (A.S.); (P.H.)
| | - Peter Hegemann
- Experimentelle Biophysik, Institut für Biologie, Humboldt Universität zu Berlin, Invalidenstraße 42, D-10115 Berlin, Germany; (A.S.); (P.H.)
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