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Ghosh M, Misra R, Bhattacharya S, Majhi K, Jung KH, Sheves M. Retinal-Carotenoid Interactions in a Sodium-Ion-Pumping Rhodopsin: Implications on Oligomerization and Thermal Stability. J Phys Chem B 2023; 127:2128-2137. [PMID: 36857147 PMCID: PMC10026069 DOI: 10.1021/acs.jpcb.2c07502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Microbial rhodopsin (also called retinal protein)-carotenoid conjugates represent a unique class of light-harvesting (LH) complexes, but their specific interactions and LH properties are not completely elucidated as only few rhodopsins are known to bind carotenoids. Here, we report a natural sodium-ion (Na+)-pumping Nonlabens (Donghaeana) dokdonensis rhodopsin (DDR2) binding with a carotenoid salinixanthin (Sal) to form a thermally stable rhodopsin-carotenoid complex. Different spectroscopic studies were employed to monitor the retinal-carotenoid interaction as well as the thermal stability of the protein, while size-exclusion chromatography (SEC) and homology modeling are performed to understand the protein oligomerization process. In analogy with that of another Na+-pumping protein Krokinobacter eikastus rhodopsin 2 (KR2), we propose that DDR2 (studied concentration range: 2 × 10-6 to 4 × 10-5 M) remains mainly as a pentamer at room temperature and neutral pH, while heating above 55 °C partially converted it into a thermally less stable oligomeric form of the protein. This process is affected by both the pH and concentration. At high concentrations (4 × 10-5 to 2 × 10-4 M), the protein adopts a pentamer form reflected in the excitonic circular dichroism (CD) spectrum. In the presence of Sal, the thermal stability of DDR2 is increased significantly, and the pigment is stable even at 85 °C. The results presented could have implications in designing stable rhodopsin-carotenoid antenna complexes.
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Affiliation(s)
- Mihir Ghosh
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ramprasad Misra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sudeshna Bhattacharya
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Koushik Majhi
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, South Korea
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76100, Israel
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2
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The chirality origin of retinal-carotenoid complex in gloeobacter rhodopsin: a temperature-dependent excitonic coupling. Sci Rep 2020; 10:13992. [PMID: 32814821 PMCID: PMC7438509 DOI: 10.1038/s41598-020-70697-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/29/2020] [Indexed: 11/08/2022] Open
Abstract
Retinal proteins play significant roles in light-induced protons/ions transport across the cell membrane. A recent studied retinal protein, gloeobacter rhodopsin (gR), functions as a proton pump, and binds the carotenoid salinixanthin (sal) in addition to the retinal chromophore. We have studied the interactions between the two chromophores as reflected in the circular dichroism (CD) spectrum of gR complex. gR exhibits a weak CD spectrum but following binding of sal, it exhibits a significant enhancement of the CD bands. To examine the CD origin, we have substituted the retinal chromophore of gR by synthetic retinal analogues, and have concluded that the CD bands originated from excitonic interaction between sal and the retinal chromophore as well as the sal chirality induced by binding to the protein. Temperature increase significantly affected the CD spectra, due to vanishing of excitonic coupling. A similar phenomenon of excitonic interaction lose between chromophores was recently reported for a photosynthetic pigment-protein complex (Nature Commmun, 9, 2018, 99). We propose that the excitonic interaction in gR is weaker due to protein conformational alterations. The excitonic interaction is further diminished following reduction of the retinal protonated Schiff base double bond. Furthermore, the intact structure of the retinal ring is necessary for obtaining the excitonic interaction.
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Ganapathy S, Kratz S, Chen Q, Hellingwerf KJ, de Groot HJM, Rothschild KJ, de Grip WJ. Redshifted and Near-infrared Active Analog Pigments Based upon Archaerhodopsin-3. Photochem Photobiol 2019; 95:959-968. [PMID: 30860604 PMCID: PMC6849744 DOI: 10.1111/php.13093] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 02/15/2019] [Indexed: 01/01/2023]
Abstract
Archaerhodopsin‐3 (AR3) is a member of the microbial rhodopsin family of hepta‐helical transmembrane proteins, containing a covalently bound molecule of all‐trans retinal as a chromophore. It displays an absorbance band in the visible region of the solar spectrum (λmax 556 nm) and functions as a light‐driven proton pump in the archaeon Halorubrum sodomense. AR3 and its mutants are widely used in neuroscience as optogenetic neural silencers and in particular as fluorescent indicators of transmembrane potential. In this study, we investigated the effect of analogs of the native ligand all‐trans retinal A1 on the spectral properties and proton‐pumping activity of AR3 and its single mutant AR3 (F229S). While, surprisingly, the 3‐methoxyretinal A2 analog did not redshift the absorbance maximum of AR3, the analogs retinal A2 and 3‐methylamino‐16‐nor‐1,2,3,4‐didehydroretinal (MMAR) did generate active redshifted AR3 pigments. The MMAR analog pigments could even be activated by near‐infrared light. Furthermore, the MMAR pigments showed strongly enhanced fluorescence with an emission band in the near‐infrared peaking around 815 nm. We anticipate that the AR3 pigments generated in this study have widespread potential for near‐infrared exploitation as fluorescent voltage‐gated sensors in optogenetics and artificial leafs and as proton pumps in bioenergy‐based applications.
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Affiliation(s)
- Srividya Ganapathy
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Svenja Kratz
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Que Chen
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Huub J M de Groot
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | - Kenneth J Rothschild
- Molecular Biophysics Laboratory, Photonics Center and Department of Physics, Boston University, Boston, MA
| | - Willem J de Grip
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.,Department of Biochemistry, Radboud University Medical Center, Nijmegen, The Netherlands
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Misra R, Eliash T, Sudo Y, Sheves M. Retinal-Salinixanthin Interactions in a Thermophilic Rhodopsin. J Phys Chem B 2018; 123:10-20. [PMID: 30525616 DOI: 10.1021/acs.jpcb.8b06795] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In microbial rhodopsins (also called retinal proteins), the retinal chromophore is used for harvesting light. A carotenoid molecule has been reported to complement the retinal as light harvesting antenna in bacterial retinal proteins, although examples are scarce. In this paper, we present the formation of a novel antenna complex between thermophilic rhodopsin (TR) and the carotenoid salinixanthin (Sal). The complex formation and its structure were studied using UV-visible absorption as well as circular dichroism (CD) spectroscopies. Our studies indicate that the complex is formed in both the trimeric and monomeric forms of TR. CD spectroscopy suggests that excitonic coupling takes place between retinal and Sal. The binding of Sal with artificial TR pigments derived from synthetic retinal analogues further supports the contribution of the retinal chromophore to the CD spectrum. These studies further support the possibility of interaction between the 4-keto ring of the Sal and the retinal in TR-Sal complexes. Temperature-dependent CD spectra indicate that the positive band (ca. 482 nm) of the bisignate CD spectra of the studied complexes originates from the contribution of excitonic coupling and induced chirality of Sal in the protein binding site. The presence of a relatively smaller glycine residue in the vicinity of the retinal chromophore in TR is proposed to be crucial for binding with Sal. The results are expected to shed light on the mechanism of retinal-carotenoid interactions in other biological systems.
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Affiliation(s)
- Ramprasad Misra
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Tamar Eliash
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical sciences , Okayama University , Kita-Ku, Okayama 700-8530 , Japan
| | - Mordechai Sheves
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel
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Jana S, Eliash T, Jung KH, Sheves M. Retinal Binding to Apo-Gloeobacter Rhodopsin: The Role of pH and Retinal-Carotenoid Interaction. J Phys Chem B 2017; 121:10759-10769. [PMID: 29111729 DOI: 10.1021/acs.jpcb.7b07523] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Over the past few decades, the structure, functions, properties, and molecular mechanisms of retinal proteins have been studied extensively. The newly studied retinal protein Gloeobacter rhodopsin (gR) acts as a light-driven proton pump, transferring a proton from the cytoplasmic region to the extracellular region of a cell following light absorption. It was previously shown that gR can bind the carotenoid salinixanthin (sal). In the present study, we report the effect of pH on the binding of retinal to the apo-protein of gR, in the presence and absence of sal, to form the gR pigment. We found that binding at different pH levels reflects the titration of two different protein residues, one at the lower pKa 3.5 and another at the higher pKa 8.4, that affect the pigment's formation. The maximum amount of pigment was formed at pH 5, both with and without the presence of sal. The introduction of sal accelerates the rate of pigment formation by a factor of 190. Furthermore, it is suggested that occupation of the binding site by the retinal chromophore induces protein conformational alterations which in turn affect the carotenoid conformation, which precedes the formation of the retinal-protein covalent bond. Our examination of synthetic retinal analogues in which the ring structure was modified revealed that, in the absence of sal, the retinal ring structure affects the rate of pigment formation and that the intact structure is needed for efficient pigment formation. However, the presence of sal abolishes this effect, and all-trans retinal and its modified ring analogues bind at a similar rate.
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Affiliation(s)
- Sankar Jana
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Tamar Eliash
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University , Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, South Korea
| | - Mordechai Sheves
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
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Smolensky Koganov E, Leitus G, Rozin R, Weiner L, Friedman N, Sheves M. Cation Binding to Xanthorhodopsin: Electron Paramagnetic Resonance and Magnetic Studies. J Phys Chem B 2017; 121:4333-4340. [PMID: 28379004 DOI: 10.1021/acs.jpcb.6b12670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Xanthorhodopsin (xR) is a member of the retinal protein family and acts as a proton pump in the cell membranes of the extremely halophilic eubacterium Salinibacter ruber. In addition to the retinal chromophore, xR contains a carotenoid, which acts as a light-harvesting antenna as it transfers 40% of the quanta it absorbs to the retinal. Our previous studies have shown that the CD and absorption spectra of xR are dramatically affected due to the protonation of two different residues. It is still unclear whether xR can bind cations. Electron paramagnetic resonance (EPR) spectroscopy used in the present study revealed that xR can bind divalent cations, such as Mn2+ and Ca2+, to deionized xR (DI-xR). We also demonstrate that xR can bind 1 equiv of Mn2+ to a high-affinity binding site followed by binding of ∼40 equiv in cooperative manner and ∼100 equiv of Mn2+ that are weakly bound. SQUID magnetic studies suggest that the high cooperative binding of Mn2+ cations to xR is due to the formation of Mn2+ clusters. Our data demonstrate that Ca2+ cations bind to DI-xR with a lower affinity than Mn2+, supporting the assumption that binding of Mn2+ occurs through cluster formation, because Ca2+ cations cannot form clusters in contrast to Mn2+.
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Affiliation(s)
- Elena Smolensky Koganov
- Department of Organic Chemistry and ‡Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Gregory Leitus
- Department of Organic Chemistry and ‡Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Rinat Rozin
- Department of Organic Chemistry and ‡Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Lev Weiner
- Department of Organic Chemistry and ‡Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Noga Friedman
- Department of Organic Chemistry and ‡Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Mordechai Sheves
- Department of Organic Chemistry and ‡Department of Chemical Research Support, Weizmann Institute of Science , Rehovot 76100, Israel
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Kanehara K, Yoshizawa S, Tsukamoto T, Sudo Y. A phylogenetically distinctive and extremely heat stable light-driven proton pump from the eubacterium Rubrobacter xylanophilus DSM 9941 T. Sci Rep 2017; 7:44427. [PMID: 28290523 PMCID: PMC5349596 DOI: 10.1038/srep44427] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
Rhodopsins are proteins that contain seven transmembrane domains with a chromophore retinal and that function as photoreceptors for light-energy conversion and light-signal transduction in a wide variety of organisms. Here we characterized a phylogenetically distinctive new rhodopsin from the thermophilic eubacterium Rubrobacter xylanophilus DSM 9941T that was isolated from thermally polluted water. Although R. xylanophilus rhodopsin (RxR) is from Actinobacteria, it is located between eukaryotic and archaeal rhodopsins in the phylogenetic tree. Escherichia coli cells expressing RxR showed a light-induced decrease in environmental pH and inhibition by a protonophore, indicating that it works as a light-driven outward proton pump. We characterized purified RxR spectroscopically, and showed that it has an absorption maximum at 541 nm and binds nearly 100% all-trans retinal. The pKa values for the protonated retinal Schiff base and its counterion were estimated to be 10.7 and 1.3, respectively. Time-resolved flash-photolysis experiments revealed the formation of a red-shifted intermediate. Of note, RxR showed an extremely high thermal stability in comparison with other proton pumping rhodopsins such as thermophilic rhodopsin TR (by 16-times) and bacteriorhodopsin from Halobacterium salinarum (HsBR, by 4-times).
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Affiliation(s)
- Kanae Kanehara
- Division of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Susumu Yoshizawa
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Takashi Tsukamoto
- Division of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Yuki Sudo
- Division of Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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Ganapathy S, Venselaar H, Chen Q, de Groot HJM, Hellingwerf KJ, de Grip WJ. Retinal-Based Proton Pumping in the Near Infrared. J Am Chem Soc 2017; 139:2338-2344. [PMID: 28094925 PMCID: PMC5342321 DOI: 10.1021/jacs.6b11366] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Proteorhodopsin (PR) and Gloeobacter rhodopsin (GR) are retinal-based light-driven proton pumps that absorb visible light (maxima at 520-540 nm). Shifting the action spectra of these proton pumps beyond 700 nm would generate new prospects in optogenetics, membrane sensor technology, and complementation of oxygenic phototrophy. We therefore investigated the effect of red-shifting analogues of retinal, combined with red-shifting mutations, on the spectral properties and pump activity of the resulting pigments. We investigated a variety of analogues, including many novel ones. One of the novel analogues we tested, 3-methylamino-16-nor-1,2,3,4-didehydroretinal (MMAR), produced exciting results. This analogue red-shifted all of the rhodopsin variants tested, accompanied by a strong broadening of the absorbance band, tailing out to 850-950 nm. In particular, MMAR showed a strong synergistic effect with the PR-D212N,F234S double mutant, inducing an astonishing 200 nm red shift in the absorbance maximum. To our knowledge, this is by far the largest red shift reported for any retinal protein. Very importantly, all MMAR-containing holoproteins are the first rhodopsins retaining significant pump activity under near-infrared illumination (730 nm light-emitting diode). Such MMAR-based rhodopsin variants present very promising opportunities for further synthetic biology modification and for a variety of biotechnological and biophysical applications.
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Affiliation(s)
- Srividya Ganapathy
- Leiden Institute of Chemistry, Leiden University , 2333 CC Leiden, The Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center , 6500 HB Nijmegen, The Netherlands
| | - Que Chen
- Swammerdam Institute for Life Sciences, University of Amsterdam , 1090 GE Amsterdam, The Netherlands
| | - Huub J M de Groot
- Leiden Institute of Chemistry, Leiden University , 2333 CC Leiden, The Netherlands
| | - Klaas J Hellingwerf
- Swammerdam Institute for Life Sciences, University of Amsterdam , 1090 GE Amsterdam, The Netherlands
| | - Willem J de Grip
- Leiden Institute of Chemistry, Leiden University , 2333 CC Leiden, The Netherlands
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Modulation of spectral properties and pump activity of proteorhodopsins by retinal analogues. Biochem J 2015; 467:333-43. [DOI: 10.1042/bj20141210] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Microbial proteorhodopsins are light-driven proton pumps, using the vitamin A derivative retinal as chromophore. We show that retinal analogues can shift their absorbance band with preservation of functionality. This may provide attractive opportunities in biotechnology, optogenetics and as potential sensors.
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Smolensky Koganov E, Brumfeld V, Friedman N, Sheves M. Origin of Circular Dichroism of Xanthorhodopsin. A Study with Artificial Pigments. J Phys Chem B 2014; 119:456-64. [DOI: 10.1021/jp510534s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Vlad Brumfeld
- Department
of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Noga Friedman
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mordechai Sheves
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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11
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Iyer ESS, Gdor I, Eliash T, Sheves M, Ruhman S. Efficient Femtosecond Energy Transfer from Carotenoid to Retinal in Gloeobacter Rhodopsin–Salinixanthin Complex. J Phys Chem B 2014; 119:2345-9. [DOI: 10.1021/jp506639w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Itay Gdor
- Institute
of Chemistry, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel 91904
| | - Tamar Eliash
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Mordechai Sheves
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot, Israel 76100
| | - Sanford Ruhman
- Institute
of Chemistry, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel 91904
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