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Nandi A, Zhang A, Chu ZT, Xie WJ, Xu Z, Dong S, Warshel A. Exploring the Light-Emitting Agents in Renilla Luciferases by an Effective QM/MM Approach. J Am Chem Soc 2024; 146:13875-13885. [PMID: 38718165 DOI: 10.1021/jacs.4c00963] [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: 05/23/2024]
Abstract
Bioluminescence is a fascinating natural phenomenon, wherein organisms produce light through specific biochemical reactions. Among these organisms, Renilla luciferase (RLuc) derived from the sea pansy Renilla reniformis is notable for its blue light emission and has potential applications in bioluminescent tagging. Our study focuses on RLuc8, a variant of RLuc with eight amino acid substitutions. Recent studies have shown that the luminescent emitter coelenteramide can adopt multiple protonation states, which may be influenced by nearby residues at the enzyme's active site, demonstrating a complex interplay between protein structure and bioluminescence. Herein, using the quantum mechanical consistent force field method and the semimacroscopic protein dipole-Langevin dipole method with linear response approximation, we show that the phenolate state of coelenteramide in RLuc8 is the primary light-emitting species in agreement with experimental results. Our calculations also suggest that the proton transfer (PT) from neutral coelenteramide to Asp162 plays a crucial role in the bioluminescence process. Additionally, we reproduced the observed emission maximum for the amide anion in RLuc8-D120A and the pyrazine anion in the presence of a Na+ counterion in RLuc8-D162A, suggesting that these are the primary emitters. Furthermore, our calculations on the neutral emitter in the engineered AncFT-D160A enzyme, structurally akin to RLuc8-D162A but with a considerably blue-shifted emission peak, aligned with the observed data, possibly explaining the variance in emission peaks. Overall, this study demonstrates an effective approach to investigate chromophores' bimolecular states while incorporating the PT process in emission spectra calculations, contributing valuable insights for future studies of PT in photoproteins.
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Affiliation(s)
- Ashim Nandi
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Aoxuan Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Zhen Tao Chu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Wen Jun Xie
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), Genetics Institute, University of Florida, Gainesville, Florida 32610, United States
| | - Zhongxin Xu
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
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2
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Natashin PV, Burakova LP, Kovaleva MI, Shevtsov MB, Dmitrieva DA, Eremeeva EV, Markova SV, Mishin AV, Borshchevskiy VI, Vysotski ES. The Role of Tyr-His-Trp Triad and Water Molecule Near the N1-Atom of 2-Hydroperoxycoelenterazine in Bioluminescence of Hydromedusan Photoproteins: Structural and Mutagenesis Study. Int J Mol Sci 2023; 24:ijms24076869. [PMID: 37047842 PMCID: PMC10095345 DOI: 10.3390/ijms24076869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Hydromedusan photoproteins responsible for the bioluminescence of a variety of marine jellyfish and hydroids are a unique biochemical system recognized as a stable enzyme-substrate complex consisting of apoprotein and preoxygenated coelenterazine, which is tightly bound in the protein inner cavity. The binding of calcium ions to the photoprotein molecule is only required to initiate the light emission reaction. Although numerous experimental and theoretical studies on the bioluminescence of these photoproteins were performed, many features of their functioning are yet unclear. In particular, which ionic state of dioxetanone intermediate decomposes to yield a coelenteramide in an excited state and the role of the water molecule residing in a proximity to the N1 atom of 2-hydroperoxycoelenterazine in the bioluminescence reaction are still under discussion. With the aim to elucidate the function of this water molecule as well as to pinpoint the amino acid residues presumably involved in the protonation of the primarily formed dioxetanone anion, we constructed a set of single and double obelin and aequorin mutants with substitutions of His, Trp, Tyr, and Ser to residues with different properties of side chains and investigated their bioluminescence properties (specific activity, bioluminescence spectra, stopped-flow kinetics, and fluorescence spectra of Ca2+-discharged photoproteins). Moreover, we determined the spatial structure of the obelin mutant with a substitution of His64, the key residue of the presumable proton transfer, to Phe. On the ground of the bioluminescence properties of the obelin and aequorin mutants as well as the spatial structures of the obelin mutants with the replacements of His64 and Tyr138, the conclusion was made that, in fact, His residue of the Tyr-His-Trp triad and the water molecule perform the "catalytic function" by transferring the proton from solvent to the dioxetanone anion to generate its neutral ionic state in complex with water, as only the decomposition of this form of dioxetanone can provide the highest light output in the light-emitting reaction of the hydromedusan photoproteins.
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Affiliation(s)
- Pavel V Natashin
- Photobiology Laboratory, Institute of Biophysics of Siberian Branch of the Russian Academy of Sciences, Federal Research Center "Krasnoyarsk Science Center" of Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036, Russia
| | - Ludmila P Burakova
- Photobiology Laboratory, Institute of Biophysics of Siberian Branch of the Russian Academy of Sciences, Federal Research Center "Krasnoyarsk Science Center" of Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036, Russia
- Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Margarita I Kovaleva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Mikhail B Shevtsov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Elena V Eremeeva
- Photobiology Laboratory, Institute of Biophysics of Siberian Branch of the Russian Academy of Sciences, Federal Research Center "Krasnoyarsk Science Center" of Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036, Russia
- Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Svetlana V Markova
- Photobiology Laboratory, Institute of Biophysics of Siberian Branch of the Russian Academy of Sciences, Federal Research Center "Krasnoyarsk Science Center" of Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036, Russia
- Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin I Borshchevskiy
- Research Center 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
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics of Siberian Branch of the Russian Academy of Sciences, Federal Research Center "Krasnoyarsk Science Center" of Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk 660036, Russia
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3
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Natashin PV, Eremeeva EV, Shevtsov MB, Kovaleva MI, Bukhdruker SS, Dmitrieva DA, Gulnov DV, Nemtseva EV, Gordeliy VI, Mishin AV, Borshchevskiy VI, Vysotski ES. Crystal structure of semi-synthetic obelin-v after calcium induced bioluminescence implies coelenteramine as the main reaction product. Sci Rep 2022; 12:19613. [PMID: 36379962 PMCID: PMC9666459 DOI: 10.1038/s41598-022-24117-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Coelenterazine-v (CTZ-v), a synthetic vinylene-bridged π-extended derivative, is able to significantly alter bioluminescence spectra of different CTZ-dependent luciferases and photoproteins by shifting them towards longer wavelengths. However, Ca2+-regulated photoproteins activated with CTZ-v display very low bioluminescence activities that hampers its usage as a substrate of photoprotein bioluminescence. Here, we report the crystal structure of semi-synthetic Ca2+-discharged obelin-v bound with the reaction product determined at 2.1 Å resolution. Comparison of the crystal structure of Ca2+-discharged obelin-v with those of other obelins before and after bioluminescence reaction reveals no considerable changes in the overall structure. However, the drastic changes in CTZ-binding cavity are observed owing to the completely different reaction product, coelenteramine-v (CTM-v). Since CTM-v is certainly the main product of obelin-v bioluminescence and is considered to be a product of the "dark" pathway of dioxetanone intermediate decomposition, it explains the low bioluminescence activity of obelin and apparently of other photoproteins with CTZ-v.
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Affiliation(s)
- Pavel V. Natashin
- grid.418863.00000 0004 0637 9162Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
| | - Elena V. Eremeeva
- grid.418863.00000 0004 0637 9162Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia ,grid.412592.90000 0001 0940 9855Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Mikhail B. Shevtsov
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Margarita I. Kovaleva
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey S. Bukhdruker
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Daria A. Dmitrieva
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmitry V. Gulnov
- grid.412592.90000 0001 0940 9855Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Elena V. Nemtseva
- grid.418863.00000 0004 0637 9162Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia ,grid.412592.90000 0001 0940 9855Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Valentin I. Gordeliy
- grid.457348.90000 0004 0630 1517Institut de Biologie Structurale (IBS), Université de Grenoble Alpes, CEA, CNRS, Grenoble, France ,grid.1957.a0000 0001 0728 696XInstitute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Alexey V. Mishin
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin I. Borshchevskiy
- grid.18763.3b0000000092721542Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia ,grid.33762.330000000406204119Joint Institute for Nuclear Research, Dubna, Russia
| | - Eugene S. Vysotski
- grid.418863.00000 0004 0637 9162Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
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4
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Hematyar M, Jafarian V, Shirdel A. Longer characteristic wavelength in a novel engineered photoprotein Mnemiopsin 2. Photochem Photobiol Sci 2022; 21:1031-1040. [PMID: 35226332 DOI: 10.1007/s43630-022-00191-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/14/2022] [Indexed: 10/19/2022]
Abstract
We designed two mutants of photoprotein Mnemiopsin 2 (Mn2) including M52I and V144I, where the mutations were applied in the EF-hand loops I and III. Far-UV CD measurements demonstrated that the stability of the helices in the wild-type (WT) protein is greater compared with the mutants. Heat-induced denaturation experiments in the apo-form of photoproteins showed that WT Mn2 has higher value of the enthalpy change for the unfolding process, indicating that it has more stabilizing interaction compared with mutants. According to the activity measurement data, both mutants, particularly V144I have lower initial intensity as well as slower decay rate as compared with the WT photoprotein. Importantly, it was found that V144I variant shows 25 nm of red shift in the characteristic wavelengths as compared with the WT photoprotein. This finding can be considered as an advantage for in vivo application of photoprotein for imaging purposes. It concluded that this position on loop III of Mn2 is a hotspot point for characteristic wavelength determination. However, further research on this mutant is needed for making stable variants of Mn2 with novel optical features.
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Affiliation(s)
- Mahsa Hematyar
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran
| | - Vahab Jafarian
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.
| | - Akram Shirdel
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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5
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Malikova NP, Eremeeva EV, Gulnov DV, Natashin PV, Nemtseva EV, Vysotski ES. Specific Activities of Hydromedusan Ca 2+ -Regulated Photoproteins. Photochem Photobiol 2021; 98:275-283. [PMID: 34727376 DOI: 10.1111/php.13556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 11/01/2021] [Indexed: 12/18/2022]
Abstract
Nowadays the recombinant Ca2+ -regulated photoproteins originating from marine luminous organisms are widely applied to monitor calcium transients in living cells due to their ability to emit light on Ca2+ binding. Here we report the specific activities of the recombinant Ca2+ -regulated photoproteins-aequorin from Aequorea victoria, obelins from Obelia longissima and Obelia geniculata, clytin from Clytia gregaria and mitrocomin from Mitrocoma cellularia. We demonstrate that along with bioluminescence spectra, kinetics of light signals and sensitivities to calcium, these photoproteins also differ in specific activities and consequently in quantum yields of bioluminescent reactions. The highest specific activities were found for obelins and mitrocomin, whereas those of aequorin and clytin were shown to be lower. To determine the factors influencing the variations in specific activities the fluorescence quantum yields for Ca2+ -discharged photoproteins were measured and found to be quite different varying in the range of 0.16-0.36. We propose that distinctions in specific activities may result from different efficiencies of singlet excited state generation and different fluorescence quantum yields of coelenteramide bound within substrate-binding cavity. This in turn may be conditioned by variations in the amino acid environment of the substrate-binding cavities and hydrogen bond distances between key residues and atoms of 2-hydroperoxycoelenterazine.
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Affiliation(s)
- Natalia P Malikova
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
| | - Elena V Eremeeva
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Dmitry V Gulnov
- Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Pavel V Natashin
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
| | - Elena V Nemtseva
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
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6
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Nemati R, Molakarimi M, Mohseni A, Taghdir M, Khalifeh K, H. Sajedi R. Thermostability of Ctenophore and Coelenterate Ca 2+-Regulated Apo-photoproteins: A Comparative Study. ACS Chem Biol 2021; 16:1538-1545. [PMID: 34181382 DOI: 10.1021/acschembio.1c00401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The stabilities of Ca2+-regulated ctenophore and coelenterate apo-photoproteins, apo-mnemiopsin (apo-Mne) and apo-aequorin (apo-Aeq), respectively, were compared biochemically, biophysically, and structurally. Despite high degrees of structural and functional conservation, drastic variations in stability and structural dynamics were found between the two proteins. Irreversible thermoinactivation experiments were performed upon incubation of apo-photoproteins at representative temperatures. The inactivation rate constants (kinact) at 50 °C were determined to be 0.001 and 0.004 min-1 for apo-Mne and apo-Aeq, respectively. Detailed analysis of the inactivation process suggests that the higher thermostability of apo-Mne is due to the higher activation energy (Ea) and subsequently higher values of ΔH* and ΔG* at a given temperature. According to molecular dynamics simulation studies, the higher hydrogen bond, electrostatic, and van der Waals energies in apo-Mne can validate the relationship between the thermal adaptation of apo-Mne and the energy barrier for the inactivation process. Our results show that favorable residues for protein thermostability such as hydrophobic, charged, and adopted α-helical structure residues are more frequent in the apo-Mne structure. Although the effect of acrylamide on fluorescence quenching suggests that the local flexibility in regions around Trp and Tyr residues of apo-Aeq is higher than that of apo-Mne, which results in it having a better ability to penetrate acrylamide molecules, the root-mean-square fluctuation of helix A in apo-Mne is higher than that in apo-Aeq. It seems that the greater flexibility of apo-Mne in these regions may be considered as a determining factor, affecting the thermal stability of apo-Mne through a balance between structural rigidity and flexibility.
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Affiliation(s)
- Robabeh Nemati
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Khosrow Khalifeh
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan 45371-38791, Iran
| | - Reza H. Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
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7
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Tomilin FN, Rogova AV, Burakova LP, Tchaikovskaya ON, Avramov PV, Fedorov DG, Vysotski ES. Unusual shift in the visible absorption spectrum of an active ctenophore photoprotein elucidated by time-dependent density functional theory. Photochem Photobiol Sci 2021; 20:10.1007/s43630-021-00039-5. [PMID: 33834429 DOI: 10.1007/s43630-021-00039-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/29/2021] [Indexed: 11/28/2022]
Abstract
Active hydromedusan and ctenophore Ca2+-regulated photoproteins form complexes consisting of apoprotein and strongly non-covalently bound 2-hydroperoxycoelenterazine (an oxygenated intermediate of coelenterazine). Whereas the absorption maximum of hydromedusan photoproteins is at 460-470 nm, ctenophore photoproteins absorb at 437 nm. Finding out a physical reason for this blue shift is the main objective of this work, and, to achieve it, the whole structure of the protein-substrate complex was optimized using a linear scaling quantum-mechanical method. Electronic excitations pertinent to the spectra of the 2-hydroperoxy adduct of coelenterazine were simulated with time-dependent density functional theory. The dihedral angle of 60° of the 6-(p-hydroxy)-phenyl group relative to the imidazopyrazinone core of 2-hydroperoxycoelenterazine molecule was found to be the key factor determining the absorption of ctenophore photoproteins at 437 nm. The residues relevant to binding of the substrate and its adopting the particular rotation were also identified.
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Affiliation(s)
- Felix N Tomilin
- Kirensky Institute of Physics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/38, Krasnoyarsk, 660036, Russia
- Siberian Federal University, Svobodny 79 pr., Krasnoyarsk, 660041, Russia
- National Research Tomsk State University, Lenin Avenue 36, Tomsk, 634050, Russia
| | - Anastasia V Rogova
- Siberian Federal University, Svobodny 79 pr., Krasnoyarsk, 660041, Russia
| | - Ludmila P Burakova
- Siberian Federal University, Svobodny 79 pr., Krasnoyarsk, 660041, Russia
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, Krasnoyarsk, 660036, Russia
| | - Olga N Tchaikovskaya
- National Research Tomsk State University, Lenin Avenue 36, Tomsk, 634050, Russia
| | - Pavel V Avramov
- Kyungpook National University, 80 Daehakro, Bukgu, Daegu, 41566, South Korea
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan.
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, Krasnoyarsk, 660036, Russia.
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8
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Burakova LP, Eremeeva EV, Vysotski ES. The interaction of C-terminal Tyr208 and Tyr13 of the first α-helix ensures a closed conformation of ctenophore photoprotein berovin. Photochem Photobiol Sci 2020; 19:313-323. [PMID: 32057065 DOI: 10.1039/c9pp00436j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light-sensitive Ca2+-regulated photoprotein berovin is responsible for the bioluminescence of the ctenophore Beroe abyssicola. It shares many properties of hydromedusan photoproteins although the degree of identity of its amino acid sequence with those of photoproteins is low. There is a hydrogen bond between C-terminal Pro and Arg situated in the N-terminal α-helix of hydromedusan photoproteins that supports a closed conformation of the internal cavity of the photoprotein molecule with bound 2-hydroperoxycoelenterazine. The C- and N-terminal hydrogen bond network is necessary to properly isolate the photoprotein active site from the solvent and consequently to provide a high quantum yield of the bioluminescence reaction. In order to find out which berovin residues perform the same function we modified the N- and C-termini of the protein by replacing or deleting various amino acid residues. The studies on berovin mutants showed that the interaction between C-terminal Tyr208 and Tyr13 localized in the first α-helix of the photoprotein is important for the stabilization and proper orientation of the oxygenated coelenterazine adduct within the internal cavity as well as for supporting the closed photoprotein conformation. We also suggest that the interplay between Tyr residues in ctenophore photoproteins occurs rather through the π-π interaction of their phenyl rings than through hydrogen bonds as in hydromedusan photoproteins.
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Affiliation(s)
- Ludmila P Burakova
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
| | - Elena V Eremeeva
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.
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9
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Griffiths TM, Oakley AJ, Yu H. Atomistic Insights into Photoprotein Formation: Computational Prediction of the Properties of Coelenterazine and Oxygen Binding in Obelin. J Comput Chem 2019; 41:587-603. [DOI: 10.1002/jcc.26125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 11/17/2019] [Accepted: 11/19/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Thomas M. Griffiths
- School of Chemistry and Molecular Bioscience University of Wollongong Wollongong New South Wales 2500 Australia
- Molecular Horizons University of Wollongong Wollongong New South Wales 2500 Australia
- Illawarra Health and Medical Research Institute, Northfields Ave Keiraville New South Wales 2500 Australia
| | - Aaron J. Oakley
- School of Chemistry and Molecular Bioscience University of Wollongong Wollongong New South Wales 2500 Australia
- Molecular Horizons University of Wollongong Wollongong New South Wales 2500 Australia
- Illawarra Health and Medical Research Institute, Northfields Ave Keiraville New South Wales 2500 Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience University of Wollongong Wollongong New South Wales 2500 Australia
- Molecular Horizons University of Wollongong Wollongong New South Wales 2500 Australia
- Illawarra Health and Medical Research Institute, Northfields Ave Keiraville New South Wales 2500 Australia
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10
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Burakova LP, Vysotski ES. Recombinant Ca 2+-regulated photoproteins of ctenophores: current knowledge and application prospects. Appl Microbiol Biotechnol 2019; 103:5929-5946. [PMID: 31172204 DOI: 10.1007/s00253-019-09939-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 11/26/2022]
Abstract
Bright bioluminescence of ctenophores is conditioned by Ca2+-regulated photoproteins. Although they share many properties characteristic of hydromedusan Ca2+-regulated photoproteins responsible for light emission of marine animals belonging to phylum Cnidaria, a substantial distinction still exists. The ctenophore photoproteins appeared to be extremely sensitive to light-they lose the ability for bioluminescence on exposure to light over the entire absorption spectrum. Inactivation is irreversible because keeping the inactivated photoprotein in the dark does not recover its activity. The capability to emit light can be restored only by incubation of inactivated photoprotein with coelenterazine in the dark at alkaline pH in the presence of oxygen. Although these photoproteins were discovered many years ago, only the cloning of cDNAs encoding these unique bioluminescent proteins in the early 2000s has provided a new impetus for their studies. To date, cDNAs encoding Ca2+-regulated photoproteins from four different species of luminous ctenophores have been cloned. The amino acid sequences of ctenophore photoproteins turned out to completely differ from those of hydromedusan photoproteins (identity less than 29%) though also similar to them having three EF-hand Ca2+-binding sites. At the same time, these photoproteins reveal the same two-domain scaffold characteristic of hydromedusan photoproteins. This review is an attempt to systemize and critically evaluate the data scattered through various articles regarding the structural features of recombinant light-sensitive Ca2+-regulated photoproteins of ctenophores and their bioluminescent and physicochemical properties as well as to compare them with those of hydromedusan photoproteins. In addition, we also discuss the prospects of their biotechnology applications.
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Affiliation(s)
- Lyudmila P Burakova
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, 660036, Russia
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, 660036, Russia.
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11
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Eremeeva EV, Vysotski ES. Exploring Bioluminescence Function of the Ca2+
-regulated Photoproteins with Site-directed Mutagenesis. Photochem Photobiol 2018; 95:8-23. [DOI: 10.1111/php.12945] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 05/25/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Elena V. Eremeeva
- Photobiology Laboratory; Institute of Biophysics SB RAS; Federal Research Center “Krasnoyarsk Science Center SB RAS”; Krasnoyarsk Russia
| | - Eugene S. Vysotski
- Photobiology Laboratory; Institute of Biophysics SB RAS; Federal Research Center “Krasnoyarsk Science Center SB RAS”; Krasnoyarsk Russia
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12
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Alieva RR, Kudryasheva NS. Variability of fluorescence spectra of coelenteramide-containing proteins as a basis for toxicity monitoring. Talanta 2017; 170:425-431. [PMID: 28501192 DOI: 10.1016/j.talanta.2017.04.043] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/10/2017] [Accepted: 04/16/2017] [Indexed: 11/30/2022]
Abstract
Nowadays, physicochemical approach to understanding toxic effects remains underdeveloped. A proper development of such mode would be concerned with simplest bioassay systems. Coelenteramide-Containing Fluorescent Proteins (CLM-CFPs) can serve as proper tools for study primary physicochemical processes in organisms under external exposures. CLM-CFPs are products of bioluminescent reactions of marine coelenterates. As opposed to Green Fluorescent Proteins, the CLM-CFPs are not widely applied in biomedical research, and their potential as colored biomarkers is undervalued now. Coelenteramide, fluorophore of CLM-CFPs, is a photochemically active molecule; it acts as a proton donor in its electron-excited states, generating several forms of different fluorescent state energy and, hence, different fluorescence color, from violet to green. Contributions of the forms to the visible fluorescence depend on the coelenteramide microenvironment in proteins. Hence, CLM-CFPs can serve as fluorescence biomarkers with color differentiation to monitor results of destructive biomolecule exposures. The paper reviews experimental and theoretical studies of spectral-luminescent and photochemical properties of CLM-CFPs, as well as their variation under different exposures - chemicals, temperature, and ionizing radiation. Application of CLM-CFPs as toxicity bioassays of a new type is justified.
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Affiliation(s)
- Roza R Alieva
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, Krasnoyarsk 660036, Russia; Siberian Federal University, Svobodny Prospect 79, Krasnoyarsk 660041, Russia
| | - Nadezhda S Kudryasheva
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, Krasnoyarsk 660036, Russia; Siberian Federal University, Svobodny Prospect 79, Krasnoyarsk 660041, Russia
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13
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Larionova MD, Markova SV, Vysotski ES. Tyr72 and Tyr80 are Involved in the Formation of an Active Site of a Luciferase of CopepodMetridia longa. Photochem Photobiol 2017; 93:503-510. [DOI: 10.1111/php.12694] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/31/2016] [Indexed: 11/27/2022]
Affiliation(s)
- Marina D. Larionova
- Photobiology Laboratory; Institute of Biophysics SB RAS; Federal Research Center “Krasnoyarsk Science Center SB RAS”; Krasnoyarsk Russia
- Chair of Biophysics; Siberian Federal University; Krasnoyarsk Russia
| | - Svetlana V. Markova
- Photobiology Laboratory; Institute of Biophysics SB RAS; Federal Research Center “Krasnoyarsk Science Center SB RAS”; Krasnoyarsk Russia
- Chair of Biophysics; Siberian Federal University; Krasnoyarsk Russia
| | - Eugene S. Vysotski
- Photobiology Laboratory; Institute of Biophysics SB RAS; Federal Research Center “Krasnoyarsk Science Center SB RAS”; Krasnoyarsk Russia
- Chair of Biophysics; Siberian Federal University; Krasnoyarsk Russia
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14
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Eremeeva EV, Bartsev SI, van Berkel WJH, Vysotski ES. Unanimous Model for Describing the Fast Bioluminescence Kinetics of Ca2+-regulated Photoproteins of Different Organisms. Photochem Photobiol 2016; 93:495-502. [DOI: 10.1111/php.12664] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/29/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Elena V. Eremeeva
- Photobiology Laboratory; Institute of Biophysics SB RAS; Federal Research Center “Krasnoyarsk Science Center SB RAS”; Krasnoyarsk Russia
| | - Sergey I. Bartsev
- Theoretical Biophysics Laboratory; Institute of Biophysics SB RAS; Federal Research Center “Krasnoyarsk Science Center SB RAS”; Krasnoyarsk Russia
| | | | - Eugene S. Vysotski
- Photobiology Laboratory; Institute of Biophysics SB RAS; Federal Research Center “Krasnoyarsk Science Center SB RAS”; Krasnoyarsk Russia
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15
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Burakova LP, Stepanyuk GA, Eremeeva EV, Vysotski ES. Role of certain amino acid residues of the coelenterazine-binding cavity in bioluminescence of light-sensitive Ca2+-regulated photoprotein berovin. Photochem Photobiol Sci 2016; 15:691-704. [DOI: 10.1039/c6pp00050a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We suggest that in the inner cavity of ctenophore photoproteins coelenterazine is bound as a 2-peroxy anion which is stabilized owing to Coulomb interaction with a guanidinium group of R41 paired with Y204.
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Affiliation(s)
- Ludmila P. Burakova
- Photobiology Laboratory
- Institute of Biophysics
- Russian Academy of Sciences
- Siberian Branch
- Krasnoyarsk 660036
| | - Galina A. Stepanyuk
- Photobiology Laboratory
- Institute of Biophysics
- Russian Academy of Sciences
- Siberian Branch
- Krasnoyarsk 660036
| | - Elena V. Eremeeva
- Photobiology Laboratory
- Institute of Biophysics
- Russian Academy of Sciences
- Siberian Branch
- Krasnoyarsk 660036
| | - Eugene S. Vysotski
- Photobiology Laboratory
- Institute of Biophysics
- Russian Academy of Sciences
- Siberian Branch
- Krasnoyarsk 660036
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16
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Moran DL, Tetteh AO, Goodman RE, Underwood MY. Safety assessment of the calcium-binding protein, apoaequorin, expressed by Escherichia coli. Regul Toxicol Pharmacol 2014; 69:243-9. [DOI: 10.1016/j.yrtph.2014.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/11/2014] [Accepted: 04/12/2014] [Indexed: 10/25/2022]
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17
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Bioluminescent properties of obelin and aequorin with novel coelenterazine analogues. Anal Bioanal Chem 2014; 406:2695-707. [DOI: 10.1007/s00216-014-7656-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/28/2013] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
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18
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Natashin PV, Ding W, Eremeeva EV, Markova SV, Lee J, Vysotski ES, Liu ZJ. Structures of the Ca2+-regulated photoprotein obelin Y138F mutant before and after bioluminescence support the catalytic function of a water molecule in the reaction. ACTA ACUST UNITED AC 2014; 70:720-32. [DOI: 10.1107/s1399004713032434] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 11/28/2013] [Indexed: 11/11/2022]
Abstract
Ca2+-regulated photoproteins, which are responsible for light emission in a variety of marine coelenterates, are a highly valuable tool for measuring Ca2+inside living cells. All of the photoproteins are a single-chain polypeptide to which a 2-hydroperoxycoelenterazine molecule is tightly but noncovalently bound. Bioluminescence results from the oxidative decarboxylation of 2-hydroperoxycoelenterazine, generating protein-bound coelenteramide in an excited state. Here, the crystal structures of the Y138F obelin mutant before and after bioluminescence are reported at 1.72 and 1.30 Å resolution, respectively. The comparison of the spatial structures of the conformational states of Y138F obelin with those of wild-type obelin gives clear evidence that the substitution of Tyr by Phe does not affect the overall structure of both Y138F obelin and its product following Ca2+discharge compared with the corresponding conformational states of wild-type obelin. Despite the similarity of the overall structures and internal cavities of Y138F and wild-type obelins, there is a substantial difference: in the cavity of Y138F obelin a water molecule corresponding to W2in wild-type obelin is not found. However, in Ca2+-discharged Y138F obelin this water molecule now appears in the same location. This finding, together with the observed much slower kinetics of Y138F obelin, clearly supports the hypothesis that the function of a water molecule in this location is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion before its decomposition into the excited-state product. Although obelin differs from other hydromedusan Ca2+-regulated photoproteins in some of its properties, they are believed to share a common mechanism.
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19
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Natashin PV, Markova SV, Lee J, Vysotski ES, Liu ZJ. Crystal structures of the F88Y obelin mutant before and after bioluminescence provide molecular insight into spectral tuning among hydromedusan photoproteins. FEBS J 2014; 281:1432-1445. [DOI: 10.1111/febs.12715] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/15/2013] [Accepted: 01/04/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Pavel V. Natashin
- National Laboratory of Biomacromolecules; Institute of Biophysics; Chinese Academy of Sciences; Beijing China
- Photobiology Laboratory; Institute of Biophysics; Russian Academy of Sciences, Siberian Branch; Krasnoyarsk Russia
- Laboratory of Bioluminescence Biotechnology; Institute of Fundamental Biology and Biotechnology; Siberian Federal University; Russia
| | - Svetlana V. Markova
- Photobiology Laboratory; Institute of Biophysics; Russian Academy of Sciences, Siberian Branch; Krasnoyarsk Russia
- Laboratory of Bioluminescence Biotechnology; Institute of Fundamental Biology and Biotechnology; Siberian Federal University; Russia
| | - John Lee
- Department of Biochemistry and Molecular Biology; University of Georgia; Athens GA USA
| | - Eugene S. Vysotski
- Photobiology Laboratory; Institute of Biophysics; Russian Academy of Sciences, Siberian Branch; Krasnoyarsk Russia
- Laboratory of Bioluminescence Biotechnology; Institute of Fundamental Biology and Biotechnology; Siberian Federal University; Russia
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules; Institute of Biophysics; Chinese Academy of Sciences; Beijing China
- iHuman Institute; ShanghaiTech University; Shanghai China
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20
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Stepanyuk GA, Liu ZJ, Burakova LP, Lee J, Rose J, Vysotski ES, Wang BC. Spatial structure of the novel light-sensitive photoprotein berovin from the ctenophore Beroe abyssicola in the Ca2+-loaded apoprotein conformation state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:2139-46. [DOI: 10.1016/j.bbapap.2013.07.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/03/2013] [Accepted: 07/17/2013] [Indexed: 11/25/2022]
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21
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Li ZS, Zou LY, Min CG, Ren AM. The effect of micro-environment on luminescence of aequorin: The role of amino acids and explicit water molecules on spectroscopic properties of coelenteramide. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 127:94-9. [DOI: 10.1016/j.jphotobiol.2013.07.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 07/20/2013] [Accepted: 07/24/2013] [Indexed: 10/26/2022]
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22
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Role of key residues of obelin in coelenterazine binding and conversion into 2-hydroperoxy adduct. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 127:133-9. [DOI: 10.1016/j.jphotobiol.2013.08.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 08/10/2013] [Accepted: 08/20/2013] [Indexed: 11/21/2022]
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23
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Li ZS, Zhao X, Zou LY, Ren AM. The Dynamics Simulation and Quantum Calculation Investigation About Luminescence Mechanism of Coelenteramide. Photochem Photobiol 2013; 89:849-55. [DOI: 10.1111/php.12073] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/07/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Zuo-Sheng Li
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry; Jilin University; Changchun; China
| | - Xi Zhao
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry; Jilin University; Changchun; China
| | - Lu-Yi Zou
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry; Jilin University; Changchun; China
| | - Ai-Min Ren
- State Key Laboratory of Theoretical and Computational Chemistry; Institute of Theoretical Chemistry; Jilin University; Changchun; China
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24
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Eremeeva EV, Markova SV, Frank LA, Visser AJWG, van Berkel WJH, Vysotski ES. Bioluminescent and spectroscopic properties of His-Trp-Tyr triad mutants of obelin and aequorin. Photochem Photobiol Sci 2013; 12:1016-24. [PMID: 23525241 DOI: 10.1039/c3pp00002h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ca(2+)-regulated photoproteins are responsible for the bioluminescence of a variety of marine organisms, mostly coelenterates. The photoproteins consist of a single polypeptide chain to which an imidazopyrazinone derivative (2-hydroperoxycoelenterazine) is tightly bound. According to photoprotein spatial structures the side chains of His175, Trp179, and Tyr190 in obelin and His169, Trp173, Tyr184 in aequorin are at distances that allow hydrogen bonding with the peroxide and carbonyl groups of the 2-hydroperoxycoelenterazine ligand. We replaced these amino acids in both photoproteins by residues with different hydrogen bond donor-acceptor capacity. All mutants exhibited luciferase-like bioluminescence activity, hardly present in the wild-type photoproteins, and showed low or no photoprotein activity, except for aeqH169Q (24% of wild-type activity), obeW179Y (23%), obeW179F (67%), obeY190F (14%), and aeqY184F (22%). The results clearly support the supposition made from photoprotein spatial structures that the hydrogen bond network formed by His-Trp-Tyr triad participates in stabilizing the 2-hydroperoxy adduct of coelenterazine. These residues are also essential for the positioning of the 2-hydroperoxycoelenterazine intermediate, light emitting reaction, and for the formation of active photoprotein. In addition, we demonstrate that although the positions of His-Trp-Tyr residues in aequorin and obelin spatial structures are almost identical the substitution effects might be noticeably different.
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Affiliation(s)
- Elena V Eremeeva
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk, Russia
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25
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Eremeeva EV, Natashin PV, Song L, Zhou Y, van Berkel WJH, Liu ZJ, Vysotski ES. Oxygen activation of apo-obelin-coelenterazine complex. Chembiochem 2013; 14:739-45. [PMID: 23494831 DOI: 10.1002/cbic.201300002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Indexed: 11/09/2022]
Abstract
Ca(2+) -regulated photoproteins use a noncovalently bound 2-hydroperoxycoelenterazine ligand to emit light in response to Ca(2+) binding. To better understand the mechanism of formation of active photoprotein from apoprotein, coelenterazine and molecular oxygen, we investigated the spectral properties of the anaerobic apo-obelin-coelenterazine complex and the kinetics of its conversion into active photoprotein after exposure to air. Our studies suggest that coelenterazine bound within the anaerobic complex might be a mixture of N7-protonated and C2(-) anionic forms, and that oxygen shifts the equilibrium in favor of the C2(-) anion as a result of peroxy anion formation. Proton removal from N7 and further protonation of peroxy anion and the resulting formation of 2-hydroperoxycoelenterazine in obelin might occur with the assistance of His175. It is proposed that this conserved His residue might play a key role both in formation of active photoprotein and in Ca(2+) -triggering of the bioluminescence reaction.
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Affiliation(s)
- Elena V Eremeeva
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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26
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Powers ML, McDermott AG, Shaner NC, Haddock SHD. Expression and characterization of the calcium-activated photoprotein from the ctenophore Bathocyroe fosteri: insights into light-sensitive photoproteins. Biochem Biophys Res Commun 2012; 431:360-6. [PMID: 23262181 DOI: 10.1016/j.bbrc.2012.12.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 12/06/2012] [Indexed: 11/19/2022]
Abstract
Calcium-binding photoproteins have been discovered in a variety of luminous marine organisms [1]. Recent interest in photoproteins from the phylum Ctenophora has stemmed from cloning and expression of several photoproteins from this group [2-5]. Additional characterization has revealed unique biochemical properties found only in ctenophore photoproteins, such as inactivation by light. Here we report the cloning, expression, and characterization of the photoprotein responsible for luminescence in the deep-sea ctenophore Bathocyroe fosteri. This animal was of particular interest due to the unique broad color spectrum observed in live specimens [6]. Full-length sequences were identified by BLAST searches of known photoprotein sequences against Bathocyroe transcripts obtained from 454 sequencing. Recombinantly expressed Bathocyroe photoprotein (BfosPP) displayed an optimal coelenterazine-loading pH of 8.5, and produced calcium-triggered luminescence with peak wavelengths closely matching the 493 nm peak observed in the spectrum of live B. fosteri specimens. Luminescence from recombinant BfosPP was inactivated most efficiently by UV and blue light. Primary structure alignment of BfosPP with other characterized photoproteins showed very strong sequence similarity to other ctenophore photoproteins and conservation of EF-hand motifs. Both alignment and structural prediction data provide more insight into the formation of the coelenterazine-binding domain and the probable mechanism of photoinactivation.
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Affiliation(s)
- Meghan L Powers
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA.
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27
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Eremeeva EV, Vysotski ES, Westphal AH, van Mierlo CP, van Berkel WJ. Ligand binding and conformational states of the photoprotein obelin. FEBS Lett 2012; 586:4173-9. [DOI: 10.1016/j.febslet.2012.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 10/05/2012] [Accepted: 10/05/2012] [Indexed: 02/02/2023]
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28
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Chen SF, Navizet I, Roca-Sanjuán D, Lindh R, Liu YJ, Ferré N. Chemiluminescence of Coelenterazine and Fluorescence of Coelenteramide: A Systematic Theoretical Study. J Chem Theory Comput 2012; 8:2796-807. [DOI: 10.1021/ct300356j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shu-Feng Chen
- Key Laboratory of Theoretical and
Computational Photochemistry (Beijing Normal University), Ministry
of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Isabelle Navizet
- Université Paris-Est, Laboratoire
Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS,
5 bd Descartes, 77454 Marne-la-Vallée, France
- Molecular Science Institute, School of Chemistry, University of the Witwatersrand, PO Wits Johannesburg
2050, South Africa
| | - Daniel Roca-Sanjuán
- Department
of Chemistry—Ångström, the Theoretical Chemistry
Programme, Uppsala University, P.O. Box
518, S-75120 Uppsala, Sweden
| | - Roland Lindh
- Department
of Chemistry—Ångström, the Theoretical Chemistry
Programme, Uppsala University, P.O. Box
518, S-75120 Uppsala, Sweden
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and
Computational Photochemistry (Beijing Normal University), Ministry
of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Nicolas Ferré
- Aix-Marseille Université, Institut
de Chimie Radicalaire, 13397 Marseille Cedex 20, France
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29
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Palmer AE, Qin Y, Park JG, McCombs JE. Design and application of genetically encoded biosensors. Trends Biotechnol 2011; 29:144-52. [PMID: 21251723 DOI: 10.1016/j.tibtech.2010.12.004] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 12/03/2010] [Accepted: 12/11/2010] [Indexed: 10/24/2022]
Abstract
In the past 5-10 years, the power of the green fluorescent protein (GFP) and its numerous derivatives has been harnessed toward the development of genetically encoded fluorescent biosensors. These sensors are incorporated into cells or organisms as plasmid DNA, which leads the transcriptional and translational machinery of the cell to express a functional sensor. To date, over 100 different genetically encoded biosensors have been developed for targets as diverse as ions, molecules and enzymes. Such sensors are instrumental in providing a window into the real-time biochemistry of living cells and whole organisms, and are providing unprecedented insight into the inner workings of a cell.
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Affiliation(s)
- Amy E Palmer
- Department of Chemistry and Biochemistry, UCB 215, University of Colorado, Boulder, CO 80309, USA.
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30
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The intrinsic fluorescence of apo-obelin and apo-aequorin and use of its quenching to characterize coelenterazine binding. FEBS Lett 2009; 583:1939-44. [PMID: 19426732 DOI: 10.1016/j.febslet.2009.04.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 04/23/2009] [Accepted: 04/28/2009] [Indexed: 11/23/2022]
Abstract
The intrinsic fluorescence of two apo-photoproteins has been characterized and its concentration-dependent quenching by coelenterazine has been for the first time applied to determine the apparent dissociation constants for coelenterazine binding with apo-aequorin (1.2+/-0.12 microM) and apo-obelin (0.2+/-0.04 microM). Stopped-flow measurements of fluorescence quenching showed that coelenterazine binding is a millisecond-scale process, in contrast to the formation of an active photoprotein complex taking several hours. This finding evidently shows that the rate-limiting step of active photoprotein formation is the conversion of coelenterazine into its 2-hydroperoxy derivative.
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31
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Stepanyuk GA, Xu H, Wu CK, Markova SV, Lee J, Vysotski ES, Wang BC. Expression, purification and characterization of the secreted luciferase of the copepod Metridia longa from Sf9 insect cells. Protein Expr Purif 2008; 61:142-8. [PMID: 18595733 DOI: 10.1016/j.pep.2008.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 05/16/2008] [Accepted: 05/21/2008] [Indexed: 11/29/2022]
Abstract
Metridia luciferase is a secreted luciferase from a marine copepod and uses coelenterazine as a substrate to produce a blue bioluminescence (lambda(max)=480 nm). This luciferase has been successfully applied as a bioluminescent reporter in mammalian cells. The main advantage of secreted luciferase as a reporter is the capability of measuring intracellular events without destroying the cells or tissues and this property is well suited for development of high throughput screening technologies. However because Metridia luciferase is a Cys-rich protein, Escherichia coli expression systems produce an incorrectly folded protein, hindering its biochemical characterization and application for development of in vitro bioluminescent assays. Here we report the successful expression of Metridia luciferase with its signal peptide for secretion, in insect (Sf9) cells using the baculovirus expression system. Functionally active luciferase secreted by insect cells into the culture media has been efficiently purified with a yield of high purity protein of 2-3 mg/L. This Metridia luciferase expressed in the insect cell system is a monomeric protein showing 3.5-fold greater bioluminescence activity than luciferase expressed and purified from E. coli. The near coincidence of the experimental mass of Metridia luciferase purified from insect cells with that calculated from amino acid sequence, indicates that luciferase does not undergo post-translational modifications such as phosphorylation or glycosylation and also, the cleavage site of the signal peptide for secretion is at VQA-KS, as predicted from sequence analysis.
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Affiliation(s)
- Galina A Stepanyuk
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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Woo J, Howell MH, von Arnim AG. Structure-function studies on the active site of the coelenterazine-dependent luciferase from Renilla. Protein Sci 2008; 17:725-35. [PMID: 18359861 DOI: 10.1110/ps.073355508] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Renilla luciferase (RLUC) is a versatile tool for gene expression assays and in vivo biosensor applications, but its catalytic mechanism remains to be elucidated. RLUC is evolutionarily related to the alpha/beta hydrolase family. Its closest known homologs are bacterial dehalogenases, raising the question of how a protein with a hydrolase fold can function as a decarboxylating oxygenase. Molecular docking simulations with the coelenterazine substrate against an RLUC homology model as well as a recently determined RLUC crystal structure were used to build hypotheses to identify functionally important residues, which were subsequently tested by site-directed mutagenesis, heterologous expression, and bioluminescence emission spectroscopy. The data highlighted two triads of residues that are critical for catalysis. The putative catalytic triad residues D120, E144, and H285 bear only limited resemblance to those found in the active site of aequorin, a coelenterazine-utilizing photoprotein, suggesting that the reaction scheme employed by RLUC differs substantially from the one established for aequorin. The role of H285 in catalysis was further supported by inhibition using diethylpyrocarbonate. Multiple substitutions of N53, W121, and P220--three other residues implicated in product binding in the homologous dehalogenase Sphingomonas LinB--also supported their involvement in catalysis. Together with luminescence spectra, our data lead us to propose that the conserved catalytic triad of RLUC is directly involved in the decarboxylation reaction of coelenterazine to produce bioluminescence, while the other active-site residues are used for binding of the substrate.
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Affiliation(s)
- Jongchan Woo
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Tennessee 37996-0840, USA
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Stepanyuk GA, Liu ZJ, Markova SS, Frank LA, Lee J, Vysotski ES, Wang BC. Crystal structure of coelenterazine-binding protein from Renilla muelleri at 1.7 Å: Why it is not a calcium-regulated photoprotein. Photochem Photobiol Sci 2008; 7:442-7. [DOI: 10.1039/b716535h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Titushin MS, Markova SV, Frank LA, Malikova NP, Stepanyuk GA, Lee J, Vysotski ES. Coelenterazine-binding protein of Renilla muelleri: cDNA cloning, overexpression, and characterization as a substrate of luciferase. Photochem Photobiol Sci 2007; 7:189-96. [PMID: 18264586 DOI: 10.1039/b713109g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Renilla bioluminescent system in vivo is comprised of three proteins--the luciferase, green-fluorescent protein, and coelenterazine-binding protein (CBP), previously called luciferin-binding protein (LBP). This work reports the cloning of the full-size cDNA encoding CBP from soft coral Renilla muelleri, its overexpression and properties of the recombinant protein. The apo-CBP was quantitatively converted to CBP by simple incubation with coelenterazine. The physicochemical properties of this recombinant CBP are determined to be practically the same as those reported for the CBP (LBP) of R. reniformis. CBP is a member of the four-EF-hand Ca(2+)-binding superfamily of proteins with only three of the EF-hand loops having the Ca(2+)-binding consensus sequences. There is weak sequence homology with the Ca(2+)-regulated photoproteins but only as a result of the necessary Ca(2+)-binding loop structure. In combination with Renilla luciferase, addition of only one Ca(2+) is sufficient to release the coelenterazine as a substrate for the luciferase for bioluminescence. This combination of the two proteins generates bioluminescence with higher reaction efficiency than using free coelenterazine alone as the substrate for luciferase. This increased quantum yield, a difference of bioluminescence spectra, and markedly different kinetics, implicate that a CBP-luciferase complex might be involved.
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Affiliation(s)
- Maxim S Titushin
- Photobiology Lab, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk, Russia
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35
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Gifford JL, Walsh MP, Vogel HJ. Structures and metal-ion-binding properties of the Ca2+-binding helix–loop–helix EF-hand motifs. Biochem J 2007; 405:199-221. [PMID: 17590154 DOI: 10.1042/bj20070255] [Citation(s) in RCA: 630] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ‘EF-hand’ Ca2+-binding motif plays an essential role in eukaryotic cellular signalling, and the proteins containing this motif constitute a large and functionally diverse family. The EF-hand is defined by its helix–loop–helix secondary structure as well as the ligands presented by the loop to bind the Ca2+ ion. The identity of these ligands is semi-conserved in the most common (the ‘canonical’) EF-hand; however, several non-canonical EF-hands exist that bind Ca2+ by a different co-ordination mechanism. EF-hands tend to occur in pairs, which form a discrete domain so that most family members have two, four or six EF-hands. This pairing also enables communication, and many EF-hands display positive co-operativity, thereby minimizing the Ca2+ signal required to reach protein saturation. The conformational effects of Ca2+ binding are varied, function-dependent and, in some cases, minimal, but can lead to the creation of a protein target interaction site or structure formation from a molten-globule apo state. EF-hand proteins exhibit various sensitivities to Ca2+, reflecting the intrinsic binding ability of the EF-hand as well as the degree of co-operativity in Ca2+ binding to paired EF-hands. Two additional factors can influence the ability of an EF-hand to bind Ca2+: selectivity over Mg2+ (a cation with very similar chemical properties to Ca2+ and with a cytoplasmic concentration several orders of magnitude higher) and interaction with a protein target. A structural approach is used in this review to examine the diversity of family members, and a biophysical perspective provides insight into the ability of the EF-hand motif to bind Ca2+ with a wide range of affinities.
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Affiliation(s)
- Jessica L Gifford
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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36
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Kirillova TN, Kudryasheva NS. Effect of heavy atoms in bioluminescent reactions. Anal Bioanal Chem 2007; 387:2009-16. [PMID: 17237922 DOI: 10.1007/s00216-006-1085-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 10/27/2006] [Accepted: 12/07/2006] [Indexed: 10/23/2022]
Abstract
Bioluminescent reactions of luminous organisms are excellent models for studying the effects of heavy atoms on enzymatic processes. The effects of potassium halides with halide anions of different atomic weight were compared in bioluminescent reactions of the firefly (Luciola mingrelica), a marine coelenterate (Obelia longissima), and a marine bacterium (Photobacterium leiognathi). Two mechanisms of the effects of the halides were examined-the physicochemical effect of the external heavy atom, based on spin-orbit interactions in electron-excited structures, and the biochemical effect, i.e. interactions with the enzymes resulting in changes of enzymatic activity. The physicochemical effect was evaluated by using photoexcitation of model fluorescent compounds (flavin mononucleotide, firefly luciferin, and coelenteramide) of similar structure to the bioluminescence emitters. The bioluminescent and photoluminescent inhibition coefficients were calculated and compared for the luminous organisms to evaluate the relative contributions of the two mechanisms. The biochemical mechanism was found to be dominant. Hence, the bioluminescent reactions can be used as assays to monitor enzyme inhibition, in metabolic processes, by Br or I-containing compounds.
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Affiliation(s)
- Tamara N Kirillova
- Laboratory of Photobiology, Institute of Biophysics, Siberian Branch of the Russian Academy of Sciences, 660036, Krasnoyarsk, Russia.
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37
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Inouye S, Sasaki S. Imidazole-assisted catalysis of luminescence reaction in blue fluorescent protein from the photoprotein aequorin. Biochem Biophys Res Commun 2007; 354:650-5. [PMID: 17254548 DOI: 10.1016/j.bbrc.2006.12.233] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Accepted: 12/30/2006] [Indexed: 11/18/2022]
Abstract
Blue fluorescent protein from the calcium-binding photoprotein aequorin (BFP-aq) is a dissociable complex of Ca(2+)-bound apoaequorin and coelenteramide, and is identified as a luciferase that catalyzes the oxidation of coelenterazine by molecular oxygen to emit light. Based on the chemical luminescence of coelenterazine oxidation by an acid-base mechanism, we found that the luminescence activity of BFP-aq was stimulated by imidazole at concentrations of 30-300mM with coelenterazine and its analogues. The kinetic analyses indicate that imidazole has no effect on the binding affinity of coelenterazine to BFP-aq and may act as a catalytic base, accepting a proton from the -NH- group of coelenterazine and stimulating luminescence activity.
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Affiliation(s)
- Satoshi Inouye
- Yokohama Research Center, Chisso Corporation, 5-1 Okawa, Kanazawa-ku, Yokohama 236-8605, Japan.
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38
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Mori K, Maki S, Niwa H, Ikeda H, Hirano T. Real light emitter in the bioluminescence of the calcium-activated photoproteins aequorin and obelin: light emission from the singlet-excited state of coelenteramide phenolate anion in a contact ion pair. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.04.044] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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40
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Inouye S, Sasaki S. Blue fluorescent protein from the calcium-sensitive photoprotein aequorin: catalytic properties for the oxidation of coelenterazine as an oxygenase. FEBS Lett 2006; 580:1977-82. [PMID: 16545379 DOI: 10.1016/j.febslet.2006.02.065] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2006] [Revised: 02/17/2006] [Accepted: 02/26/2006] [Indexed: 11/17/2022]
Abstract
Blue fluorescent protein from the calcium-binding photoprotein aequorin (BFP-aq) is a complex of Ca2+ -bound apoaequorin and coelenteramide, and shows luminescence activity like a luciferase, catalyzing the oxidation of coelenterazine with molecular oxygen. To understand the catalytic properties of BFP-aq, various fluorescent proteins (FP-aq) have been prepared from semi-synthetic aequorin and characterized in comparison with BFP-aq. FP-aq has luciferase activity and could be regenerated into native aequorin by incubation with coelenterazine. The results from substrate specificity studies of FP-aq using various coelenterazine analogues have suggested that the oxidation of coelenterazine by BFP-aq in the luciferase reaction and the regeneration process to aequorin might involve the same catalytic site of BFP-aq.
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Affiliation(s)
- Satoshi Inouye
- Yokohama Research Center, Chisso Co., 5-1 Okawa, Kanazawa-ku, Yokohama 236-8605, Japan.
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41
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Liu ZJ, Stepanyuk GA, Vysotski ES, Lee J, Markova SV, Malikova NP, Wang BC. Crystal structure of obelin after Ca2+-triggered bioluminescence suggests neutral coelenteramide as the primary excited state. Proc Natl Acad Sci U S A 2006; 103:2570-5. [PMID: 16467137 PMCID: PMC1413834 DOI: 10.1073/pnas.0511142103] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The crystal structure at 1.93-A resolution is determined for the Ca2+-discharged obelin containing three bound calcium ions as well as the product of the bioluminescence reaction, coelenteramide. This finding extends the series of available spatial structures of the ligand-dependent conformations of the protein to four, the obelin itself, and those after the bioluminescence reaction with or without bound Ca2+ and/or coelenteramide. Among these structures, global conformational changes are small, typical of the class of "calcium signal modulators" within the EF-hand protein superfamily. Nevertheless, in the active site there are significant repositions of two residues. The His-175 imidazole ring flips becoming almost perpendicular to the original orientation corroborating the crucial importance of this residue for triggering bioluminescence. Tyr-138 hydrogen bonded to the coelenterazine N1-atom in unreacted obelin is moved away from the binding cavity after reaction. However, this Tyr is displaced by a water molecule from within the cavity, which now forms a hydrogen bond to the same atom, the amide N of coelenteramide. From this observation, a reaction scheme is proposed that would result in the neutral coelenteramide as the primary excited state product in photoprotein bioluminescence. From such a higher energy state it is now energetically feasible to account for the shorter wavelength bioluminescence spectra obtained from some photoprotein mutants or to populate the lower energy state of the phenolate anion to yield the blue bioluminescence ordinarily observed from native photoproteins.
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Affiliation(s)
- Zhi-Jie Liu
- *Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China; and
| | - Galina A. Stepanyuk
- *Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk 660036, Russia
| | - Eugene S. Vysotski
- *Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk 660036, Russia
| | - John Lee
- *Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
- To whom correspondence should be addressed. E-mail:
| | - Svetlana V. Markova
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk 660036, Russia
| | - Natalia P. Malikova
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk 660036, Russia
| | - Bi-Cheng Wang
- *Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
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Oliveira V, Garrido PAG, Rodrigues CC, Colquhoun A, Castro LM, Almeida PC, Shida CS, Juliano MA, Juliano L, Camargo ACM, Hyslop S, Roberts JL, Grum-Tokars V, Glucksman MJ, Ferro ES. Calcium modulates endopeptidase 24.15 (EC 3.4.24.15) membrane association, secondary structure and substrate specificity. FEBS J 2005; 272:2978-92. [PMID: 15955058 DOI: 10.1111/j.1742-4658.2005.04692.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The metalloendopeptidase 24.15 (EP24.15) is ubiquitously present in the extracellular environment as a secreted protein. Outside the cell, this enzyme degrades several neuropeptides containing from 5 to 17 amino acids (e.g. gonadotropin releasing hormone, bradykinin, opioids and neurotensin). The constitutive secretion of EP24.15 from glioma C6 cells was demonstrated to be stimulated linearly by reduced concentrations of extracellular calcium. In the present report we demonstrate that extracellular calcium concentration has no effect on the total amount of the extracellular (cell associated + medium) enzyme. Indeed, immuno-cytochemical analyses by confocal and electron microscopy suggested that the absence of calcium favors the enzyme shedding from the plasma membrane into the medium. Two putative calcium-binding sites on EP24.15 (D93 and D159) were altered by site-directed mutagenesis to investigate their possible contribution to binding of the enzyme at the cell surface. These mutated recombinant proteins behave similarly to the wild-type enzyme regarding enzymatic activity, secondary structure, calcium sensitivity and immunoreactivity. However, immunocytochemical analyses by confocal microscopy consistently show a reduced ability of the D93A mutant to associate with the plasma membrane of glioma C6 cells when compared with the wild-type enzyme. These data and the model of the enzyme's structure as determined by X-ray diffraction suggest that D93 is located at the enzyme surface and is consistent with membrane association of EP24.15. Moreover, calcium was also observed to induce a major change in the EP24.15 cleavage site on distinctive fluorogenic substrates. These data suggest that calcium may be an important modulator of ep24.15 cell function.
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Affiliation(s)
- Vitor Oliveira
- Laboratório de Neurociências, Universidade da Cidade de São Paulo, Brazil
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Deng L, Vysotski ES, Markova SV, Liu ZJ, Lee J, Rose J, Wang BC. All three Ca2+-binding loops of photoproteins bind calcium ions: the crystal structures of calcium-loaded apo-aequorin and apo-obelin. Protein Sci 2005; 14:663-75. [PMID: 15689515 PMCID: PMC2279293 DOI: 10.1110/ps.041142905] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The crystal structures of calcium-loaded apo-aequorin and apo-obelin have been determined at resolutions 1.7A and 2.2 A, respectively. A calcium ion is observed in each of the three EF-hand loops that have the canonical calcium-binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium-loaded apo-protein retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2-hyroperoxycoelenterazine, and also the same as the Ca2+-discharged obelin bound with product, coleneteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.
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Affiliation(s)
- Lu Deng
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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44
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Stepanyuk GA, Golz S, Markova SV, Frank LA, Lee J, Vysotski ES. Interchange of aequorin and obelin bioluminescence color is determined by substitution of one active site residue of each photoprotein. FEBS Lett 2005; 579:1008-14. [PMID: 15710383 DOI: 10.1016/j.febslet.2005.01.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2004] [Revised: 01/03/2005] [Accepted: 01/06/2005] [Indexed: 11/20/2022]
Abstract
The bioluminescence spectra from the Ca2+-regulated photoproteins aequorin (lambdamax=469 nm) and obelin (lambdamax=482 nm) differ because aequorin has an H-bond from its Tyr82 to the bound coelenteramide, not present in obelin at the corresponding Phe88. Substitutions of this Phe88 by Tyr, Trp, or His shifted the obelin bioluminescence to shorter wavelength with F88Y having lambdamax=453 nm. Removal of the H-bond by the substitution of Y82F in aequorin shifted its bioluminescence to lambdamax=501 nm. All mutants were stable with good activity and were expressible in mammalian cells, thereby demonstrating potential for monitoring multiple events in cells using multi-color detection.
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Affiliation(s)
- Galina A Stepanyuk
- Photobiology Laboratory, Institute of Biophysics, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
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