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Xie JM, Leng Y, Cui XY, Min CG, Ren AM, Liu G, Yin Q. Theoretical Study on the Formation and Decomposition Mechanisms of Coelenterazine Dioxetanone. J Phys Chem A 2023; 127:3804-3813. [PMID: 37083412 DOI: 10.1021/acs.jpca.3c00453] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Bioluminescence has been drawing broad attention due to its high signal-to-noise ratio and high bioluminescence quantum yields, which has been widely applied in the fields of biomedicine, bioanalysis, and so on. Among numerous bioluminescent substrates, coelenterazine is famous for its wide distribution. However, the oxygenation reaction mechanism of coelenterazine is far from being completely understood. In this paper, the formation and decomposition mechanisms of coelenterazine dioxetanone were investigated via density functional theory (DFT) and time-dependent (TD) DFT approaches. The results showed that the oxygenation reaction first occurred along the triplet-state potential energy surface (PES), after the intersystem crossing (ISC), second jumped to the diradical-state PES, and ultimately formed coelenterazine dioxetanone. For the decomposition mechanism of dioxetanone, the computational results showed that the chemiexcitation of neutral dioxetanone was more efficient than that of other dioxetanone species. Moreover, the diradical properties and the degree of ionic character are modified by the counter ions.
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Affiliation(s)
- Jin-Mei Xie
- School of Materials Science and Engineering, Kunming University of Science and Technology, Kunming 650093, P. R. China
| | - Yan Leng
- Research Center for Analysis and Measurement, Kunming University of Science and Technology, Kunming 650093 P. R. China
| | - Xiao-Ying Cui
- Research Center for Analysis and Measurement, Kunming University of Science and Technology, Kunming 650093 P. R. China
| | - Chun-Gang Min
- Research Center for Analysis and Measurement, Kunming University of Science and Technology, Kunming 650093 P. R. China
| | - Ai-Min Ren
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Gang Liu
- Institute of Chemical and Industrial Bioengineering, Jilin Engineering Normal University, Changchun 130052, P. R. China
| | - Qinhong Yin
- Faculty of Narcotics Control, Yunnan Police College, Kunming 650223, P. R. China
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Larionova MD, Wu L, Eremeeva EV, Natashin PV, Gulnov DV, Nemtseva EV, Liu D, Liu Z, Vysotski ES. Crystal structure of semisynthetic obelin-v. Protein Sci 2022; 31:454-469. [PMID: 34802167 PMCID: PMC8819848 DOI: 10.1002/pro.4244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 02/03/2023]
Abstract
Coelenterazine-v (CTZ-v), a synthetic derivative with an additional benzyl ring, yields a bright bioluminescence of Renilla luciferase and its "yellow" mutant with a significant shift in the emission spectrum toward longer wavelengths, which makes it the substrate of choice for deep tissue imaging. Although Ca2+ -regulated photoproteins activated with CTZ-v also display red-shifted light emission, in contrast to Renilla luciferase their bioluminescence activities are very low, which makes photoproteins activated by CTZ-v unusable for calcium imaging. Here, we report the crystal structure of Ca2+ -regulated photoprotein obelin with 2-hydroperoxycoelenterazine-v (obelin-v) at 1.80 Å resolution. The structures of obelin-v and obelin bound with native CTZ revealed almost no difference; only the minor rearrangement in hydrogen-bond pattern and slightly increased distances between key active site residues and some atoms of 2-hydroperoxycoelenterazine-v were found. The fluorescence quantum yield (ΦFL ) of obelin bound with coelenteramide-v (0.24) turned out to be even higher than that of obelin with native coelenteramide (0.19). Since both obelins are in effect the enzyme-substrate complexes containing the 2-hydroperoxy adduct of CTZ-v or CTZ, we reasonably assume the chemical reaction mechanisms and the yields of the reaction products (ΦR ) to be similar for both obelins. Based on these findings we suggest that low bioluminescence activity of obelin-v is caused by the low efficiency of generating an electronic excited state (ΦS ). In turn, the low ΦS value as compared to that of native CTZ might be the result of small changes in the substrate microenvironment in the obelin-v active site.
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Affiliation(s)
- Marina D. Larionova
- Photobiology LaboratoryInstitute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”KrasnoyarskRussia,iHuman Institute, ShanghaiTech UniversityShanghaiChina
| | - Lijie Wu
- iHuman Institute, ShanghaiTech UniversityShanghaiChina
| | - Elena V. Eremeeva
- Photobiology LaboratoryInstitute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”KrasnoyarskRussia,Institute of Fundamental Biology and Biotechnology, Siberian Federal UniversityKrasnoyarskRussia
| | - Pavel V. Natashin
- Photobiology LaboratoryInstitute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”KrasnoyarskRussia
| | - Dmitry V. Gulnov
- Institute of Fundamental Biology and Biotechnology, Siberian Federal UniversityKrasnoyarskRussia
| | - Elena V. Nemtseva
- Photobiology LaboratoryInstitute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”KrasnoyarskRussia,Institute of Fundamental Biology and Biotechnology, Siberian Federal UniversityKrasnoyarskRussia
| | - Dongsheng Liu
- iHuman Institute, ShanghaiTech UniversityShanghaiChina
| | - Zhi‐Jie Liu
- iHuman Institute, ShanghaiTech UniversityShanghaiChina,School of Life Science and Technology, ShanghaiTech UniversityShanghaiChina
| | - Eugene S. Vysotski
- Photobiology LaboratoryInstitute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”KrasnoyarskRussia
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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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Molakarimi M, Mohseni A, Taghdir M, Pashandi Z, Gorman MA, Parker MW, Naderi-Manesh H, Sajedi RH. QM/MM simulations provide insight into the mechanism of bioluminescence triggering in ctenophore photoproteins. PLoS One 2017; 12:e0182317. [PMID: 28777808 PMCID: PMC5544205 DOI: 10.1371/journal.pone.0182317] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/16/2017] [Indexed: 11/28/2022] Open
Abstract
Photoproteins are responsible for light emission in a variety of marine ctenophores and coelenterates. The mechanism of light emission in both families occurs via the same reaction. However, the arrangement of amino acid residues surrounding the chromophore, and the catalytic mechanism of light emission is unknown for the ctenophore photoproteins. In this study, we used quantum mechanics/molecular mechanics (QM/MM) and site-directed mutagenesis studies to investigate the details of the catalytic mechanism in berovin, a member of the ctenophore family. In the absence of a crystal structure of the berovin-substrate complex, molecular docking was used to determine the binding mode of the protonated (2-hydroperoxy) and deprotonated (2-peroxy anion) forms of the substrate to berovin. A total of 13 mutants predicted to surround the binding site were targeted by site-directed mutagenesis which revealed their relative importance in substrate binding and catalysis. Molecular dynamics simulations and MM-PBSA (Molecular Mechanics Poisson-Boltzmann/surface area) calculations showed that electrostatic and polar solvation energy are +115.65 and -100.42 kcal/mol in the deprotonated form, respectively. QM/MM calculations and pKa analysis revealed the deprotonated form of substrate is unstable due to the generation of a dioxetane intermediate caused by nucleophilic attack of the substrate peroxy anion at its C3 position. This work also revealed that a hydrogen bonding network formed by a D158- R41-Y204 triad could be responsible for shuttling the proton from the 2- hydroperoxy group of the substrate to bulk solvent.
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Affiliation(s)
- Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Zaiddodine Pashandi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Michael A. Gorman
- Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
| | - Michael W. Parker
- Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent’s Institute of Medical Research, Fitzroy, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail: (RHS); (MNM)
| | - Reza H. Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail: (RHS); (MNM)
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5
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Lee J. Perspectives on Bioluminescence Mechanisms. Photochem Photobiol 2016; 93:389-404. [PMID: 27748947 DOI: 10.1111/php.12650] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/24/2016] [Indexed: 11/27/2022]
Abstract
The molecular mechanisms of the bioluminescence systems of the firefly, bacteria and those utilizing imidazopyrazinone luciferins such as coelenterazine are gradually being uncovered using modern biophysical methods such as dynamic (ns-ps) fluorescence spectroscopy, NMR, X-ray crystallography and computational chemistry. The chemical structures of all reactants are well defined, and the spatial structures of the luciferases are providing important insight into interactions within the active cavity. It is generally accepted that the firefly and coelenterazine systems, although proceeding by different chemistries, both generate a dioxetanone high-energy species that undergoes decarboxylation to form directly the product in its S1 state, the bioluminescence emitter. More work is still needed to establish the structure of the products completely. In spite of the bacterial system receiving the most research attention, the chemical pathway for excitation remains mysterious except that it is clearly not by a decarboxylation. Both the coelenterazine and bacterial systems have in common of being able to employ "antenna proteins," lumazine protein and the green-fluorescent protein, for tuning the color of the bioluminescence. Spatial structure information has been most valuable in informing the mechanism of the Ca2+ -regulated photoproteins and the antenna protein interactions.
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Affiliation(s)
- John Lee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA
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Min C, Pinto da Silva L, Esteves da Silva JCG, Yang X, Huang S, Ren A, Zhu Y. A Computational Investigation of the Equilibrium Constants for the Fluorescent and Chemiluminescent States of Coelenteramide. Chemphyschem 2016; 18:117-123. [DOI: 10.1002/cphc.201600850] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/04/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Chun‐Gang Min
- Research Center for Analysis and Measurement Kunming University of Science and Technology Kunming 650093 P. R. China
| | - Luís Pinto da Silva
- Centro de Investigaçäo em Química (CIQ-UP), Departamento de Química e Bioquímica Faculdade de Ciências da Universidade do Porto Rua Campo Alegra 687 4169-007 Porto Portugal
| | - Joaquim C. G. Esteves da Silva
- Centro de Investigaçäo em Química (CIQ-UP), Departamento de Química e Bioquímica Faculdade de Ciências da Universidade do Porto Rua Campo Alegra 687 4169-007 Porto Portugal
| | - Xi‐Kun Yang
- Research Center for Analysis and Measurement Kunming University of Science and Technology Kunming 650093 P. R. China
| | - Shao‐Jun Huang
- Research Center for Analysis and Measurement Kunming University of Science and Technology Kunming 650093 P. R. China
| | - Ai‐Min Ren
- Institute of Theoretical Chemistry Jilin University Changchun 130023 P. R. China
| | - Yan‐Qin Zhu
- Research Center for Analysis and Measurement Kunming University of Science and Technology Kunming 650093 P. R. China
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7
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Qu X, Rowe L, Dikici E, Ensor M, Daunert S. Aequorin mutants with increased thermostability. Anal Bioanal Chem 2014; 406:5639-43. [PMID: 25084737 DOI: 10.1007/s00216-014-8039-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/27/2014] [Accepted: 07/16/2014] [Indexed: 12/01/2022]
Abstract
Bioluminescent labels can be especially useful for in vivo and live animal studies due to the negligible bioluminescence background in cells and most animals, and the non-toxicity of bioluminescent reporter systems. Significant thermal stability of bioluminescent labels is essential, however, due to the longitudinal nature and physiological temperature conditions of many bioluminescent-based studies. To improve the thermostability of the bioluminescent protein aequorin, we employed random and rational mutagenesis strategies to create two thermostable double mutants, S32T/E156V and M36I/E146K, and a particularly thermostable quadruple mutant, S32T/E156V/Q168R/L170I. The double aequorin mutants, S32T/E156V and M36I/E146K, retained 4 and 2.75 times more of their initial bioluminescence activity than wild-type aequorin during thermostability studies at 37 °C. Moreover, the quadruple aequorin mutant, S32T/E156V/Q168R/L170I, exhibited more thermostability at a variety of temperatures than either double mutant alone, producing the most thermostable aequorin mutant identified thus far.
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Affiliation(s)
- Xiaoge Qu
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA
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8
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Yue L, Liu YJ. Mechanism of AMPPD Chemiluminescence in a Different Voice. J Chem Theory Comput 2013; 9:2300-12. [DOI: 10.1021/ct400206k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ling Yue
- Key Laboratory
of Theoretical and Computational Photochemistry,
Ministry of Education, College of Chemistry, Beijing Normal University,
Beijing 100875, China
| | - Ya-Jun Liu
- Key Laboratory
of Theoretical and Computational Photochemistry,
Ministry of Education, College of Chemistry, Beijing Normal University,
Beijing 100875, China
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9
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Min CG, Li ZS, Ren AM, Zou LY, Guo JF, Goddard JD. The fluorescent properties of coelenteramide, a substrate of aequorin and obelin. J Photochem Photobiol A Chem 2013. [DOI: 10.1016/j.jphotochem.2012.10.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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10
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Giuliani G, Molinari P, Ferretti G, Cappelli A, Anzini M, Vomero S, Costa T. New red-shifted coelenterazine analogues with an extended electronic conjugation. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.07.041] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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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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