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Choudhury A, Santra S, Ghosh D. Understanding the Photoprocesses in Biological Systems: Need for Accurate Multireference Treatment. J Chem Theory Comput 2024; 20:4951-4964. [PMID: 38864715 DOI: 10.1021/acs.jctc.4c00027] [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: 06/13/2024]
Abstract
Light-matter interaction is crucial to life itself and revolves around many of the central processes in biology. The need for understanding these photochemical and photophysical processes cannot be overemphasized. Interaction of light with biological systems starts with the absorption of light and subsequent phenomena that occur in the excited states of the system. However, excited states are typically difficult to understand within the mean field approximation of quantum chemical methods. Therefore, suitable multireference methods and methodologies have been developed to understand these phenomena. In this Perspective, we will describe a few methods and methodologies suitable for these descriptions and discuss some persisting difficulties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriyo Santra
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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2
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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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3
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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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4
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Deventer MH, Persson M, Laus A, Pottie E, Cannaert A, Tocco G, Gréen H, Stove CP. Off-target activity of NBOMes and NBOMe analogs at the µ opioid receptor. Arch Toxicol 2023; 97:1367-1384. [PMID: 36853332 DOI: 10.1007/s00204-023-03465-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/16/2023] [Indexed: 03/01/2023]
Abstract
New psychoactive substances (NPS) are introduced on the illicit drug market at a rapid pace. Their molecular targets are often inadequately elucidated, which contributes to the delayed characterization of their pharmacological effects. Inspired by earlier findings, this study set out to investigate the µ opioid receptor (MOR) activation potential of a large set of psychedelics, substances which typically activate the serotonin (5-HT2A) receptor as their target receptor. We observed that some substances carrying the N-benzyl phenethylamine (NBOMe) structure activated MOR, as confirmed by both the NanoBiT® βarr2 recruitment assay and the G protein-based AequoScreen® Ca2+ release assay. The use of two orthogonal systems proved beneficial as some aspecific, receptor independent effects were found for various analogs when using the Ca2+ release assay. The specific 'off-target' effects at MOR could be blocked by the opioid antagonist naloxone, suggesting that these NBOMes occupy the same common opioid binding pocket as conventional opioids. This was corroborated by molecular docking, which revealed the plausibility of multiple interactions of 25I-NBOMe with MOR, similar to those observed for opioids. Additionally, structure-activity relationship findings seen in vitro were rationalized in silico for two 25I-NBOMe isomers. Overall, as MOR activity of these psychedelics was only noticed at high concentrations, we consider it unlikely that for the tested compounds there will be a relevant opioid toxicity in vivo at physiologically relevant concentrations. However, small modifications to the original NBOMe structure may result in a panel of more efficacious and potent MOR agonists, potentially exhibiting a dual MOR/5-HT2A activation potential.
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Affiliation(s)
- Marie H Deventer
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Mattias Persson
- Department of Forensic Genetic and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden
| | - Antonio Laus
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Eline Pottie
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Annelies Cannaert
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Graziella Tocco
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Henrik Gréen
- Department of Forensic Genetic and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden.,Division of Clinical Chemistry and Pharmacology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Christophe P Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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5
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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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6
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Xie JM, Leng Y, Dong K, Cui XY, Yang XK, Min CG, Liu CX, Ren AM. Effect of double bond on electronic and optical properties of coelenteramide: A time-dependent density functional theory investigation. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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Liu YJ. Understanding the complete bioluminescence cycle from a multiscale computational perspective: A review. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2022. [DOI: 10.1016/j.jphotochemrev.2022.100537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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8
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Recombinant light-sensitive photoprotein berovin from ctenophore Beroe abyssicola: Bioluminescence and absorbance characteristics. Biochem Biophys Res Commun 2022; 624:23-27. [DOI: 10.1016/j.bbrc.2022.07.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/20/2022] [Indexed: 11/20/2022]
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9
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Vysotski ES. “Bioluminescence and Photonics of Fluorescent Proteins” session at the 9th Congress of the Russian Photobiology Society (Shepsi, Krasnodar region, Russia; September 12–19, 2021). Biophys Rev 2022; 14:765-767. [DOI: 10.1007/s12551-022-00971-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
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10
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Quan Z, Mao L, Tang YQ, Lei M, Zhu BZ, Liu YJ. Mechanistic Investigation of H 2 O 2 -dependent Chemiluminescence from Tetrabromo-1,4-Benzoquinone. Chemphyschem 2022; 23:e202100885. [PMID: 35106876 DOI: 10.1002/cphc.202100885] [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: 12/14/2021] [Revised: 01/13/2022] [Indexed: 11/11/2022]
Abstract
As a H2 O2 -dependent bioluminescent substrate, tetrabromo-1,4-benzoquinone (TBBQ) was first isolated from acorn worm. The mechanism of chemiluminescence (CL) corresponding to the bioluminescence (BL) of acorn worm is largely unknown, let alone the mechanism of BL. In this article, we firstly studied the chemical and physical processes, and mechanism of H2 O2 -dependent CL from TBBQ by theoretical and experimental methods. The research results indicate: the CL process is initiated by a nucleophilic substitution reaction, which leads to the formation of an anionic dioxetane through five consecutive reactions; the anionic dioxetane decomposes to the first singlet excited state (S1 ) via a conical interaction of the potential energy surfaces (PESs) between the ground (S0 ) and S1 state; the anionic S1 -state changes to its neutral form by a proton transfer from the solvent and this neutral product is assigned as the actual luminophore. Moreover, the experimental detection of CL, . OH and the identifications of 2,3-dibromo maleic acid and 2-bromo malonic acid as the major final products provide direct evidence of the theoretically suggested mechanism. Finally, this study proves that the activity of the H2 O2 -dependent CL from TBBQ is significantly lower than the one from tetrachloro-1,4-benzoquinone (TCBQ), which is caused by the weaker electron withdrawing effect and the stronger heavy atomic effect of bromine.
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Affiliation(s)
- Zhuo Quan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P.R. China
| | - Li Mao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, The Chinese Academy of Sciences, Beijing 100085, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi-Qi Tang
- Center for Advanced Materials Research, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, 519087, P.R. China
| | - Ming Lei
- State Key Laboratory of Chemical Resource Engineering, Institute of Computational Chemistry, College of Chemistry, Beijing University of Chemical Technology, Beijing, 100029, P.R. China
| | - Ben-Zhan Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, The Chinese Academy of Sciences, Beijing 100085, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P.R. China.,Center for Advanced Materials Research, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, 519087, P.R. China
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11
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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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12
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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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13
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Chen SF, Vysotski ES, Liu YJ. H 2O-Bridged Proton-Transfer Channel in Emitter Species Formation in Obelin Bioluminescence. J Phys Chem B 2021; 125:10452-10458. [PMID: 34520210 DOI: 10.1021/acs.jpcb.1c03985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bioluminescence of a number of marine organisms is conditioned by Ca2+-regulated photoprotein (CaRP) with coelenterazine as the reaction substrate. The reaction product, coelenteramide, at the first singlet excited state (S1) is the emitter of CaRP. The S1-state coelenteramide is produced via the decomposition of coelenterazine dioxetanone. Experiments suggested that the neutral S1-coelenteramide is the primary emitter species. This supposition contradicts with theoretical calculations showing that the anionic S1-coelenteramide is a primary product of the decomposition of coelenterazine dioxetanone. In this study, applying molecular dynamic (MD) simulations and the hybrid quantum mechanics/molecular mechanics (QM/MM) method, we investigated a proton-transfer (PT) process taking place in CaRP obelin from Obelia longissima for emitter formation. Our calculations demonstrate a concerted PT process with a water molecule as a bridge between anionic S1-coelenteramide and the nearest histidine residue. The low activation barrier as well as the strong hydrogen-bond network between the proton donor and the proton acceptor suggests a fast PT process comparable with that of the lifetime of excited anionic S1-coelenteramide. The existence of the PT process eliminates the discrepancy between experimental and theoretical studies. The fast PT process at emitter formation can also take place in other CaRPs.
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Affiliation(s)
- Shu-Feng Chen
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai 201418, People's Republic of China
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia
| | - Ya-Jun Liu
- Center for Advanced Materials Research, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai 519087, China.,Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
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14
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Burakova LP, Lyakhovich MS, Mineev KS, Petushkov VN, Zagitova RI, Tsarkova AS, Kovalchuk SI, Yampolsky IV, Vysotski ES, Kaskova ZM. Unexpected Coelenterazine Degradation Products of Beroe abyssicola Photoprotein Photoinactivation. Org Lett 2021; 23:6846-6849. [PMID: 34416112 DOI: 10.1021/acs.orglett.1c02410] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ca2+-regulated photoproteins of ctenophores lose bioluminescence activity when exposed to visible light. Little is known about the chemical nature of chromophore photoinactivation. Using a total synthesis strategy, we have established the structures of two unusual coelenterazine products, isolated from recombinant berovin of the ctenophore Beroe abyssicola, which are Z/E isomers. We propose that during light irradiation, these derivatives are formed from 2-hydroperoxycoelenterazine via the intermediate 8a-peroxide by a mechanism reminiscent of that previously described for the auto-oxidation of green-fluorescent-protein-like chromophores.
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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 660036, Russia
| | - Maria S Lyakhovich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin N Petushkov
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia
| | - Renata I Zagitova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Aleksandra S Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia.,Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Sergey I Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Ilia V Yampolsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia.,Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia
| | - Zinaida M Kaskova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia.,Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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15
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Haghdoust F, Molakarimi M, Mirshahi M, Sajedi RH. Engineering aequorin to improve thermostability through rigidifying flexible sites. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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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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17
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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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18
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Syed AJ, Anderson JC. Applications of bioluminescence in biotechnology and beyond. Chem Soc Rev 2021; 50:5668-5705. [DOI: 10.1039/d0cs01492c] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Bioluminescent probes have hugely benefited from the input of synthetic chemistry and protein engineering. Here we review the latest applications of these probes in biotechnology and beyond, with an eye on current limitations and future directions.
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Affiliation(s)
- Aisha J. Syed
- Department of Chemistry
- University College London
- London
- UK
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19
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RedquorinXS Mutants with Enhanced Calcium Sensitivity and Bioluminescence Output Efficiently Report Cellular and Neuronal Network Activities. Int J Mol Sci 2020; 21:ijms21217846. [PMID: 33105848 PMCID: PMC7660078 DOI: 10.3390/ijms21217846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 01/14/2023] Open
Abstract
Considerable efforts have been focused on shifting the wavelength of aequorin Ca2+-dependent blue bioluminescence through fusion with fluorescent proteins. This approach has notably yielded the widely used GFP-aequorin (GA) Ca2+ sensor emitting green light, and tdTomato-aequorin (Redquorin), whose bioluminescence is completely shifted to red, but whose Ca2+ sensitivity is low. In the present study, the screening of aequorin mutants generated at twenty-four amino acid positions in and around EF-hand Ca2+-binding domains resulted in the isolation of six aequorin single or double mutants (AequorinXS) in EF2, EF3, and C-terminal tail, which exhibited markedly higher Ca2+ sensitivity than wild-type aequorin in vitro. The corresponding Redquorin mutants all showed higher Ca2+ sensitivity than wild-type Redquorin, and four of them (RedquorinXS) matched the Ca2+ sensitivity of GA in vitro. RedquorinXS mutants exhibited unaltered thermostability and peak emission wavelengths. Upon stable expression in mammalian cell line, all RedquorinXS mutants reported the activation of the P2Y2 receptor by ATP with higher sensitivity and assay robustness than wt-Redquorin, and one, RedquorinXS-Q159T, outperformed GA. Finally, wide-field bioluminescence imaging in mouse neocortical slices showed that RedquorinXS-Q159T and GA similarly reported neuronal network activities elicited by the removal of extracellular Mg2+. Our results indicate that RedquorinXS-Q159T is a red light-emitting Ca2+ sensor suitable for the monitoring of intracellular signaling in a variety of applications in cells and tissues, and is a promising candidate for the transcranial monitoring of brain activities in living mice.
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20
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Krasitskaya VV, Bashmakova EE, Frank LA. Coelenterazine-Dependent Luciferases as a Powerful Analytical Tool for Research and Biomedical Applications. Int J Mol Sci 2020; 21:E7465. [PMID: 33050422 PMCID: PMC7590018 DOI: 10.3390/ijms21207465] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022] Open
Abstract
: The functioning of bioluminescent systems in most of the known marine organisms is based on the oxidation reaction of the same substrate-coelenterazine (CTZ), catalyzed by luciferase. Despite the diversity in structures and the functioning mechanisms, these enzymes can be united into a common group called CTZ-dependent luciferases. Among these, there are two sharply different types of the system organization-Ca2+-regulated photoproteins and luciferases themselves that function in accordance with the classical enzyme-substrate kinetics. Along with deep and comprehensive fundamental research on these systems, approaches and methods of their practical use as highly sensitive reporters in analytics have been developed. The research aiming at the creation of artificial luciferases and synthetic CTZ analogues with new unique properties has led to the development of new experimental analytical methods based on them. The commercial availability of many ready-to-use assay systems based on CTZ-dependent luciferases is also important when choosing them by first-time-users. The development of analytical methods based on these bioluminescent systems is currently booming. The bioluminescent systems under consideration were successfully applied in various biological research areas, which confirms them to be a powerful analytical tool. In this review, we consider the main directions, results, and achievements in research involving these luciferases.
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Affiliation(s)
- Vasilisa V. Krasitskaya
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
| | - Eugenia E. Bashmakova
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
| | - Ludmila A. Frank
- Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia; (V.V.K.); (E.E.B.)
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
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21
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Eremeeva EV, Jiang T, Malikova NP, Li M, Vysotski ES. Bioluminescent Properties of Semi-Synthetic Obelin and Aequorin Activated by Coelenterazine Analogues with Modifications of C-2, C-6, and C-8 Substituents. Int J Mol Sci 2020; 21:E5446. [PMID: 32751691 PMCID: PMC7432523 DOI: 10.3390/ijms21155446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022] Open
Abstract
Ca2+-regulated photoproteins responsible for bioluminescence of a variety of marine organisms are single-chain globular proteins within the inner cavity of which the oxygenated coelenterazine, 2-hydroperoxycoelenterazine, is tightly bound. Alongside with native coelenterazine, photoproteins can also use its synthetic analogues as substrates to produce flash-type bioluminescence. However, information on the effect of modifications of various groups of coelenterazine and amino acid environment of the protein active site on the bioluminescent properties of the corresponding semi-synthetic photoproteins is fragmentary and often controversial. In this paper, we investigated the specific bioluminescence activity, light emission spectra, stopped-flow kinetics and sensitivity to calcium of the semi-synthetic aequorins and obelins activated by novel coelenterazine analogues and the recently reported coelenterazine derivatives. Several semi-synthetic photoproteins activated by the studied coelenterazine analogues displayed sufficient bioluminescence activities accompanied by various changes in the spectral and kinetic properties as well as in calcium sensitivity. The poor activity of certain semi-synthetic photoproteins might be attributed to instability of some coelenterazine analogues in solution and low efficiency of 2-hydroperoxy adduct formation. In most cases, semi-synthetic obelins and aequorins displayed different properties upon being activated by the same coelenterazine analogue. The results indicated that the OH-group at the C-6 phenyl ring of coelenterazine is important for the photoprotein bioluminescence and that the hydrogen-bond network around the substituent in position 6 of the imidazopyrazinone core could be the reason of different bioluminescence activities of aequorin and obelin with certain coelenterazine analogues.
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Affiliation(s)
- Elena V. Eremeeva
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia; (E.V.E.); (N.P.M.)
| | - Tianyu Jiang
- Key Laboratory of Chemical Biology (MOE), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China;
- State Key Laboratory of Microbial Technology, Shandong University–Helmholtz Institute of Biotechnology, Shandong University, Qingdao 266237, China
| | - Natalia P. Malikova
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia; (E.V.E.); (N.P.M.)
| | - Minyong Li
- Key Laboratory of Chemical Biology (MOE), Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China;
| | - Eugene S. Vysotski
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia; (E.V.E.); (N.P.M.)
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22
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Tang YQ, Liu YJ. Theoretical Study on Chemiluminescence of H2O2-dependent Tetrachloro-1,4-benzoquinone. J Org Chem 2020; 85:9042-9050. [DOI: 10.1021/acs.joc.0c00955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yi-Qi Tang
- 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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23
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Ding BW, Eremeeva EV, Vysotski ES, Liu YJ. Luminescence Activity Decreases When v-coelenterazine Replaces Coelenterazine in Calcium-Regulated Photoprotein-A Theoretical and Experimental Study. Photochem Photobiol 2020; 96:1047-1060. [PMID: 32416626 DOI: 10.1111/php.13280] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/23/2020] [Indexed: 11/27/2022]
Abstract
Calcium-regulated photoproteins are found in at least five phyla of organisms. The light emitted by those photoproteins can be tuned by mutating the photoprotein and/or by modifying the substrate coelenterazine (CTZ). Thirty years ago, Shimomura observed that the luminescence activity of aequorin was dramatically reduced when the substrate CTZ was replaced by its analog v-CTZ. The latter is formed by adding a phenyl ring to the π-conjugated moiety of CTZ. The decrease in luminescence activity has not been understood until now. In this paper, through combined quantum mechanics and molecular mechanics calculations as well as molecular dynamics simulations, we discovered the reason for this observation. Modification of the substrate changes the conformation of nearby aromatic residues and enhances the π-π stacking interactions between the conjugated moiety of v-CTZ and the residues, which weakens the charge transfer to form light emitter and leads to a lower luminescence activity. The microenvironments of CTZ in obelin and in aequorin are very similar, so we predicted that the luminescence activity of obelin will also dramatically decrease when CTZ is replaced by v-CTZ. This prediction has received strong evidence from currently theoretical calculations and has been verified by experiments.
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Affiliation(s)
- Bo-Wen Ding
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - 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
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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24
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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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25
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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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26
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Gao M, Ding BW, Liu YJ. Tuning the fluorescence of calcium-discharged photoprotein obelin via mutating at the His22-Phe88-Trp92 triad - a QM/MM study. Photochem Photobiol Sci 2019; 18:1823-1832. [PMID: 31165126 DOI: 10.1039/c9pp00191c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The fluorescence (FL) of calcium-discharged photoprotein (CaDP) can be altered by easily mutating CaDP without modifying coelenteramide (CLM), which is the decarboxylation product of coelenterazine in calcium-regulated photoprotein. The His22-Phe88-Trp92 triad (the ordering numbers of three amino acids are sorted by a crystal structure (PDB: 2F8P) of calcium-discharged obelin, i.e., CaDP-obelin) is closely related to CaDP-obelin FL, since it exists in close proximity to the 5-p-hydroxyphenyl of CLM. Therefore, it is important to thoroughly investigate how the mutations of this triad affect the emission color of CaDP-obelin FL. In this study, by mutating wild-type CaDP-obelin (WT) at the His22-Phe88-Trp92 triad, we theoretically constructed its nine mutants of separable FL colors. Through combined quantum mechanics and molecular mechanics (QM/MM) calculations and molecular dynamics (MD) simulations, the influence of the mutations of this triad on the CaDP-obelin FL was analyzed considering the H-bond effect and the charge effect. This study demonstrated that the mutations at the His22-Phe88-Trp92 triad redistribute the charges on the D-π-A molecule, CLM, change the charge transfer from the D to the (π + A) moiety, and thereby alter the FL emission. Appending more negative charges on the phenolate moiety of CLM benefits the FL redshift.
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Affiliation(s)
- Meng Gao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, P. R. China.
| | - Bo-Wen Ding
- School of Environment, Beijing Normal University, Beijing, P. R. China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, P. R. China.
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27
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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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28
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Markova SV, Larionova MD, Vysotski ES. Shining Light on the Secreted Luciferases of Marine Copepods: Current Knowledge and Applications. Photochem Photobiol 2019; 95:705-721. [PMID: 30585639 DOI: 10.1111/php.13077] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 12/18/2018] [Indexed: 01/02/2023]
Abstract
Copepod luciferases-a family of small secretory proteins of 18.4-24.3 kDa, including a signal peptide-are responsible for bright secreted bioluminescence of some marine copepods. The copepod luciferases use coelenterazine as a substrate to produce blue light in a simple oxidation reaction without any additional cofactors. They do not share sequence or structural similarity with other identified bioluminescent proteins including coelenterazine-dependent Renilla and Oplophorus luciferases. The small size, strong luminescence activity and high stability, including thermostability, make secreted copepod luciferases very attractive candidates as reporter proteins which are particularly useful for nondisruptive reporter assays and for high-throughput format. The most known and extensively investigated representatives of this family are the first cloned GpLuc and MLuc luciferases from copepods Gaussia princeps and Metridia longa, respectively. Immediately after cloning, these homologous luciferases were successfully applied as bioluminescent reporters in vivo and in vitro, and since then, the scope of their applications continues to grow. This review is an attempt to systemize and critically evaluate the data scattered through numerous articles regarding the main structural features of copepod luciferases, their luminescent and physicochemical properties. We also review the main trends of their application as bioluminescent reporters in cell and molecular biology.
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Affiliation(s)
- Svetlana V Markova
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,Siberian Federal University, Krasnoyarsk, Russia.,N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia, Moscow, Russia
| | - Marina D Larionova
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia, Moscow, Russia
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia.,N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of Russia, Moscow, Russia
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29
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Molakarimi M, Gorman MA, Mohseni A, Pashandi Z, Taghdir M, Naderi-Manesh H, Sajedi RH, Parker MW. Reaction mechanism of the bioluminescent protein mnemiopsin1 revealed by X-ray crystallography and QM/MM simulations. J Biol Chem 2019; 294:20-27. [PMID: 30420427 PMCID: PMC6322872 DOI: 10.1074/jbc.ra118.006053] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/05/2018] [Indexed: 11/06/2022] Open
Abstract
Bioluminescence of a variety of marine organisms, mostly cnidarians and ctenophores, is carried out by Ca2+-dependent photoproteins. The mechanism of light emission operates via the same reaction in both animal families. Despite numerous studies on the ctenophore photoprotein family, the detailed catalytic mechanism and arrangement of amino acid residues surrounding the chromophore in this family are a mystery. Here, we report the crystal structure of Cd2+-loaded apo-mnemiopsin1, a member of the ctenophore family, at 2.15 Å resolution and used quantum mechanics/molecular mechanics (QM/MM) to investigate its reaction mechanism. The simulations suggested that an Asp-156-Arg-39-Tyr-202 triad creates a hydrogen-bonded network to facilitate the transfer of a proton from the 2-hydroperoxy group of the chromophore coelenterazine to bulk solvent. We identified a water molecule in the coelenteramide-binding cavity that forms a hydrogen bond with the amide nitrogen atom of coelenteramide, which, in turn, is hydrogen-bonded via another water molecule to Tyr-131. This observation supports the hypothesis that the function of the coelenteramide-bound water molecule is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion, thereby triggering the bioluminescence reaction in the ctenophore photoprotein family.
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Affiliation(s)
- Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Michael A Gorman
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia; Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Zaiddodine Pashandi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-175, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran.
| | - Michael W Parker
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia; Australian Cancer Research Foundation Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.
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30
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Lee J, Müller F, Visser AJWG. The Sensitized Bioluminescence Mechanism of Bacterial Luciferase. Photochem Photobiol 2018; 95:679-704. [PMID: 30485901 DOI: 10.1111/php.13063] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 11/17/2018] [Indexed: 11/27/2022]
Abstract
After more than one-half century of investigations, the mechanism of bioluminescence from the FMNH2 assisted oxygen oxidation of an aliphatic aldehyde on bacterial luciferase continues to resist elucidation. There are many types of luciferase from species of bioluminescent bacteria originating from both marine and terrestrial habitats. The luciferases all have close sequence homology, and in vitro, a highly efficient light generation is obtained from these natural metabolites as substrates. Sufficient exothermicity equivalent to the energy of a blue photon is available in the chemical oxidation of the aldehyde to the corresponding carboxylic acid, and a luciferase-bound FMNH-OOH is a key player. A high energy species, the source of the exothermicity, is unknown except that it is not a luciferin cyclic peroxide, a dioxetanone, as identified in the pathway of the firefly and the marine bioluminescence systems. Besides these natural substrates, variable bioluminescence properties are found using other reactants such as flavin analogs or aldehydes, but results also depend on the luciferase type. Some rationalization of the mechanism has resulted from spatial structure determination, NMR of intermediates and dynamic optical spectroscopy. The overall light path appears to fall into the sensitized class of chemiluminescence mechanism, distinct from the dioxetanone types.
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Affiliation(s)
- John Lee
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA
| | | | - Antonie J W G Visser
- Laboratory of Biochemistry Microspectroscopy Centre, Wageningen University, Wageningen, The Netherlands
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31
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Petrova AS, Lukonina AA, Dementyev DV, Ya Bolsunovsky A, Popov AV, Kudryasheva NS. Protein-based fluorescent bioassay for low-dose gamma radiation exposures. Anal Bioanal Chem 2018; 410:6837-6844. [PMID: 30062510 DOI: 10.1007/s00216-018-1282-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/10/2018] [Accepted: 07/17/2018] [Indexed: 01/30/2023]
Abstract
The study suggests an application of a coelenteramide-containing fluorescent protein (CLM-CFP) as a simplest bioassay for gamma radiation exposures. "Discharged obelin," a product of the bioluminescence reaction of the marine coelenterate Obelia longissima, was used as a representative of the CLM-CFP group. The bioassay is based on a simple enzymatic reaction-photochemical proton transfer in the coelenteramide-apoprotein complex. Components of this reaction differ in fluorescence color, providing, by this, an evaluation of the proton transfer efficiency in the photochemical process. This efficiency depends on the microenvironment of the coelenteramide within the protein complex, and, hence, can evaluate a destructive ability of gamma radiation. The CLM-CFP samples were exposed to gamma radiation (137Cs, 2 mGy/h) for 7 and 16 days at 20 °C and 5 °C, respectively. As a result, two fluorescence characteristics (overall fluorescence intensity and contributions of color components to the fluorescence spectra) were identified as bioassay parameters. Both parameters demonstrated high sensitivity of the CLM-CFP-based bioassay to the low-dose gamma radiation exposure (up to 100 mGy). Higher temperature (20 °C) enhanced the response of CLM-CFP to gamma radiation. This new bioassay can provide fluorescent multicolor assessment of protein destruction in cells and physiological liquids under exposure to low doses of gamma radiation. Graphical abstract ᅟ.
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Affiliation(s)
- Alena S Petrova
- Krasnoyarsk State Agrarian University, Mira Avenue 90, Krasnoyarsk, 660049, Russia
| | - Anna A Lukonina
- Siberian Federal University, Svobodnyy Ave 79, Krasnoyarsk, 660041, Russia
| | - Dmitry V Dementyev
- Institute of Biophysics SB RAS, FRC KSC SB RAS, Krasnoyarsk, 660036, Russia
| | | | - Anatoliy V Popov
- Department of Radiology, University of Pennsylvania, 3401 N Broad St., Philadelphia, PA, 19140, USA
| | - Nadezhda S Kudryasheva
- Siberian Federal University, Svobodnyy Ave 79, Krasnoyarsk, 660041, Russia. .,Institute of Biophysics SB RAS, FRC KSC SB RAS, Krasnoyarsk, 660036, Russia.
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32
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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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33
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Vacher M, Fdez Galván I, Ding BW, Schramm S, Berraud-Pache R, Naumov P, Ferré N, Liu YJ, Navizet I, Roca-Sanjuán D, Baader WJ, Lindh R. Chemi- and Bioluminescence of Cyclic Peroxides. Chem Rev 2018; 118:6927-6974. [PMID: 29493234 DOI: 10.1021/acs.chemrev.7b00649] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Bioluminescence is a phenomenon that has fascinated mankind for centuries. Today the phenomenon and its sibling, chemiluminescence, have impacted society with a number of useful applications in fields like analytical chemistry and medicine, just to mention two. In this review, a molecular-orbital perspective is adopted to explain the chemistry behind chemiexcitation in both chemi- and bioluminescence. First, the uncatalyzed thermal dissociation of 1,2-dioxetane is presented and analyzed to explain, for example, the preference for triplet excited product states and increased yield with larger nonreactive substituents. The catalyzed fragmentation reaction and related details are then exemplified with substituted 1,2-dioxetanone species. In particular, the preference for singlet excited product states in that case is explained. The review also examines the diversity of specific solutions both in Nature and in artificial systems and the difficulties in identifying the emitting species and unraveling the color modulation process. The related subject of excited-state chemistry without light absorption is finally discussed. The content of this review should be an inspiration to human design of new molecular systems expressing unique light-emitting properties. An appendix describing the state-of-the-art experimental and theoretical methods used to study the phenomena serves as a complement.
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Affiliation(s)
- Morgane Vacher
- Department of Chemistry-Ångström , Uppsala University , P.O. Box 538, SE-751 21 Uppsala , Sweden
| | - Ignacio Fdez Galván
- Department of Chemistry-Ångström , Uppsala University , P.O. Box 538, SE-751 21 Uppsala , Sweden
| | - Bo-Wen Ding
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Stefan Schramm
- New York University Abu Dhabi , P.O. Box 129188, Abu Dhabi , United Arab Emirates
| | - Romain Berraud-Pache
- Université Paris-Est , Laboratoire Modélisation et Simulation Multi Échelle, MSME, UMR 8208 CNRS, UPEM , 5 bd Descartes , 77454 Marne-la-Vallée , France
| | - Panče Naumov
- New York University Abu Dhabi , P.O. Box 129188, Abu Dhabi , United Arab Emirates
| | | | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry , Beijing Normal University , Beijing 100875 , China
| | - Isabelle Navizet
- Université Paris-Est , Laboratoire Modélisation et Simulation Multi Échelle, MSME, UMR 8208 CNRS, UPEM , 5 bd Descartes , 77454 Marne-la-Vallée , France
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular , Universitat de València , P.O. Box 22085 , Valencia , Spain
| | - Wilhelm J Baader
- Departamento de Química Fundamental, Instituto de Química , Universidade de São Paulo , Av. Prof. Lineu Prestes, 748 , 05508-000 São Paulo , SP , Brazil
| | - Roland Lindh
- Department of Chemistry-Ångström , Uppsala University , P.O. Box 538, SE-751 21 Uppsala , Sweden.,Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
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Wang ZX, Yu XH, Li F, Kong FY, Lv WX, Wang W. Multiplexed ratiometric photoluminescent detection of pyrophosphate using anisotropic boron-doped nitrogen-rich carbon rugby ball-like nanodots. J Mater Chem B 2018; 6:1771-1781. [DOI: 10.1039/c7tb02708g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
B-doped N-rich carbon rugby ball-like nanodots have been synthesized by a heterophase polymerization route and can act not only as a ratiometric sensor for Hg2+ but also as a dual-mode PPi-selective sensor.
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Affiliation(s)
- Zhong-Xia Wang
- School of Chemistry and Chemical Engineering
- Yancheng Institute of Technology
- Yancheng 224051
- China
| | - Xian-He Yu
- School of Chemistry and Chemical Engineering
- Yancheng Institute of Technology
- Yancheng 224051
- China
| | - Feng Li
- School of Chemistry and Chemical Engineering
- Yancheng Institute of Technology
- Yancheng 224051
- China
| | - Fen-Ying Kong
- School of Chemistry and Chemical Engineering
- Yancheng Institute of Technology
- Yancheng 224051
- China
| | - Wei-Xin Lv
- School of Chemistry and Chemical Engineering
- Yancheng Institute of Technology
- Yancheng 224051
- China
| | - Wei Wang
- School of Chemistry and Chemical Engineering
- Yancheng Institute of Technology
- Yancheng 224051
- China
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35
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Ebrahimi M, Mohseni A, Khalifeh K, Ranjbar B, Sajedi RH. Evolutionary conservation of EF-hand ΙΙ loop in aequorin: Priority of intensity to decay rate in bioluminescence emission. Arch Biochem Biophys 2017; 634:29-37. [PMID: 28970088 DOI: 10.1016/j.abb.2017.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/15/2017] [Accepted: 09/28/2017] [Indexed: 12/15/2022]
Abstract
As a Ca2+-regulated photoprotein, aequorin (Aeq) contains four EF-hand motifs, the second one lacks the standard sequence for Ca2+ coordination and doesn't bind to Ca2+. Here, we replaced this loop with a functional loop. According to structural studies, although the global stability of modified aequorin (4EFAeq) is higher than that of Aeq; increasing the local flexibility accompanied by internal structural rearrangements in 4EFAeq result in its penetrability to urea and acrylamide. A fast decay rate was observed for 4EFAeq. Assuming the presence of intermediate states in the luminescent reaction, this observation indicate that the loop replacement leads to the lowering of the half-life of intermediate states which results in increasing the rate of conformational switching of 4EFAeq to light emitting form. However, considerable reduction in initial luminescence intensity of 4EFAeq suggests that the number of functional complexes is reduced. Our findings demonstrate that the conformational effects of the second loop in Aeq elicit a delicate balance between local flexibility and global stability which may be considered as an important functional parameter in photoproteins. It was also concluded that evolutionary conservation of EF-hand ΙΙ in the current form is a consequence of priority of intensity to decay rate in bioluminescent organisms.
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Affiliation(s)
- Mahsa Ebrahimi
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran
| | - Ammar Mohseni
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Khosrow Khalifeh
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.
| | - Bijan Ranjbar
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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36
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Bioluminescent and biochemical properties of Cys-free Ca 2+ -regulated photoproteins obelin and aequorin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 174:97-105. [DOI: 10.1016/j.jphotobiol.2017.07.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 11/18/2022]
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37
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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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Photoinactivation related dynamics of ctenophore photoproteins: Insights from molecular dynamics simulation under electric-field. Biochem Biophys Res Commun 2017; 490:265-270. [PMID: 28610920 DOI: 10.1016/j.bbrc.2017.06.034] [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: 05/30/2017] [Accepted: 06/09/2017] [Indexed: 11/24/2022]
Abstract
Photoinactivation is a common phenomenon in bioluminescence ctenophore photoproteins (e.g mnemiopsin, berovin and BfosPP) with still unknown mechanism. The activity of coelenterate photoproteins (e.g aequorin), which has high structural similarity with ctenophore photoproteins, is not affected by light. Recently, we have characterized the effects of light on ctenophore photoprotein mnemiopsin, in different conformations, which has demonstrated light induced structural changes, uniquely secondary structures, of both apo and holo mnemiopsin. This paper is further expansion of our previous work, by applying molecular dynamics simulations to investigate photoinactivation related dynamics of berovin at atomistic level, in comparison with aequorin, under the influence of electric component of electromagnetic field. The results have indicated that the intense electric filed could influence structure of both berovin and aequorin but in different manner, whereas moderate electric field only effects on berovin's structure remarkably. In this case, increased helicity of residues E180-M193 and decreased helical contents of L38-D46 and L125-D138 segments are considerable in berovin as well as flexibility elevation of calcium binding loops. These changes cause structural expansion of berovin, especially at N-terminal domain, in direction of electric field. In conclusion, the induced structural changes of mentioned helical parts together with elevated fluctuation of their adjacent segments, N26-D46 and M193-Y206, indicate the influence of light on substrate stabilizing residues, Arg41 and Y204. This condition could presumably leads to inactivation of bioluminescence reaction due to separation of substrate from the cavity of the protein.
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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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40
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Bakayan A, Domingo B, Vaquero CF, Peyriéras N, Llopis J. Fluorescent Protein-photoprotein Fusions and Their Applications in Calcium Imaging. Photochem Photobiol 2017; 93:448-465. [PMID: 27925224 DOI: 10.1111/php.12682] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022]
Abstract
Calcium-activated photoproteins, such as aequorin, have been used as luminescent Ca2+ indicators since 1967. After the cloning of aequorin in 1985, microinjection was substituted by its heterologous expression, which opened the way for a widespread use. Molecular fusion of green fluorescent protein (GFP) to aequorin recapitulated the nonradiative energy transfer process that occurs in the jellyfish Aequorea victoria, from which these two proteins were obtained, resulting in an increase of light emission and a shift to longer wavelength. The abundance and location of the chimera are seen by fluorescence, whereas its luminescence reports Ca2+ levels. GFP-aequorin is broadly used in an increasing number of studies, from organelles and cells to intact organisms. By fusing other fluorescent proteins to aequorin, the available luminescence color palette has been expanded for multiplexing assays and for in vivo measurements. In this report, we will attempt to review the various photoproteins available, their reported fusions with fluorescent proteins and their biological applications to image Ca2+ dynamics in organelles, cells, tissue explants and in live organisms.
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Affiliation(s)
- Adil Bakayan
- BioEmergences Unit (CNRS, USR3695), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Beatriz Domingo
- Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, Albacete, Spain
| | - Cecilia F Vaquero
- Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, Albacete, Spain
| | - Nadine Peyriéras
- BioEmergences Unit (CNRS, USR3695), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Juan Llopis
- Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, Albacete, Spain
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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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42
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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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43
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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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Salehi F, Emamzadeh R, Nazari M, Rasa SMM. Probing the emitter site of Renilla luciferase using small organic molecules; an attempt to understand the molecular architecture of the emitter site. Int J Biol Macromol 2016; 93:1253-1260. [PMID: 27651278 DOI: 10.1016/j.ijbiomac.2016.09.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/16/2016] [Indexed: 11/29/2022]
Abstract
Renilla luciferase is a sensitive enzyme and has wide applications in biotechnology such as drug screening. Previous studies have tried to show the catalytic residues, nevertheless, the accurate architecture and molecular behavior of its emitter site remains uncharacterized. In this study, the activity of Renilla luciferase, in the presence of two small organic molecules including dimethyl sulfoxide (DMSO) and isopropanol was considered and the structure was studied by circular dichroism (CD) and fluorescence spectroscopy. Moreover, the interaction of small organic molecules with the Renilla luciferase was studied using molecular dynamics simulations. Kinetics studies showed that at low concentration of DMSO (16.6-66mM) and isopropanol (19.3-76mM) the Km changed and a competitive inhibition pattern was observed. Moreover, spectroscopy studies reveled that the changes of activity of Renilla luciferase in the presence of low concentrations of small organic molecules was not associated with structural collapse or severe changes in the enzyme conformation. Molecular dynamics simulations indicated that DMSO and isopropanol, as probing molecules, were both able to bind to the emitter site and remained with the residues of the emitter site. Based on the probing data, the architecture of the emitter site in the "non-binding" model was proposed.
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Affiliation(s)
| | | | - Mahboobeh Nazari
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
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Andronico LA, Quintavalla A, Lombardo M, Mirasoli M, Guardigli M, Trombini C, Roda A. Synthesis of 1,2-Dioxetanes as Thermochemiluminescent Labels for Ultrasensitive Bioassays: Rational Prediction of Olefin Photooxygenation Outcome by Using a Chemometric Approach. Chemistry 2016; 22:18156-18168. [DOI: 10.1002/chem.201603765] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/07/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Luca A. Andronico
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Arianna Quintavalla
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Marco Lombardo
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Mara Mirasoli
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Massimo Guardigli
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Claudio Trombini
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Aldo Roda
- Department of Chemistry “G. Ciamician”; Alma Mater Studiorum; University of Bologna; Via Selmi 2 40126 Bologna Italy
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47
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Pashandi Z, Molakarimi M, Sajedi RH, Taghdir M, Naderi-Manesh H. Light induced structural changes of the photoprotein mnemiopsin: Characterization and contribution in photoinactivation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 165:133-140. [PMID: 27780117 DOI: 10.1016/j.jphotobiol.2016.10.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/14/2016] [Indexed: 10/20/2022]
Abstract
Mnemiopsin, an EF-hand Ca2+ binding photoprotein isolated from luminous ctenophore Mnemiopsis leidyi, emits blue light from its chromophore, coelenterazine, which is non-covalently bond in its central hydrophobic core. Previous studies have revealed unique biochemical properties for ctenophore photoproteins such as inactivation by light, but only few have focused on photoinactivation process. To understand the nature of photoinactivation process we have investigated the impact of light alone and in the presence of Ca2+ ion on the structure of this photoprotein. We used UV-Vis, circular dichroism (CD) and fluorescence spectroscopy following Ca2+ binding assay to analyze the light effects on mnemiopsin conformation in comparison with aequorin at both apo and holo form. Our results showed light induced structural changes which resulted into photoinactivation. These changes include significant modification on secondary structure of mnemiopsin in comparison with aequorin. Our data also revealed that light could influence structure of apo protein regardless of presence of coelenterazine. The comparative studies of Ca2+ ion binding affinity following light exposure, also showed that light induced structural changes could presumably affect coelenterazine binding or its conformation in binding site in such a way that causes photoinactivation. In conclusion, we have proposed that structural rearrangement of helix 5 and C-terminal motif could be responsible for light induced structural changes.
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Affiliation(s)
- Zaiddodine Pashandi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Maryam Molakarimi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza H Sajedi
- 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
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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48
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Malikova NP, Borgdorff AJ, Vysotski ES. Semisynthetic photoprotein reporters for tracking fast Ca(2+) transients. Photochem Photobiol Sci 2016; 14:2213-24. [PMID: 26508209 DOI: 10.1039/c5pp00328h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Changes in the intracellular concentration of free ionized calcium ([Ca(2+)]i) control a host of cellular processes as varied as vision, muscle contraction, neuronal signal transmission, proliferation, apoptosis etc. The disturbance in Ca(2+)-signaling causes many severe diseases. To understand the mechanisms underlying the control by calcium and how disorder of this regulation relates to pathological conditions, it is necessary to measure [Ca(2+)]i. The Ca(2+)-regulated photoproteins which are responsible for bioluminescence of marine coelenterates have been successfully used for this purpose over the years. Here we report the results on comparative characterization of bioluminescence properties of aequorin from Aequorea victoria, obelin from Obelia longissima, and clytin from Clytia gregaria charged by native coelenterazine and coelenterazine analogues f, i, and hcp. The comparison of specific bioluminescence activity, stability, emission spectra, stopped-flow kinetics, sensitivity to calcium, and effect of physiological concentrations of Mg(2+) establishes obelin-hcp as an excellent semisynthetic photoprotein to keep track of fast intracellular Ca(2+) transients. The rate of rise of its light signal on a sudden change of [Ca(2+)] is almost 3- and 11-fold higher than those of obelin and aequorin with native coelenterazine, respectively, and 20 times higher than that of the corresponding aequorin-hcp. In addition, obelin-hcp preserves a high specific bioluminescence activity and displays higher Ca(2+)-sensitivity as compared to obelin charged by native coelenterazine and sensitivity to Ca(2+) comparable with those of aequorin-f and aequorin-hcp.
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Affiliation(s)
- Natalia P Malikova
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk 660036, Russia
| | - Aren J Borgdorff
- Institut des Neurosciences Alfred Fessard, UPR 3294, Centre National de la Recherche Scientifique, Avenue de la Terrasse, 91198 Gif-sur-Yvette, France.
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk 660036, Russia
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Burakova LP, Natashin PV, Markova SV, Eremeeva EV, Malikova NP, Cheng C, Liu ZJ, Vysotski ES. Mitrocomin from the jellyfish Mitrocoma cellularia with deleted C-terminal tyrosine reveals a higher bioluminescence activity compared to wild type photoprotein. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:286-297. [PMID: 27395792 DOI: 10.1016/j.jphotobiol.2016.06.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/30/2016] [Accepted: 06/30/2016] [Indexed: 10/21/2022]
Abstract
The full-length cDNA genes encoding five new isoforms of Ca(2+)-regulated photoprotein mitrocomin from a small tissue sample of the outer bell margin containing photocytes of only one specimen of the luminous jellyfish Mitrocoma cellularia were cloned, sequenced, and characterized after their expression in Escherichia coli and subsequent purification. The analysis of cDNA nucleotide sequences encoding mitrocomin isoforms allowed suggestion that two isoforms might be the products of two allelic genes differing in one amino acid residue (64R/Q) whereas other isotypes appear as a result of transcriptional mutations. In addition, the crystal structure of mitrocomin was determined at 1.30Å resolution which expectedly revealed a high similarity with the structures of other hydromedusan photoproteins. Although mitrocomin isoforms reveal a high degree of identity of amino acid sequences, they vary in specific bioluminescence activities. At that, all isotypes displayed the identical bioluminescence spectra (473-474nm with no shoulder at 400nm). Fluorescence spectra of Ca(2+)-discharged mitrocomins were almost identical to their light emission spectra similar to the case of Ca(2+)-discharged aequorin, but different from Ca(2+)-discharged obelins and clytin which fluorescence is red-shifted by 25-30nm from bioluminescence spectra. The main distinction of mitrocomin from other hydromedusan photoproteins is an additional Tyr at the C-terminus. Using site-directed mutagenesis, we showed that this Tyr is not important for bioluminescence because its deletion even increases specific activity and efficiency of apo-mitrocomin conversion into active photoprotein, in contrast to C-terminal Pro of other photoproteins. Since genes in a population generally exist as different isoforms, it makes us anticipate the cloning of even more isoforms of mitrocomin and other hydromedusan photoproteins with different bioluminescence properties.
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Affiliation(s)
- Ludmila P Burakova
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk 660036, Russia
| | - Pavel V Natashin
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk 660036, Russia; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Svetlana V Markova
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk 660036, Russia
| | - Elena V Eremeeva
- 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
| | - Chongyun Cheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, China; iHuman Institute, ShanghaiTech University, Shanghai 201210, China.
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Krasnoyarsk 660036, Russia.
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50
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Improving the luminescence properties of aequorin by conjugating to CdSe/ZnS quantum dot nanoparticles: Red shift and slowing decay rate. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:153-161. [PMID: 27371914 DOI: 10.1016/j.jphotobiol.2016.06.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/22/2016] [Indexed: 12/11/2022]
Abstract
Changing the properties of photoprotein aequorin such as the wavelength emission and decay half-life by using bioluminescence resonance energy transfer (BRET) phenomenon is the main aim in this paper. BRET system was set up with CdSe/ZnS quantum dot nanoparticles as an acceptor molecule and photoprotein as an energy donor molecule. Quantum dots are semiconductor nanoparticles with very interesting optical properties, including broad excitation spectra, narrow and the symmetric band width emission spectra, tunable by their sizes, compositions, negligible photo-bleaching and good chemical and photo-stability. In this QD-BRET system, aequorin is conjugated to the carboxyl groups on quantum dot surface by EDC/NHS chemistry as cross linker. Bioluminescence energy generates by aequorin upon adding Ca(2+) and transfers to the quantum dots in a radiationless manner and emits at a longer wavelength. The determined bioluminescent parameters for this method included aequorin activity, emission spectra and decay half-life time. In fact, this spectrum tuning strategy resulted in a change in bioluminescent properties of photoprotein, therefore, the maximum emission wavelength shifted from 455 to 540nm and the decay time increased from 3.76 to 12.11s. Nowadays, photoproteins with different characteristics are capable of being employed as a reporter in multi-analyte detections and in vivo imaging.
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