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Hematyar M, Jafarian V, Shirdel A. Longer characteristic wavelength in a novel engineered photoprotein Mnemiopsin 2. Photochem Photobiol Sci 2022; 21:1031-1040. [PMID: 35226332 DOI: 10.1007/s43630-022-00191-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/14/2022] [Indexed: 10/19/2022]
Abstract
We designed two mutants of photoprotein Mnemiopsin 2 (Mn2) including M52I and V144I, where the mutations were applied in the EF-hand loops I and III. Far-UV CD measurements demonstrated that the stability of the helices in the wild-type (WT) protein is greater compared with the mutants. Heat-induced denaturation experiments in the apo-form of photoproteins showed that WT Mn2 has higher value of the enthalpy change for the unfolding process, indicating that it has more stabilizing interaction compared with mutants. According to the activity measurement data, both mutants, particularly V144I have lower initial intensity as well as slower decay rate as compared with the WT photoprotein. Importantly, it was found that V144I variant shows 25 nm of red shift in the characteristic wavelengths as compared with the WT photoprotein. This finding can be considered as an advantage for in vivo application of photoprotein for imaging purposes. It concluded that this position on loop III of Mn2 is a hotspot point for characteristic wavelength determination. However, further research on this mutant is needed for making stable variants of Mn2 with novel optical features.
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Affiliation(s)
- Mahsa Hematyar
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran
| | - Vahab Jafarian
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran.
| | - Akram Shirdel
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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2
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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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3
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Dopp JL, Reuel NF. Simple, functional, inexpensive cell extract for in vitro prototyping of proteins with disulfide bonds. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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4
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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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Yu X, Scott D, Dikici E, Joel S, Deo S, Daunert S. Multiplexing cytokine analysis: towards reducing sample volume needs in clinical diagnostics. Analyst 2019; 144:3250-3259. [PMID: 31049499 DOI: 10.1039/c9an00297a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2024]
Abstract
The trend for improved more precise diagnostics and management of disease heavily relies on the measurement of panels of biomarkers in physiological samples of patients. Ideally, the ultimate goal would be to detect as many clinically relevant biomarkers as possible in a single drop of blood, achieving quick, sensitive, reproducible, and affordable detection in small volume physiological samples. Bioluminescent (BL) proteins provide many of the desired characteristics required for such labels, including detection at extremely low concentrations, no interference from physiological fluids leading to excellent detection limits, and compatibility with many miniaturized systems. However, to date the use of BL proteins has been restricted by their limited multiplexing capabilities. BL proteins typically exhibit a single emission profile and decay kinetics making the simultaneous detection of multiple analytes difficult. Recent progresses in this area include the use of two different engineered luminescent proteins to achieve resolved signals via one-dimensional time resolution. This approach, however, to date only lead to a dual analyte detection. Herein, we have demonstrated that using a two-dimensional approach that combines both temporal and spatial resolution, we can expand the multiplexing capabilities of bioluminescent proteins. To that end, the photoprotein aequorin (AEQ) has been employed for the simultaneous detection of three separate analytes in a single well, differentiated through the use of three discrete time/wavelength windows. Through a combination of site-specific mutations and synthetic coelenterazines "semi-synthetic" AEQ variants have been developed with altered emission profiles and decay kinetics. In this study, two AEQ mutant proteins were genetically conjugated to three pro-inflammatory cytokines (tumor necrosis factor alpha, interleukins 6 and 8) resulting in AEQ-labeled cytokines. These fusion proteins were combined with synthetic coelenterazines resulting in proteins with differing emission maxima and half-lives to allow for the simultaneous detection of all three cytokines in a single sample. The validity of the assay was demonstrated in serum by employing human physiological samples and comparing our results with commercially available individual tests for each of the three cytokines.
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Affiliation(s)
- Xiaowen Yu
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33136, USA.
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Rahmani H, Sajedi RH. Aequorin as a sensitive and selective reporter for detection of dopamine: A photoprotein inhibition assay approach. Int J Biol Macromol 2018; 122:677-683. [PMID: 30391428 DOI: 10.1016/j.ijbiomac.2018.10.221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/23/2018] [Accepted: 10/30/2018] [Indexed: 01/03/2023]
Abstract
Dopamine is a metabolite that plays a key role in the human body and in biomedical and diagnostic applications. Thus, the concentration of this analyte has been considered in various diseases in therapeutic drug monitoring (TDM). In the present study, for the first time, a photoprotein inhibition assay strategy was developed by utilizing aequorin for the direct detection of dopamine as a receptor and reporter simultaneously. The results showed that bioluminescence emission of aequorin was effectively quenched by increasing concentration of dopamine at the range of 1 nM to 100 μM with a detection limit of 53 nM. The viability of this method for the monitoring of dopamine in spiked biological fluids was also established and it was successfully applied for the direct determination of dopamine in a blood serum and urine without preliminary treatment with satisfactory quantitative recovery 90-95% and 82-93%, respectively. The structural investigation using circular dichroism, fluorescence spectroscopy, and docking simulation indicated that, changes in the microenvironment of aromatic residues were significant, while minor conformational alterations of the protein were observed. It seems dopamine inhibits bioluminescence activity with specific binding to the residues involved in the light production.
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Affiliation(s)
- Hossein Rahmani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran.
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7
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Bioluminescence and kinetic aspects of double mutated aequorin variants. Int J Biol Macromol 2018; 112:163-168. [DOI: 10.1016/j.ijbiomac.2018.01.170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 11/21/2022]
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Sharifian S, Homaei A, Hemmati R, B Luwor R, Khajeh K. The emerging use of bioluminescence in medical research. Biomed Pharmacother 2018; 101:74-86. [PMID: 29477474 DOI: 10.1016/j.biopha.2018.02.065] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 02/13/2018] [Accepted: 02/15/2018] [Indexed: 01/01/2023] Open
Abstract
Bioluminescence is the light produced by a living organism and is commonly emitted by sea life with Ca2+-regulated photoproteins being the most responsible for bioluminescence emission. Marine coelenterates provide important functions involved in essential purposes such as defense, feeding, and breeding. In this review, the main characteristics of marine photoproteins including aequorin, clytin, obelin, berovin, pholasin and symplectin from different marine organisms will be discussed. We will focused on the recent use of recombinant photoproteins in different biomedical research fields including the measurement of Ca2+ in different intracellular compartments of animal cells, as labels in the design and development of binding assays. This review will also outline how bioluminescent photoproteins have been used in a plethora of analytical methods including ultra-sensitive assays and in vivo imaging of cellular processes. Due to their unique properties including elective intracellular distribution, wide dynamic range, high signal-to-noise ratio and low Ca2+-buffering effect, recombinant photoproteins represent a promising future analytical tool in several in vitro and in vivo experiments.
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Affiliation(s)
- Sana Sharifian
- Department of Marine Biology, Faculty of Sciences, University of Hormozgan, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Biochemistry, Faculty of Sciences, University of Hormozgan, Bandar Abbas, Iran.
| | - Roohullah Hemmati
- Department of Biology, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Rodney B Luwor
- Department of Surgery, Level 5, Clinical Sciences Building, The University of Melbourne, The Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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9
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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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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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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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Hakiminia F, Molakarimi M, Khalifeh K, Jahani Z, Sajedi RH, Ranjbar B. Adjustment of local conformational flexibility and accessible surface area alterations of Serine128 and Valine183 in mnemiopsin. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.03.082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Grinstead KM, Rowe L, Ensor CM, Joel S, Daftarian P, Dikici E, Zingg JM, Daunert S. Red-Shifted Aequorin Variants Incorporating Non-Canonical Amino Acids: Applications in In Vivo Imaging. PLoS One 2016; 11:e0158579. [PMID: 27367859 PMCID: PMC4930207 DOI: 10.1371/journal.pone.0158579] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 06/17/2016] [Indexed: 11/18/2022] Open
Abstract
The increased importance of in vivo diagnostics has posed new demands for imaging technologies. In that regard, there is a need for imaging molecules capable of expanding the applications of current state-of-the-art imaging in vivo diagnostics. To that end, there is a desire for new reporter molecules capable of providing strong signals, are non-toxic, and can be tailored to diagnose or monitor the progression of a number of diseases. Aequorin is a non-toxic photoprotein that can be used as a sensitive marker for bioluminescence in vivo imaging. The sensitivity of aequorin is due to the fact that bioluminescence is a rare phenomenon in nature and, therefore, it does not suffer from autofluorescence, which contributes to background emission. Emission of bioluminescence in the blue-region of the spectrum by aequorin only occurs when calcium, and its luciferin coelenterazine, are bound to the protein and trigger a biochemical reaction that results in light generation. It is this reaction that endows aequorin with unique characteristics, making it ideally suited for a number of applications in bioanalysis and imaging. Herein we report the site-specific incorporation of non-canonical or non-natural amino acids and several coelenterazine analogues, resulting in a catalog of 72 cysteine-free, aequorin variants which expand the potential applications of these photoproteins by providing several red-shifted mutants better suited to use in vivo. In vivo studies in mouse models using the transparent tissue of the eye confirmed the activity of the aequorin variants incorporating L-4-iodophehylalanine and L-4-methoxyphenylalanine after injection into the eye and topical addition of coelenterazine. The signal also remained localized within the eye. This is the first time that aequorin variants incorporating non-canonical amino acids have shown to be active in vivo and useful as reporters in bioluminescence imaging.
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Affiliation(s)
- Kristen M. Grinstead
- Department of Biochemistry and Molecular Biology, R. Bunn Gautier Bldg., 1011 NW 15th Street, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States of America
| | - Laura Rowe
- Department of Chemistry, 1610 Campus Drive East, Valparaiso University, Valparaiso, IN, 46385, United States of America
| | - Charles M. Ensor
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, 40536, United States of America
| | - Smita Joel
- Department of Biochemistry and Molecular Biology, R. Bunn Gautier Bldg., 1011 NW 15th Street, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States of America
| | - Pirouz Daftarian
- Department of Biochemistry and Molecular Biology, R. Bunn Gautier Bldg., 1011 NW 15th Street, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States of America
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, R. Bunn Gautier Bldg., 1011 NW 15th Street, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States of America
| | - Jean-Marc Zingg
- Department of Biochemistry and Molecular Biology, R. Bunn Gautier Bldg., 1011 NW 15th Street, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States of America
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, R. Bunn Gautier Bldg., 1011 NW 15th Street, Miller School of Medicine, University of Miami, Miami, FL, 33136, United States of America
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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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15
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Lim D, Bertoli A, Sorgato M, Moccia F. Generation and usage of aequorin lentiviral vectors for Ca2+ measurement in sub-cellular compartments of hard-to-transfect cells. Cell Calcium 2016; 59:228-39. [DOI: 10.1016/j.ceca.2016.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/01/2016] [Indexed: 12/18/2022]
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Hakiminia F, Khalifeh K, Sajedi RH, Ranjbar B. Determination of structural elements on the folding reaction of mnemiopsin by spectroscopic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 158:49-55. [PMID: 26803749 DOI: 10.1016/j.saa.2016.01.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 11/19/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
Mnemiopsin 1 is a member of photoprotein family, made up of 206 amino acid residues. These Ca(2+)-regulated photoproteins are responsible for light emission in a variety of marine cnidarians and ctenophores. They composed of an apoprotein, a single polypeptide chain of 25 kDa, molecular oxygen and the non-covalently bound chromophore. In this study, we examined whether three mutations, namely R39K, S128G and V183T affect the thermodynamic stability as well as refolding and unfolding kinetics of mnemiopsin 1. Conformational stability measurements using fluorescence and far-UV CD spectroscopies revealed that all variants unfold in multi-step manner in which the secondary and tertiary structures are lost in different steps. However kinetic studies showed that point mutation S128G destabilizes both kinetic intermediate and native conformation; while, these structural elements are stabilized in V183T. We also found that the stability of folded and intermediate states increases in R39K. We concluded that the initial packing of helical segments within the protein structure is more facilitated when Lys with smaller side chain is present in the protein chain.
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Affiliation(s)
- Forough Hakiminia
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Khosrow Khalifeh
- Department of Biology, Faculty of Sciences, University of Zanjan, P.O. Box 45195-313, Zanjan, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
| | - Bijan Ranjbar
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
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Grinstead K, Joel S, Zingg JM, Dikici E, Daunert S. Enabling Aequorin for Biotechnology Applications Through Genetic Engineering. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015:149-179. [PMID: 26475468 DOI: 10.1007/10_2015_336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In recent years, luminescent proteins have been studied for their potential application in a variety of detection systems. Bioluminescent proteins, which do not require an external excitation source, are especially well-suited as reporters in analytical detection. The photoprotein aequorin is a bioluminescent protein that can be engineered for use as a molecular reporter under a wide range of conditions while maintaining its sensitivity. Herein, the characteristics of aequorin as well as the engineering and production of aequorin variants and their impact on signal detection in biological systems are presented. The structural features and activity of aequorin, its benefits as a label for sensing and applications in highly sensitive detection, as well as in gaining insight into biological processes are discussed. Among those, focus has been placed on the highly sensitive calcium detection in vivo, in vitro DNA and small molecule sensing, and development of in vivo imaging technologies. Graphical Abstract.
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Affiliation(s)
- Kristen Grinstead
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Smita Joel
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Jean-Marc Zingg
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Emre Dikici
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
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Coutant EP, Janin YL. Synthetic Routes to Coelenterazine and Other Imidazo[1,2-a]pyrazin-3-one Luciferins: Essential Tools for Bioluminescence-Based Investigations. Chemistry 2015; 21:17158-71. [DOI: 10.1002/chem.201501531] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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19
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Mahdavi A, Sajedi RH, Hosseinkhani S, Taghdir M. Hyperactive Arg39Lys mutated mnemiopsin: implication of positively charged residue in chromophore binding cavity. Photochem Photobiol Sci 2015; 14:792-800. [DOI: 10.1039/c4pp00191e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mnemiopsin, a Ca2+-regulated photoprotein isolated fromMnemiopsis leidyi, belongs to the family of ctenophore photoproteins. While there are no charged amino acid residues in the coelenterazine binding cavity of cnidarian photoproteins, ctenophore photoproteins have a positively charged residue (Arg) in this region.
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Affiliation(s)
- Atiyeh Mahdavi
- Department of Biological Sciences
- Institute for Advanced Studies in Basic Sciences (IASBS)
- Zanjan 45195-1159
- Iran
| | - Reza H. Sajedi
- Department of Biochemistry
- Faculty of Biological Sciences
- Tarbiat Modares University
- Tehran 14115-154
- Iran
| | - Saman Hosseinkhani
- 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
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20
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Bakayan A, Domingo B, Miyawaki A, Llopis J. Imaging Ca(2+) activity in mammalian cells and zebrafish with a novel red-emitting aequorin variant. Pflugers Arch 2014; 467:2031-42. [PMID: 25355614 PMCID: PMC4537489 DOI: 10.1007/s00424-014-1639-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 10/15/2014] [Accepted: 10/21/2014] [Indexed: 02/04/2023]
Abstract
Ca2+ monitoring with aequorin is an established bioluminescence technique, whereby the photoprotein emits blue light when it binds to Ca2+. However, aequorin’s blue emission and low quantum yield limit its application for in vivo imaging because blue-green light is greatly attenuated in animal tissues. In earlier work, aequorin was molecularly fused with green, yellow, and red fluorescent proteins, producing an emission shift through bioluminescence resonance energy transfer (BRET). We have previously shown that the chimera tandem dimer Tomato-aequorin (tdTA) emits red light in mammalian cells and across the skin and other tissues of mice [1]. In this work, we varied the configuration of the linker in tdTA to maximize energy transfer. One variant, named Redquorin, improved BRET from aequorin to tdTomato to almost a maximum value, and the emission above 575 nm exceeded 73 % of total counts. By pairing Redquorin with appropriate synthetic coelenterazines, agonist-induced and spontaneous Ca2+ oscillations in single HEK-293 cells were imaged. In addition, we also imaged Ca2+ transients associated with twitching behavior in developing zebrafish embryos expressing Redquorin during the segmentation period. Furthermore, the emission profile of Redquorin resulted in significant luminescence crossing a blood sample, a highly absorbing tissue. This new tool will facilitate in vivo imaging of Ca2+ from deep tissues of animals.
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Affiliation(s)
- Adil Bakayan
- Centro Regional de Investigaciones Biomédicas (CRIB) and Facultad de Medicina de Albacete, Universidad Castilla-La Mancha, C/ Almansa 14, 02008, Albacete, Spain
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21
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Qu X, Rowe L, Dikici E, Ensor M, Daunert S. Aequorin mutants with increased thermostability. Anal Bioanal Chem 2014; 406:5639-43. [PMID: 25084737 DOI: 10.1007/s00216-014-8039-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 06/27/2014] [Accepted: 07/16/2014] [Indexed: 12/01/2022]
Abstract
Bioluminescent labels can be especially useful for in vivo and live animal studies due to the negligible bioluminescence background in cells and most animals, and the non-toxicity of bioluminescent reporter systems. Significant thermal stability of bioluminescent labels is essential, however, due to the longitudinal nature and physiological temperature conditions of many bioluminescent-based studies. To improve the thermostability of the bioluminescent protein aequorin, we employed random and rational mutagenesis strategies to create two thermostable double mutants, S32T/E156V and M36I/E146K, and a particularly thermostable quadruple mutant, S32T/E156V/Q168R/L170I. The double aequorin mutants, S32T/E156V and M36I/E146K, retained 4 and 2.75 times more of their initial bioluminescence activity than wild-type aequorin during thermostability studies at 37 °C. Moreover, the quadruple aequorin mutant, S32T/E156V/Q168R/L170I, exhibited more thermostability at a variety of temperatures than either double mutant alone, producing the most thermostable aequorin mutant identified thus far.
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Affiliation(s)
- Xiaoge Qu
- Department of Chemistry, University of Kentucky, Lexington, KY, 40506, USA
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Mahdavi A, Sajedi RH, Hosseinkhani S, Taghdir M, Sariri R. Site-directed mutagenesis of photoprotein mnemiopsin: implication of some conserved residues in bioluminescence properties. Photochem Photobiol Sci 2013. [DOI: 10.1039/c2pp25320h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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23
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Teasley Hamorsky K, Ensor CM, Dikici E, Pasini P, Bachas L, Daunert S. Bioluminescence inhibition assay for the detection of hydroxylated polychlorinated biphenyls. Anal Chem 2012; 84:7648-55. [PMID: 22908962 DOI: 10.1021/ac301872u] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxylated polychlorinated biphenyls (OH-PCBs) are an important class of contaminants that mainly originate from polychlorinated biphenyl metabolism. They may conceivably be as dangerous and persistent as the parent compounds; most prominently, OH-PCBs are endocrine disruptors. Due to increasing evidence of the presence of OH-PCBs in the environment and in living organisms, including humans, and of their toxicity, methods of detection for OH-PCBs are needed in the environmental and medical fields. Herein, we describe the development and optimization of a protein-based inhibition assay for the quantification of OH-PCBs. Specifically, the photoprotein aequorin was utilized for the detection of OH-PCBs. We hypothesized that OH-PCBs interact with aequorin, and we established that OH-PCBs actually inhibit the bioluminescence of aequorin in a dose-dependent manner. We took advantage of this phenomenon to develop an assay that is capable of detecting a wide variety of OH-PCBs with a range of detection limits, the best detection limit being 11 nM for the compound 2-hydroxy-2',3,4',5',6-pentachorobiphenyl. The viability of this system for the screening of OH-PCBs in spiked biological and environmental samples was also established. We envision the implementation of this novel bioluminescence inhibition assay as a rapid, sensitive, and cost-effective method for monitoring OH-PCBs. Furthermore, to the best of our knowledge, this is the first time aequorin has been employed to detect an analyte by the inhibition of its bioluminescence reaction. Hence, this strategy may prove to be a general approach for the development of a new generation of protein-based inhibition assays.
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Roda A, Guardigli M. Analytical chemiluminescence and bioluminescence: latest achievements and new horizons. Anal Bioanal Chem 2011; 402:69-76. [PMID: 22002591 DOI: 10.1007/s00216-011-5455-8] [Citation(s) in RCA: 161] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 09/23/2011] [Accepted: 09/26/2011] [Indexed: 01/13/2023]
Abstract
Chemiluminescence (CL) and bioluminescence (BL) are the detection techniques of choice for the development of highly sensitive analytical methods, from immunoassays and nucleic acid hybridization assays to whole-cell biosensors. Nevertheless, basic and applied research on CL and BL aimed at further improving their analytical performance is still very active. This research covers diverse and complementary fields, including (among others) enhancing the light emission efficiency of CL systems, the use of nanomaterials to catalyze or enhance CL/BL reactions, the study of BL proteins to elucidate the color modulation mechanism, the discovery of new BL systems, the production of thermostable BL protein mutants with altered emission spectra, the development of BL imaging techniques to expand our understanding of living systems, and the implementation of CL/BL detection in miniaturized analytical devices. In the near future, we expect even greater diffusion of CL/BL-based analytical methods, especially in portable analytical devices intended for applications ranging from environmental analysis to companion diagnostics for personalized medicine.
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Affiliation(s)
- Aldo Roda
- Department of Pharmaceutical Sciences, University of Bologna, Alma Mater Studiorum, Bologna, Italy.
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25
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Cloning, Sequencing, Expression and Structural Investigation of Mnemiopsin from Mnemiopsis leidyi: An Attempt Toward Understanding Ca2+-Regulated Photoproteins. Protein J 2011; 30:566-74. [DOI: 10.1007/s10930-011-9363-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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26
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27
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Scott D, Dikici E, Ensor M, Daunert S. Bioluminescence and its impact on bioanalysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2011; 4:297-319. [PMID: 21456969 DOI: 10.1146/annurev-anchem-061010-113855] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
There is an increasing need for versatile yet sensitive labels, posed by the demands for low detection in bioanalysis. Bioluminescent proteins have many desirable characteristics, including the ability to be detected at extremely low concentrations; no background interference from autofluorescent compounds present in samples; and compatibility with many miniaturized platforms, such as lab-on-a-chip and lab-on-a-CD systems. Bioluminescent proteins have found a plethora of analytical applications in intracellular monitoring, genetic regulation and detection, immuno- and binding assays, and whole-cell biosensors, among others. As new bioluminescent organisms are discovered and new bioluminescence proteins are characterized, use of these proteins will continue to dramatically improve our understanding of molecular and cellular events, as well as their applications for detection of environmental and biomedical samples.
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Affiliation(s)
- Daniel Scott
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33101, USA
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28
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Ca2+-regulated photoproteins: effective immunoassay reporters. SENSORS 2010; 10:11287-300. [PMID: 22163526 PMCID: PMC3231056 DOI: 10.3390/s101211287] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 11/24/2010] [Accepted: 12/03/2010] [Indexed: 11/19/2022]
Abstract
Ca2+-regulated photoproteins of luminous marine coelenterates are of interest and a challenge for researchers as a unique bioluminescent system and as a promising analytical instrument for both in vivo and in vitro applications. The proteins are comprehensively studied as to biochemical properties, tertiary structures, bioluminescence mechanism, etc. This knowledge, along with available recombinant proteins serves the basis for development of unique bioluminescent detection systems that are “self-contained”, triggerable, fast, highly sensitive, and non-hazardous. In the paper, we focus on the use of photoproteins as reporters in binding assays based on immunological recognition element—bioluminescent immunoassay and hybridization immunoassay, their advantages and prospects.
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29
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Rowe L, Ensor M, Mehl R, Daunert S. Modulating the bioluminescence emission of photoproteins by in vivo site-directed incorporation of non-natural amino acids. ACS Chem Biol 2010; 5:455-60. [PMID: 20230005 DOI: 10.1021/cb9002909] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The in vivo incorporation of non-natural amino acids into specific sites within proteins has become an extremely powerful tool for bio- and protein chemists in recent years. One avenue that has yet to be explored, however, is whether or not the incorporation of non-natural amino acids can tune the color of light emitted by bioluminescent proteins, whose light emission mechanisms are more complex and less well understood than their fluorescent counterparts. Bioluminescent proteins are becoming increasingly important in a variety of research fields, such as in situ imaging and the study of protein-protein interactions in vivo, and an increased spectral variety of bioluminescent reporters is needed for further progress. Thus, herein we report the first successful spectral shifting (44 nm) of a bioluminescent protein, aequorin, via the site-specific incorporation of several non-natural amino acids into an integral amino acid position within the aequorin structure in vivo.
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Affiliation(s)
- Laura Rowe
- Department of Chemistry, University of Kentucky, Rose Street, Lexington, Kentucky 40506
| | - Mark Ensor
- Department of Chemistry, University of Kentucky, Rose Street, Lexington, Kentucky 40506
| | - Ryan Mehl
- Department of Chemistry, Franklin and Marshall College, 415 Harrisburg Avenue, Lancaster, Pennsylvania, 17603
| | - Sylvia Daunert
- Department of Chemistry, University of Kentucky, Rose Street, Lexington, Kentucky 40506
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Rowe L, Dikici E, Daunert S. Engineering bioluminescent proteins: expanding their analytical potential. Anal Chem 2010; 81:8662-8. [PMID: 19725502 DOI: 10.1021/ac9007286] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bioluminescent proteins are used in a plethora of analytical methods, from ultrasensitive assay development to the in vivo imaging of cellular processes. This article reviews the most pertinent current bioluminescent-protein-based technologies and suggests the future direction of this vein of research. (To listen to a podcast about this feature, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html .).
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Abstract
Bioluminescence spans all oceanic dimensions and has evolved many times--from bacteria to fish--to powerfully influence behavioral and ecosystem dynamics. New methods and technology have brought great advances in understanding of the molecular basis of bioluminescence, its physiological control, and its significance in marine communities. Novel tools derived from understanding the chemistry of natural light-producing molecules have led to countless valuable applications, culminating recently in a related Nobel Prize. Marine organisms utilize bioluminescence for vital functions ranging from defense to reproduction. To understand these interactions and the distributions of luminous organisms, new instruments and platforms allow observations on individual to oceanographic scales. This review explores recent advances, including the chemical and molecular, phylogenetic and functional, community and oceanographic aspects of bioluminescence.
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Affiliation(s)
- Steven H D Haddock
- Monterey Bay Aquarium Research Institute, Moss Landing, California 95039, USA.
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