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Stepanov AI, Zhurlova PA, Shuvaeva AA, Sokolinskaya EL, Gurskaya NG, Lukyanov KA, Putlyaeva LV. Optogenetics for sensors: On-demand fluorescent labeling of histone epigenetics. Biochem Biophys Res Commun 2023; 687:149174. [PMID: 37939505 DOI: 10.1016/j.bbrc.2023.149174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 10/26/2023] [Indexed: 11/10/2023]
Abstract
Post-translational modifications of histones to a large extent determine the functional state of chromatin loci. Dynamic visualization of histone modifications with genetically encoded fluorescent sensors makes it possible to monitor changes in the epigenetic state of a single living cell. At the same time, the sensors can potentially compete with endogenous factors recognizing these modifications. Thus, prolonged binding of the sensors to chromatin can affect normal epigenetic regulation. Here, we report an optogenetic sensor for live-cell visualization of histone H3 methylated at lysine-9 (H3K9me3) named MPP8-LAMS (MPP8-based light-activated modification sensor). MPP8-LAMS consists of several fusion protein parts (from N- to C-terminus): i) nuclear export signal (NES), ii) far-red fluorescent protein Katushka, iii) H3K9me3-binding reader domain of the human M phase phosphoprotein 8 (MPP8), iv) the light-responsive AsLOV2 domain, which exposes a nuclear localization signal (NLS) upon blue light stimulation. In the dark, due to the NES, MPP8-LAMS is localized in the cytosol. Under blue light illumination, MPP8-LAMS underwent an efficient translocation from cytosol to nucleus, enabling visualization of H3K9me3-enriched loci. Such an on-demand visualization minimizes potential impact on cell physiology as most of the time the sensor is separated from its target. In general, the present work extends the application of optogenetics to the area of advanced use of genetically encoded sensors.
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Affiliation(s)
- Afanasii I Stepanov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Polina A Zhurlova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia
| | - Alexandra A Shuvaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, 141701 Dolgoprudny, Russia
| | - Elena L Sokolinskaya
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia
| | - Nadya G Gurskaya
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | - Lidia V Putlyaeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, 121205 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
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Lukyanov KA. Fluorescent proteins for a brighter science. Biochem Biophys Res Commun 2022; 633:29-32. [DOI: 10.1016/j.bbrc.2022.08.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/06/2022]
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Simonyan TR, Protasova EA, Mamontova AV, Shakhov AM, Lukyanov KA, Maksimov EG, Bogdanov AM. A Single Fluorescent Protein-Based Indicator with a Time-Resolved Fluorescence Readout for Precise pH Measurements in the Alkaline Range. Int J Mol Sci 2022; 23:12907. [PMID: 36361706 PMCID: PMC9658282 DOI: 10.3390/ijms232112907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/22/2022] [Accepted: 10/23/2022] [Indexed: 09/19/2023] Open
Abstract
The real-time monitoring of the intracellular pH in live cells with high precision represents an important methodological challenge. Although genetically encoded fluorescent indicators can be considered as a probe of choice for such measurements, they are hindered mostly by the inability to determine an absolute pH value and/or a narrow dynamic range of the signal, making them inefficient for recording the small pH changes that typically occur within cellular organelles. Here, we study the pH sensitivity of a green-fluorescence-protein (GFP)-based emitter (EGFP-Y145L/S205V) with the alkaline-shifted chromophore's pKa and demonstrate that, in the pH range of 7.5-9.0, its fluorescence lifetime changes by a factor of ~3.5 in a quasi-linear manner in mammalian cells. Considering the relatively strong lifetime response in a narrow pH range, we proposed the mitochondria, which are known to have a weakly alkaline milieu, as a target for live-cell pH measurements. Using fluorescence lifetime imaging microscopy (FLIM) to visualize the HEK293T cells expressing mitochondrially targeted EGFP-Y145L/S205V, we succeeded in determining the absolute pH value of the mitochondria and recorded the ETC-uncoupler-stimulated pH shift with a precision of 0.1 unit. We thus show that a single GFP with alkaline-shifted pKa can act as a high-precision indicator that can be used in a specific pH range.
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Affiliation(s)
- Tatiana R. Simonyan
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Elena A. Protasova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anastasia V. Mamontova
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Aleksander M. Shakhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Semenov Federal Research Center for Chemical Physics, 119991 Moscow, Russia
| | | | - Eugene G. Maksimov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
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Stepanov AI, Besedovskaia ZV, Moshareva MA, Lukyanov KA, Putlyaeva LV. Studying Chromatin Epigenetics with Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms23168988. [PMID: 36012253 PMCID: PMC9409072 DOI: 10.3390/ijms23168988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/29/2022] Open
Abstract
Epigenetic modifications of histones (methylation, acetylation, phosphorylation, etc.) are of great importance in determining the functional state of chromatin. Changes in epigenome underlay all basic biological processes, such as cell division, differentiation, aging, and cancerous transformation. Post-translational histone modifications are mainly studied by immunoprecipitation with high-throughput sequencing (ChIP-Seq). It enables an accurate profiling of target modifications along the genome, but suffers from the high cost of analysis and the inability to work with living cells. Fluorescence microscopy represents an attractive complementary approach to characterize epigenetics. It can be applied to both live and fixed cells, easily compatible with high-throughput screening, and provide access to rich spatial information down to the single cell level. In this review, we discuss various fluorescent probes for histone modification detection. Various types of live-cell imaging epigenetic sensors suitable for conventional as well as super-resolution fluorescence microscopy are described. We also focus on problems and future perspectives in the development of fluorescent probes for epigenetics.
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Affiliation(s)
- Afanasii I. Stepanov
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
| | - Zlata V. Besedovskaia
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
| | - Maria A. Moshareva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklay St. 16/10, 117997 Moscow, Russia
| | - Konstantin A. Lukyanov
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
- Correspondence: (K.A.L.); (L.V.P.)
| | - Lidia V. Putlyaeva
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205 Moscow, Russia
- Correspondence: (K.A.L.); (L.V.P.)
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Sokolinskaya EL, Putlyaeva LV, Polinovskaya VS, Lukyanov KA. Genetically Encoded Fluorescent Sensors for SARS-CoV-2 Papain-like Protease PLpro. Int J Mol Sci 2022; 23:ijms23147826. [PMID: 35887174 PMCID: PMC9318946 DOI: 10.3390/ijms23147826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/07/2022] [Accepted: 07/14/2022] [Indexed: 02/04/2023] Open
Abstract
In the SARS-CoV-2 lifecycle, papain-like protease PLpro cuts off the non-structural proteins nsp1, nsp2, and nsp3 from a large polyprotein. This is the earliest viral enzymatic activity, which is crucial for all downstream steps. Here, we designed two genetically encoded fluorescent sensors for the real-time detection of PLpro activity in live cells. The first sensor was based on the Förster resonance energy transfer (FRET) between the red fluorescent protein mScarlet as a donor and the biliverdin-binding near-infrared fluorescent protein miRFP670 as an acceptor. A linker with the PLpro recognition site LKGG in between made this FRET pair sensitive to PLpro cleavage. Upon the co-expression of mScarlet-LKGG-miRFP670 and PLpro in HeLa cells, we observed a gradual increase in the donor fluorescence intensity of about 1.5-fold. In the second sensor, both PLpro and its target—green mNeonGreen and red mScarletI fluorescent proteins separated by an LKGG-containing linker—were attached to the endoplasmic reticulum (ER) membrane. Upon cleavage by PLpro, mScarletI diffused from the ER throughout the cell. About a two-fold increase in the nucleus/cytoplasm ratio was observed as a result of the PLpro action. We believe that the new PLpro sensors can potentially be used to detect the earliest stages of SARS-CoV-2 propagation in live cells as well as for the screening of PLpro inhibitors.
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Moshareva MA, Lukyanov KA, Putlyaeva LV. Fluorescence imaging of epigenetic genome modifications. Biochem Biophys Res Commun 2022; 622:86-92. [PMID: 35843098 DOI: 10.1016/j.bbrc.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Abstract
Epigenome contains a lot of information about cell state. Epigenetic analysis includes primarily sequence-based methods, which provide detailed data on distribution of modifications along the genome, but are poorly applicable for screenings. Specific fluorescence labeling and imaging of epigenetic modifications is an attractive complementary approach. It is currently based mainly on histone modifications study. We expect that inclusion of DNA modifications into imaging-based study would empower the method. In this review we discuss methods for fluorescence imaging of DNA modifications (mainly 5-methylcytosine). It opens an easy way to single cell analysis and high-throughput screening. Moreover, tracking epigenome changes in live cells becomes possible with genetically encoded probes.
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Affiliation(s)
- Maria A Moshareva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Konstantin A Lukyanov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lidia V Putlyaeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia.
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Sokolinskaya EL, Putlyaeva LV, Gorshkova AA, Lukyanov KA. Intermembrane oligomerization of SARS-CoV-2 M-protein: possible role in viral budding. BRSMU 2022. [DOI: 10.24075/brsmu.2022.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Despite the extensive research spurred by the catastrophic effects of COVID-19 pandemic, precise molecular mechanisms of some stages in SARS-CoV-2 life cycle remain elusive. One of such stages is the detachment of viral particles during budding. Using confocal fluorescence microscopy, we observed formation of specific structures by endoplasmic reticulum in human cells expressing SARS-CoV-2 M-protein, implicating oligomerization of M-protein across parallel membranes. In our opinion, such intermembrane oligomerization may provide a driving force for pinching off the viral particles during SARS-CoV-2 budding.
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Affiliation(s)
- EL Sokolinskaya
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - LV Putlyaeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - AA Gorshkova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - KA Lukyanov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
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Shirmanova MV, Gavrina AI, Kovaleva TF, Dudenkova VV, Zelenova EE, Shcheslavskiy VI, Mozherov AM, Snopova LB, Lukyanov KA, Zagaynova EV. Insight into redox regulation of apoptosis in cancer cells with multiparametric live-cell microscopy. Sci Rep 2022; 12:4476. [PMID: 35296739 PMCID: PMC8927414 DOI: 10.1038/s41598-022-08509-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 02/25/2022] [Indexed: 02/07/2023] Open
Abstract
Cellular redox status and the level of reactive oxygen species (ROS) are important regulators of apoptotic potential, playing a crucial role in the growth of cancer cell and their resistance to apoptosis. However, the relationships between the redox status and ROS production during apoptosis remain poorly explored. In this study, we present an investigation on the correlations between the production of ROS, the redox ratio FAD/NAD(P)H, the proportions of the reduced nicotinamide cofactors NADH and NADPH, and caspase-3 activity in cancer cells at the level of individual cells. Two-photon excitation fluorescence lifetime imaging microscopy (FLIM) was applied to monitor simultaneously apoptosis using the genetically encoded sensor of caspase-3, mKate2-DEVD-iRFP, and the autofluorescence of redox cofactors in colorectal cancer cells upon stimulation of apoptosis with staurosporine, cisplatin or hydrogen peroxide. We found that, irrespective of the apoptotic stimulus used, ROS accumulation correlated well with both the elevated pool of mitochondrial, enzyme-bound NADH and caspase-3 activation. Meanwhile, a shift in the contribution of bound NADH could develop independently of the apoptosis, and this was observed in the case of cisplatin. An increase in the proportion of bound NADPH was detected only in staurosporine-treated cells, this likely being associated with a high level of ROS production and their resulting detoxification. The results of the study favor the discovery of new therapeutic strategies based on manipulation of the cellular redox balance, which could help improve the anti-tumor activity of drugs and overcome apoptotic resistance.
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Affiliation(s)
- Marina V Shirmanova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia.
| | - Alena I Gavrina
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Tatiana F Kovaleva
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Varvara V Dudenkova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Ekaterina E Zelenova
- National Medical Research Radiological Centre of the Ministry of Health of the Russian Federation, 2nd Botkinsky proezd, 3, Moscow, Russia, 125284
| | - Vladislav I Shcheslavskiy
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia.,Becker&Hickl GmbH, Nunsdorfer Ring 7-9, 12277, Berlin, Germany
| | - Artem M Mozherov
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Ludmila B Snopova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Konstantin A Lukyanov
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, Russia, 121205
| | - Elena V Zagaynova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia.,Lobachevsky State University of Nizhny Novgorod, Gagarin Avenue 23, Nizhny Novgorod, Russia, 603950
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Bozhanova NG, Harp JM, Bender BJ, Gavrikov AS, Gorbachev DA, Baranov MS, Mercado CB, Zhang X, Lukyanov KA, Mishin AS, Meiler J. Computational redesign of a fluorogen activating protein with Rosetta. PLoS Comput Biol 2021; 17:e1009555. [PMID: 34748541 PMCID: PMC8601599 DOI: 10.1371/journal.pcbi.1009555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/18/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
The use of unnatural fluorogenic molecules widely expands the pallet of available genetically encoded fluorescent imaging tools through the design of fluorogen activating proteins (FAPs). While there is already a handful of such probes available, each of them went through laborious cycles of in vitro screening and selection. Computational modeling approaches are evolving incredibly fast right now and are demonstrating great results in many applications, including de novo protein design. It suggests that the easier task of fine-tuning the fluorogen-binding properties of an already functional protein in silico should be readily achievable. To test this hypothesis, we used Rosetta for computational ligand docking followed by protein binding pocket redesign to further improve the previously described FAP DiB1 that is capable of binding to a BODIPY-like dye M739. Despite an inaccurate initial docking of the chromophore, the incorporated mutations nevertheless improved multiple photophysical parameters as well as the overall performance of the tag. The designed protein, DiB-RM, shows higher brightness, localization precision, and apparent photostability in protein-PAINT super-resolution imaging compared to its parental variant DiB1. Moreover, DiB-RM can be cleaved to obtain an efficient split system with enhanced performance compared to a parental DiB-split system. The possible reasons for the inaccurate ligand binding pose prediction and its consequence on the outcome of the design experiment are further discussed. Computational approaches have recently made significant progress in the protein engineering field evolving from a tool for helping experimentalists to prioritize or short-list mutations for testing to being capable of making fully reliable predictions. However, not all the fields of protein modeling are evolving at a similar pace. That is why evaluating the capabilities of computational tools on different tasks is important to provide other scientists with up-to-date information on the state of the field. Here we tested the performance of Rosetta (one of the leading macromolecule modeling tools) in improving small molecule-binding proteins. We successfully redesigned a fluorogen binding protein DiB1 –a protein that binds a non-fluorescent molecule and enforces its fluorescence in the obtained complex–for improved brightness and better performance in super-resolution imaging. Our results suggest that such tasks can be already achieved without laborious library screenings. However, the flexibility of the proteins might still be underestimated during standard modeling protocols and should be closely evaluated.
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Affiliation(s)
- Nina G. Bozhanova
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Joel M. Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brian J. Bender
- Department of Pharmacology and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Alexey S. Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Christina B. Mercado
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Xuan Zhang
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | | | - Alexander S. Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- * E-mail:
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Perfilov MM, Gavrikov AS, Lukyanov KA, Mishin AS. Transient Fluorescence Labeling: Low Affinity-High Benefits. Int J Mol Sci 2021; 22:11799. [PMID: 34769228 PMCID: PMC8583718 DOI: 10.3390/ijms222111799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
Fluorescent labeling is an established method for visualizing cellular structures and dynamics. The fundamental diffraction limit in image resolution was recently bypassed with the development of super-resolution microscopy. Notably, both localization microscopy and stimulated emission depletion (STED) microscopy impose tight restrictions on the physico-chemical properties of labels. One of them-the requirement for high photostability-can be satisfied by transiently interacting labels: a constant supply of transient labels from a medium replenishes the loss in the signal caused by photobleaching. Moreover, exchangeable tags are less likely to hinder the intrinsic dynamics and cellular functions of labeled molecules. Low-affinity labels may be used both for fixed and living cells in a range of nanoscopy modalities. Nevertheless, the design of optimal labeling and imaging protocols with these novel tags remains tricky. In this review, we highlight the pros and cons of a wide variety of transiently interacting labels. We further discuss the state of the art and future perspectives of low-affinity labeling methods.
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Affiliation(s)
| | | | | | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.P.); (A.S.G.); (K.A.L.)
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Yuzhakova DV, Shirmanova MV, Klimenko VV, Lukina MM, Gavrina AI, Komarova AD, Gorbachev DA, Sapogova NV, Lukyanov KA, Kamensky VA. PDT with genetically encoded photosensitizer miniSOG on a tumor spheroid model: A comparative study of continuous-wave and pulsed irradiation. Biochim Biophys Acta Gen Subj 2021; 1865:129978. [PMID: 34487824 DOI: 10.1016/j.bbagen.2021.129978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Therapeutic effects of PDT depend on many factors, including the amount of singlet oxygen, localization of photosensitizer and irradiation protocol. The present study was aimed to compare the cytotoxic mechanisms of PDT under continuous-wave (CW) and pulsed irradiation using a tumor spheroid model and a genetically encoded photosensitizer miniSOG. METHODS 1O2 detection in miniSOG and flavin mononucleotide (FMN) solutions was performed. Photobleaching of miniSOG in solution and in HeLa tumor spheroids was analyzed. Tumor spheroid morphology and growth and the cell death mechanisms after PDT in CW and pulsed modes were assessed. RESULTS We found a more rapid 1O2 generation and a higher photobleaching rate in miniSOG solution upon irradiation in pulsed mode compared to CW mode. Photobleaching of miniSOG in tumor spheroids was also higher after irradiation in the pulsed mode. PDT of spheroids in CW mode resulted in a moderate expansion of the necrotic core of tumor spheroids and a slight inhibition of spheroid growth. The pulsed mode was more effective in induction of cell death, including apoptosis, and suppression of spheroid growth. CONCLUSIONS Comparison of CW and pulsed irradiation modes in PDT with miniSOG showed more pronounced cytotoxic effects of the pulsed mode. Our results suggest that the pulsed irradiation regimen enables enhanced 1O2 production by photosensitizer and stimulates apoptosis. GENERAL SIGNIFICANCE Our results provide more insights into the cellular mechanisms of anti-cancer PDT and open the way to improvement of light irradiation protocols.
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Affiliation(s)
- Diana V Yuzhakova
- Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia.
| | - Marina V Shirmanova
- Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia
| | - Vladimir V Klimenko
- Saint-Petersburg Clinical Scientific and Practical Center of Specialized Types of Medical Care (Oncological), 68A Leningradskaya St., Pesochny Settlement, 197758 St. Petersburg, Russia
| | - Maria M Lukina
- Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia
| | - Alena I Gavrina
- Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia
| | - Anastasya D Komarova
- Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia
| | - Dmitry A Gorbachev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., GSP-7, 117997 Moscow, Russia
| | - Natalya V Sapogova
- Institute of Applied Physics of the Russian Academy of Sciences, 46 Ulyanov St., 603950 Nizhny Novgorod, Russia
| | - Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 30/1 Bolshoy Boulevard, 121205 Moscow, Russia
| | - Vladislav A Kamensky
- Institute of Applied Physics of the Russian Academy of Sciences, 46 Ulyanov St., 603950 Nizhny Novgorod, Russia
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Abstract
The COVID-19 pandemic caused by SARS-CoV-2 coronavirus deeply affected the world community. It gave a strong impetus to the development of not only approaches to diagnostics and therapy, but also fundamental research of the molecular biology of this virus. Fluorescence microscopy is a powerful technology enabling detailed investigation of virus-cell interactions in fixed and live samples with high specificity. While spatial resolution of conventional fluorescence microscopy is not sufficient to resolve all virus-related structures, super-resolution fluorescence microscopy can solve this problem. In this paper, we review the use of fluorescence microscopy to study SARS-CoV-2 and related viruses. The prospects for the application of the recently developed advanced methods of fluorescence labeling and microscopy-which in our opinion can provide important information about the molecular biology of SARS-CoV-2-are discussed.
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Affiliation(s)
| | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
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13
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Kolesov DV, Ivanova VO, Sokolinskaya EL, Kost LA, Balaban PM, Lukyanov KA, Nikitin ES, Bogdanov AM. Impacts of OrX and cAMP-insensitive Orco to the insect olfactory heteromer activity. Mol Biol Rep 2021; 48:4549-4561. [PMID: 34129187 DOI: 10.1007/s11033-021-06480-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/05/2021] [Indexed: 11/24/2022]
Abstract
Insect odorant receptors (ORs) have been suggested to function as ligand-gated cation channels, with OrX/Orco heteromers combining ionotropic and metabotropic activity. The latter is mediated by different G proteins and results in Orco self-activation by cyclic nucleotide binding. In this contribution, we co-express the odor-specific subunits DmOr49b and DmOr59b with either wild-type Orco or an Orco-PKC mutant lacking cAMP activation heterologously in mammalian cells. We show that the characteristics of heteromers strongly depend on both the OrX type and the coreceptor variant. Thus, methyl acetate-sensitive Or59b/Orco demonstrated 25-fold faster response kinetics over o-cresol-specific Or49b/Orco, while the latter required a 10-100 times lower ligand concentration to evoke a similar electrical response. Compared to wild-type Orco, Orco-PKC decreased odorant sensitivity in both heteromers, and blocked an outward current rectification intrinsic to the Or49b/Orco pair. Our observations thus provide an insight into insect OrX/Orco functioning, highlighting their natural and artificial tuning features and laying the groundwork for their application in chemogenetics, drug screening, and repellent design.
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Affiliation(s)
- Danila V Kolesov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Violetta O Ivanova
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russia
| | | | - Liubov A Kost
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Pavel M Balaban
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russia
| | | | - Evgeny S Nikitin
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russia
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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14
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Protasova EA, Mishin AS, Lukyanov KA, Maksimov EG, Bogdanov AM. Chromophore reduction plus reversible photobleaching: how the mKate2 "photoconversion" works. Photochem Photobiol Sci 2021; 20:791-803. [PMID: 34085171 DOI: 10.1007/s43630-021-00060-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
mKate red-to-green photoconversion is a non-canonical type of phototransformation in fluorescent proteins, with a poorly understood mechanism. We have hypothesized that the daughter mKate2 protein may also be photoconvertible, and that this phenomenon would be connected with mKate(2) chromophore photoreduction. Indeed, upon the intense irradiation of the protein sample supplemented by sodium dithionite, the accumulation of green as well as blue spectral forms is enhanced. The reaction was shown to be reversible upon the reductant's removal. However, an analysis of the fluorescence microscopy data, absorption spectra, kinetics and time-resolved fluorescence spectroscopy revealed that the short-wavelength spectral forms of mKate(2) exist before photoactivation, that their fractions increase light-independently after dithionite addition, and that the conversion is facilitated by the photobleaching of the red chromophore form.
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Affiliation(s)
- Elena A Protasova
- Faculty of Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia
| | | | - Eugene G Maksimov
- Faculty of Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia.
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15
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Pletneva NV, Maksimov EG, Protasova EA, Mamontova AV, Simonyan TR, Ziganshin RH, Lukyanov KA, Muslinkina L, Pletnev S, Bogdanov AM, Pletnev VZ. Amino acid residue at the 165th position tunes EYFP chromophore maturation. A structure-based design. Comput Struct Biotechnol J 2021; 19:2950-2959. [PMID: 34136094 PMCID: PMC8163865 DOI: 10.1016/j.csbj.2021.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 01/07/2023] Open
Abstract
For the whole GFP family, a few cases, when a single mutation in the chromophore environment strongly inhibits maturation, were described. Here we study EYFP-F165G - a variant of the enhanced yellow fluorescent protein - obtained by a single F165G replacement, and demonstrated multiple fluorescent states represented by the minor emission peaks in blue and yellow ranges (~470 and ~530 nm), and the major peak at ~330 nm. The latter has been assigned to tryptophan fluorescence, quenched due to excitation energy transfer to the mature chromophore in the parental EYFP protein. EYFP-F165G crystal structure revealed two general independent routes of post-translational chemistry, resulting in two main states of the polypeptide chain with the intact chromophore forming triad (~85%) and mature chromophore (~15%). Our experiments thus highlighted important stereochemical role of the 165th position strongly affecting spectral characteristics of the protein. On the basis of the determined EYFP-F165G three-dimensional structure, new variants with ~ 2-fold improved brightness were engineered.
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Key Words
- Ala (A), alanine
- Arg (R), arginine
- Asn (R), asparagine
- Chromophore maturation
- DTT, dithiothreitol
- EC, extinction coefficient
- EET, excitation energy transfer
- EGFP, enhanced green fluorescent protein
- ESET, excited-state electron transfer
- EYFP
- EYFP, enhanced yellow fluorescent protein
- Excitation energy transfer
- FLIM, fluorescence lifetime imaging microscopy
- FP, fluorescent protein
- FQY, fluorescence quantum yield
- FRET, Förster resonance energy transfer
- FTIR, Fourier-transform infrared (spectroscopy
- Femtosecond spectroscopy
- Fluorescent proteins
- GFP, green fluorescent protein
- GYG, glycine-tyrosine-glycine
- Gln (Q), glutamine
- Glu (E), glutamic acid
- Gly (G), glycine
- His (H), histidine
- IVA-cloning, in vivo assembly cloning
- Leu (L), leucine
- PBS, phosphate buffered saline
- PCR, polymerase chain reaction
- Phe (F), phenylalanine
- REACh, resonance energy-accepting chromoprotein
- Ser (S), serine
- Structure-guided mutagenesis
- Trp (W), tryptophan
- Tryptophan fluorescence
- Tyr (Y), tyrosine
- Val (V), valine
- X-ray structure
- avGFP, Aequorea victoria green fluorescent protein
- sfGFP, superfolder GFP
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Affiliation(s)
- Nadya V. Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Eugene G. Maksimov
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Elena A. Protasova
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anastasia V. Mamontova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Tatiana R. Simonyan
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Liya Muslinkina
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia,Corresponding authors at: Depatment of biophotonics (both), Laboratory of genetically encoded molecular tools ( A.M.B.), Laboratory of of X-ray study ( V.Z.P.).
| | - Vladimir Z. Pletnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia,Corresponding authors at: Depatment of biophotonics (both), Laboratory of genetically encoded molecular tools ( A.M.B.), Laboratory of of X-ray study ( V.Z.P.).
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16
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Shirmanova MV, Gorbachev DA, Sarkisyan KS, Parnes AP, Gavrina AI, Polozova AV, Kovaleva TF, Snopova LB, Dudenkova VV, Zagaynova EV, Lukyanov KA. FUCCI-Red: a single-color cell cycle indicator for fluorescence lifetime imaging. Cell Mol Life Sci 2021; 78:3467-3476. [PMID: 33555392 DOI: 10.1007/s00018-020-03712-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/23/2020] [Accepted: 11/16/2020] [Indexed: 01/23/2023]
Abstract
The phase of the cell cycle determines numerous aspects of cancer cell behaviour including invasiveness, ability to migrate and responsiveness to cytotoxic drugs. To non-invasively monitor progression of cell cycle in vivo, a family of genetically encoded fluorescent indicators, FUCCI (fluorescent ubiquitination-based cell cycle indicator), has been developed. Existing versions of FUCCI are based on fluorescent proteins of two or more different colors fused to cell-cycle-dependent degradation motifs. Thus, FUCCI-expressing cells emit light of different colors in different phases providing a robust way to monitor cell cycle progression by fluorescence microscopy and flow cytometry but limiting the possibility to simultaneously visualize other markers. To overcome this limitation, we developed a single-color variant of FUCCI, called FUCCI-Red, which utilizes two red fluorescent proteins with distinct fluorescence lifetimes, mCherry and mKate2. Similarly to FUCCI, these proteins carry cell cycle-dependent degradation motifs to resolve G1 and S/G2/M phases. We showed utility of FUCCI-Red by visualizing cell cycle progression of cancer cells in 2D and 3D cultures and monitoring development of tumors in vivo by confocal and fluorescence lifetime imaging microscopy (FLIM). Single-channel registration and red-shifted spectra make FUCCI-Red sensor a promising instrument for multiparameter in vivo imaging applications, which was demonstrated by simultaneous detection of cellular metabolic state using endogenous fluorescence in the blue range.
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Affiliation(s)
- Marina V Shirmanova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Dmitry A Gorbachev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205, Moscow, Russia
| | - Karen S Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alina P Parnes
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alena I Gavrina
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Anastasia V Polozova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Tatyana F Kovaleva
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Ludmila B Snopova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Varvara V Dudenkova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Elena V Zagaynova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
- Lobachevsky State University of Nizhny Novgorod, Gagarin Ave. 23, 603950, Nizhny Novgorod, Russia
| | - Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205, Moscow, Russia.
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17
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Gorbachev DA, Staroverov DB, Lukyanov KA, Sarkisyan KS. Genetically Encoded Red Photosensitizers with Enhanced Phototoxicity. Int J Mol Sci 2020; 21:E8800. [PMID: 33233801 PMCID: PMC7709005 DOI: 10.3390/ijms21228800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/09/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
Genetically encoded photosensitizers are increasingly used as optogenetic tools to control cell fate or trigger intracellular processes. A monomeric red fluorescent protein called SuperNova has been recently developed, however, it demonstrates suboptimal characteristics in most phototoxicity-based applications. Here, we applied directed evolution to this protein and identified SuperNova2, a protein with S10R substitution that results in enhanced brightness, chromophore maturation and phototoxicity in bacterial and mammalian cell cultures.
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Affiliation(s)
- Dmitry A Gorbachev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Dmitry B Staroverov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Karen S Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, UK
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18
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Mamontova AV, Shakhov AM, Lukyanov KA, Bogdanov AM. Deciphering the Role of Positions 145 and 165 in Fluorescence Lifetime Shortening in the EGFP Variants. Biomolecules 2020; 10:biom10111547. [PMID: 33202759 PMCID: PMC7696298 DOI: 10.3390/biom10111547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 01/15/2023] Open
Abstract
The bright ultimately short lifetime enhanced emitter (BrUSLEE) green fluorescent protein, which differs from the enhanced green fluorescent protein (EGFP) in three mutations, exhibits an extremely short fluorescence lifetime at a relatively high brightness. An important contribution to shortening the BrUSLEE fluorescence lifetime compared to EGFP is provided by the T65G substitution of chromophore-forming residue and the Y145M mutation touching the chromophore environment. Although the influence of the T65G mutation was studied previously, the role of the 145th position in determining the GFPs physicochemical characteristics remains unclear. In this work, we show that the Y145M substitution, both alone and in combination with the F165Y mutation, does not shorten the fluorescence lifetime of EGFP-derived mutants. Thus, the unlocking of Y145M as an important determinant of lifetime tuning is possible only cooperatively with mutations at position 65. We also show here that the introduction of a T65G substitution into EGFP causes complex photobehavior of the respective mutants in the lifetime domain, namely, the appearance of two fluorescent states with different lifetimes, preserved in any combination with the Y145M and F165Y substitutions.
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Affiliation(s)
- Anastasia V. Mamontova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.V.M.); (K.A.L.)
| | | | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.V.M.); (K.A.L.)
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Correspondence:
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19
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Gorbachev DA, Petrusevich EF, Kabylda AM, Maksimov EG, Lukyanov KA, Bogdanov AM, Baranov MS, Bochenkova AV, Mishin AS. A General Mechanism of Green-to-Red Photoconversions of GFP. Front Mol Biosci 2020; 7:176. [PMID: 32850965 PMCID: PMC7405548 DOI: 10.3389/fmolb.2020.00176] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 07/07/2020] [Indexed: 12/20/2022] Open
Abstract
Here we dissect the phenomena of oxidative and reductive green-to-red photoconversion of the Green Fluorescent Protein. We characterize distinct orange- and red-emitting forms (λabs/λem = 490/565 nm; λabs/λem = 535/600 nm) arising during the Enhanced Green Fluorescent Protein (EGFP) photoconversion under low-oxygen conditions in the presence of reductants. These forms spectroscopically differ from that observed previously in oxidative redding (λabs/λem = 575/607 nm). We also report on a new green-emitting state (λabs/λem = 405/525 nm), which is formed upon photoconversion under the low-oxygen conditions. Based on the spectral properties of these forms, their light-independent time evolution, and the high-level computational studies, we provide a structural basis for various photoproducts. Under the low-oxygen conditions, the neutral quinoid-like structure formed via a two-electron oxidation process is found to be a key intermediate and a most likely candidate for the novel green-emitting state of the chromophore. The observed large Stokes shift is traced to the formation of the zwitterionic form of the chromophore in the excited state. Subsequently, this form undergoes two types of cyclization reactions, resulting in the formation of either the orange-emitting state (λabs/λem = 490/565 nm) or the red-emitting form (λabs/λem = 535/600 nm). The T65G mutant lacks one of the proposed cyclization pathways and, indeed, the photoconverted T65G EGFP exhibits a single orange-emitting state. In oxidative redding, the red-emitting state resembles the structure of the chromophore from asFP595 (λabs/λem = 572/595 nm), which is directly formed upon two-electron oxidation and deprotonation bypassing the formation of the quinoid-like structure. Our results disclose a general “oxidative” mechanism of various green-to-red photoconversions of EGFP, providing a link between oxidative redding and the photoconversion under low-oxygen conditions.
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Affiliation(s)
- Dmitry A Gorbachev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Adil M Kabylda
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Eugene G Maksimov
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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20
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Serebrovskaya EO, Podvalnaya NM, Dudenkova VV, Efremova AS, Gurskaya NG, Gorbachev DA, Luzhin AV, Kantidze OL, Zagaynova EV, Shram SI, Lukyanov KA. Genetically Encoded Fluorescent Sensor for Poly-ADP-Ribose. Int J Mol Sci 2020; 21:ijms21145004. [PMID: 32679873 PMCID: PMC7404130 DOI: 10.3390/ijms21145004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 11/29/2022] Open
Abstract
Poly-(ADP-ribosyl)-ation (PARylation) is a reversible post-translational modification of proteins and DNA that plays an important role in various cellular processes such as DNA damage response, replication, transcription, and cell death. Here we designed a fully genetically encoded fluorescent sensor for poly-(ADP-ribose) (PAR) based on Förster resonance energy transfer (FRET). The WWE domain, which recognizes iso-ADP-ribose internal PAR-specific structural unit, was used as a PAR-targeting module. The sensor consisted of cyan Turquoise2 and yellow Venus fluorescent proteins, each in fusion with the WWE domain of RNF146 E3 ubiquitin ligase protein. This bipartite sensor named sPARroW (sensor for PARrelying on WWE) enabled monitoring of PAR accumulation and depletion in live mammalian cells in response to different stimuli, namely hydrogen peroxide treatment, UV irradiation and hyperthermia.
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Affiliation(s)
- Ekaterina O. Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.O.S.); (N.M.P.); (N.G.G.); (D.A.G.)
| | - Nadezda M. Podvalnaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.O.S.); (N.M.P.); (N.G.G.); (D.A.G.)
- Institute of Molecular Genetics, Kurchatova Sq. 2, 123182 Moscow, Russia; (A.S.E.); (S.I.S.)
| | - Varvara V. Dudenkova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia; (V.V.D.); (E.V.Z.)
| | - Anna S. Efremova
- Institute of Molecular Genetics, Kurchatova Sq. 2, 123182 Moscow, Russia; (A.S.E.); (S.I.S.)
| | - Nadya G. Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.O.S.); (N.M.P.); (N.G.G.); (D.A.G.)
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Dmitry A. Gorbachev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.O.S.); (N.M.P.); (N.G.G.); (D.A.G.)
| | - Artem V. Luzhin
- Institute of Gene Biology, Vavilova 34/5, 119334 Moscow, Russia; (A.V.L.); (O.L.K.)
| | - Omar L. Kantidze
- Institute of Gene Biology, Vavilova 34/5, 119334 Moscow, Russia; (A.V.L.); (O.L.K.)
| | - Elena V. Zagaynova
- Institute of Experimental Oncology and Biomedical Technologies, Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia; (V.V.D.); (E.V.Z.)
- Lobachevsky State University of Nizhny Novgorod, Gagarin Ave. 23, 603950 Nizhny Novgorod, Russia
| | - Stanislav I. Shram
- Institute of Molecular Genetics, Kurchatova Sq. 2, 123182 Moscow, Russia; (A.S.E.); (S.I.S.)
| | - Konstantin A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (E.O.S.); (N.M.P.); (N.G.G.); (D.A.G.)
- Correspondence:
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21
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Nazarov PA, Kirsanov RS, Denisov SS, Khailova LS, Karakozova MV, Lyamzaev KG, Korshunova GA, Lukyanov KA, Kotova EA, Antonenko YN. Fluorescein Derivatives as Antibacterial Agents Acting via Membrane Depolarization. Biomolecules 2020; 10:biom10020309. [PMID: 32075319 PMCID: PMC7072581 DOI: 10.3390/biom10020309] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/03/2020] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
Appending a lipophylic alkyl chain by ester bond to fluorescein has been previously shown to convert this popular dye into an effective protonophoric uncoupler of oxidative phosphorylation in mitochondria, exhibiting neuro- and nephroprotective effects in murine models. In line with this finding, we here report data on the pronounced depolarizing effect of a series of fluorescein decyl esters on bacterial cells. The binding of the fluorescein derivatives to Bacillus subtilis cells was monitored by fluorescence microscopy and fluorescence correlation spectroscopy (FCS). FCS revealed the energy-dependent accumulation of the fluorescein esters with decyl(triphenyl)- and decyl(tri-p-tolyl)phosphonium cations in the bacterial cells. The latter compound proved to be the most potent in suppressing B. subtilis growth.
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Affiliation(s)
- Pavel A. Nazarov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (R.S.K.); (L.S.K.); (K.G.L.); (G.A.K.); (Y.N.A.)
- Correspondence: (P.A.N.); (E.A.K.)
| | - Roman S. Kirsanov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (R.S.K.); (L.S.K.); (K.G.L.); (G.A.K.); (Y.N.A.)
| | - Stepan S. Denisov
- Department of Biochemistry, University of Maastricht, Cardiovascular Research Institute Maastricht, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands;
| | - Ljudmila S. Khailova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (R.S.K.); (L.S.K.); (K.G.L.); (G.A.K.); (Y.N.A.)
| | - Marina V. Karakozova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (M.V.K.); (K.A.L.)
| | - Konstantin G. Lyamzaev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (R.S.K.); (L.S.K.); (K.G.L.); (G.A.K.); (Y.N.A.)
| | - Galina A. Korshunova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (R.S.K.); (L.S.K.); (K.G.L.); (G.A.K.); (Y.N.A.)
| | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (M.V.K.); (K.A.L.)
| | - Elena A. Kotova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (R.S.K.); (L.S.K.); (K.G.L.); (G.A.K.); (Y.N.A.)
- Correspondence: (P.A.N.); (E.A.K.)
| | - Yuri N. Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (R.S.K.); (L.S.K.); (K.G.L.); (G.A.K.); (Y.N.A.)
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22
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Perfilov MM, Gurskaya NG, Serebrovskaya EO, Melnikov PA, Kharitonov SL, Lewis TR, Arshavsky VY, Baklaushev VP, Mishin AS, Lukyanov KA. Highly photostable fluorescent labeling of proteins in live cells using exchangeable coiled coils heterodimerization. Cell Mol Life Sci 2020; 77:4429-4440. [PMID: 31894363 DOI: 10.1007/s00018-019-03426-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/10/2019] [Accepted: 12/13/2019] [Indexed: 10/25/2022]
Abstract
Fluorescent proteins are commonly used to label target proteins in live cells. However, the conventional approach based on covalent fusion of targeted proteins with fluorescent protein probes is limited by the slow rate of fluorophore maturation and irretrievable loss of fluorescence due to photobleaching. Here, we report a genetically encoded protein labeling system utilizing transient interactions of small, 21-28 residues-long helical protein tags (K/E coils, KEC). In this system, a protein of interest, covalently tagged with a single coil, is visualized through binding to a cytoplasmic fluorescent protein carrying a complementary coil. The reversible heterodimerization of KECs, whose affinity can be tuned in a broad concentration range from nanomolar to micromolar, allows continuous exchange and replenishment of the tag bound to a targeted protein with the entire cytosolic pool of soluble fluorescent coils. We found that, under conditions of partial illumination of living cells, the photostability of labeling with KECs exceeds that of covalently fused fluorescent probes by approximately one order of magnitude. Similarly, single-molecule localization microscopy with KECs provided higher labeling density and allowed a much longer duration of imaging than with conventional fusion to fluorescent proteins. We also demonstrated that this method is well suited for imaging newly synthesized proteins, because the labeling efficiency by KECs is not dependent on the rate of fluorescent protein maturation. In conclusion, KECs can be used to visualize various target proteins which are directly exposed to the cytosol, thereby enabling their advanced characterization in time and space.
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Affiliation(s)
- Maxim M Perfilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia
| | - Nadya G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov St. 1, 117997, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia.,Department of Ophthalmology, Duke University, Durham, NC, 27710, USA
| | - Pavel A Melnikov
- Serbsky National Medical Research Center for Psychiatry and Narcology, Kropotkinsky Lane 23, 119034, Moscow, Russia
| | - Sergey L Kharitonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University, Durham, NC, 27710, USA
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University, Durham, NC, 27710, USA.,Department of Pharmacology, Duke University, Durham, NC, 27710, USA
| | - Vladimir P Baklaushev
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, Orekhovy Blvd. 28, 115682, Moscow, Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia.
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia. .,Skolkovo Institute of Science and Technology, Bolshoy Blvd. 30, 121205, Moscow, Russia.
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23
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Affiliation(s)
- Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.
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24
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Kost LA, Ivanova VO, Balaban PM, Lukyanov KA, Nikitin ES, Bogdanov AM. Red Fluorescent Genetically Encoded Voltage Indicators with Millisecond Responsiveness. Sensors (Basel) 2019; 19:E2982. [PMID: 31284557 PMCID: PMC6651345 DOI: 10.3390/s19132982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/02/2019] [Accepted: 07/04/2019] [Indexed: 01/09/2023]
Abstract
Genetically encoded fluorescent indicators typically consist of the sensitive and reporter protein domains connected with the amino acid linkers. The final performance of a particular indicator may depend on the linker length and composition as strong as it depends on the both domains nature. Here we aimed to optimize interdomain linkers in VSD-FR189-188-a recently described red fluorescent protein-based voltage indicator. We have tested 13 shortened linker versions and monitored the dynamic range, response speed and polarity of the corresponding voltage indicator variants. While the new indicators didn't show a contrast enhancement, some of them carrying very short interdomain linkers responded 25-fold faster than the parental VSD-FR189-188. Also we found the critical linker length at which fluorescence response to voltage shift changes its polarity from negative to positive slope. Our observations thus make an important contribution to the designing principles of the fluorescent protein-derived voltage indicators.
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Affiliation(s)
- Liubov A Kost
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Violetta O Ivanova
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Pavel M Balaban
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Evgeny S Nikitin
- Institute of Higher Nervous Activity and Neurophysiology, Moscow 117485, Russia
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.
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25
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Abstract
Super-resolution fluorescence microscopy (nanoscopy) enables imaging with a spatial resolution much higher than the diffraction limit of optical microscopy. However, the methods of fluorescence nanoscopy are still poorly suitable for studying living cells. In this review, we describe some of methods for nanoscopy and specific fluorescent labeling aimed to decrease the damaging effects of light illumination on live samples.
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Affiliation(s)
- A S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - K A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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26
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Povarova NV, Barinov NA, Baranov MS, Markina NM, Varizhuk AM, Pozmogova GE, Klinov DV, Kozhemyako VB, Lukyanov KA. Efficient silica synthesis from tetra(glycerol)orthosilicate with cathepsin- and silicatein-like proteins. Sci Rep 2018; 8:16759. [PMID: 30425281 PMCID: PMC6233156 DOI: 10.1038/s41598-018-34965-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/24/2018] [Indexed: 12/21/2022] Open
Abstract
Silicateins play a key role in biosynthesis of spicules in marine sponges; they are also capable to catalyze formation of amorphous silica in vitro. Silicateins are highly homologous to cathepsins L – a family of cysteine proteases. Molecular mechanisms of silicatein activity remain controversial. Here site-directed mutagenesis was used to clarify significance of selected residues in silica polymerization. A number of mutations were introduced into two sponge proteins – silicatein A1 and cathepsin L from Latrunculia oparinae, as well as into human cathepsin L. First direction was alanine scanning of the proposed catalytic residues. Also, reciprocal mutations were introduced at selected positions that differ between cathepsins L and silicateins. Surprisingly, all the wild type and mutant proteins were capable to catalyze amorphous silica formation with a water-soluble silica precursor tetra(glycerol)orthosilicate. Some mutants possessed several-fold enhanced silica-forming activity and can potentially be useful for nanomaterial synthesis applications. Our findings contradict to the previously suggested mechanisms of silicatein action via a catalytic triad analogous to that in cathepsins L. Instead, a surface-templated biosilification by silicateins and related proteins can be proposed.
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Affiliation(s)
- Natalia V Povarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435, Moscow, Russia
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997, Moscow, Russia
| | - Nadezhda M Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Anna M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435, Moscow, Russia
| | - Galina E Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435, Moscow, Russia
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435, Moscow, Russia
| | - Valery B Kozhemyako
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 690022, Vladivostok, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
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27
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Mamontova AV, Solovyev ID, Savitsky AP, Shakhov AМ, Lukyanov KA, Bogdanov AM. Bright GFP with subnanosecond fluorescence lifetime. Sci Rep 2018; 8:13224. [PMID: 30185895 PMCID: PMC6125319 DOI: 10.1038/s41598-018-31687-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/23/2018] [Indexed: 11/09/2022] Open
Abstract
Fluorescence lifetime imaging microscopy (FLIM) measures fluorescence decay rate at every pixel of an image. FLIM can separate probes of the same color but different fluorescence lifetimes (FL), thus it is a promising approach for multiparameter imaging. However, available GFP-like fluorescent proteins (FP) possess a narrow range of FLs (commonly, 2.3-3.5 ns) which limits their applicability for multiparameter FLIM. Here we report a new FP probe showing both subnanosecond fluorescence lifetime and exceptional fluorescence brightness (80% of EGFP). To design this probe we applied semi-rational amino acid substitutions selection. Critical positions (Thr65, Tyr145, Phe165) were altered based on previously reported effect on FL or excited state electron transfer. The resulting EGFP triple mutant, BrUSLEE (Bright Ultimately Short Lifetime Enhanced Emitter), allows for both reliable detection of the probe and recording FL signal clearly distinguishable from that of the spectrally similar commonly used GFPs. We demonstrated high performance of this probe in multiparameter FLIM experiment. We suggest that amino acid substitutions described here lead to a significant shift in radiative and non-radiative excited state processes equilibrium.
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Affiliation(s)
| | - Ilya D Solovyev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander P Savitsky
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.,Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander М Shakhov
- Semenov Institute of Chemical Physics, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
| | | | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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28
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Pennacchietti F, Serebrovskaya EO, Faro AR, Shemyakina II, Bozhanova NG, Kotlobay AA, Gurskaya NG, Bodén A, Dreier J, Chudakov DM, Lukyanov KA, Verkhusha VV, Mishin AS, Testa I. Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy. Nat Methods 2018; 15:601-604. [PMID: 29988095 DOI: 10.1038/s41592-018-0052-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/18/2018] [Indexed: 11/09/2022]
Abstract
Reversibly photoswitchable fluorescent proteins (rsFPs) are gaining popularity as tags for optical nanoscopy because they make it possible to image with lower light doses. However, green rsFPs need violet-blue light for photoswitching, which is potentially phototoxic and highly scattering. We developed new rsFPs based on FusionRed that are reversibly photoswitchable with green-orange light. The rsFusionReds are bright and exhibit rapid photoswitching, thereby enabling nanoscale imaging of living cells.
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Affiliation(s)
- Francesca Pennacchietti
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Aline R Faro
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Irina I Shemyakina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey A Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nadya G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Andreas Bodén
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jes Dreier
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dmitry M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation.
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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29
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Shcheslavskiy VI, Shirmanova MV, Dudenkova VV, Lukyanov KA, Gavrina AI, Shumilova AV, Zagaynova E, Becker W. Fluorescence time-resolved macroimaging. Opt Lett 2018; 43:3152-3155. [PMID: 29957804 DOI: 10.1364/ol.43.003152] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/08/2018] [Indexed: 06/08/2023]
Abstract
While laser scanning fluorescence lifetime imaging (FLIM) is a powerful approach for cell biology, its small field of view (typically less than 1 mm) makes it impractical for the imaging of large biological samples that is often required for biomedical applications. Here we present a system that allows performing FLIM on macroscopic samples as large as 18 mm with a lateral resolution of 15 μm. The performance of the system is verified with FLIM of endogenous metabolic cofactor reduced nicotinamide adenine dinucleotide (phosphate), NAD(P)H, and genetically encoded fluorescent protein mKate2 in a mouse tumor in vivo.
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30
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Lidsky PV, Lukyanov KA, Misra T, Handke B, Mishin AS, Lehner CF. A genetically encoded fluorescent probe for imaging of oxygenation gradients in living Drosophila. Development 2018; 145:dev.156257. [PMID: 29437781 DOI: 10.1242/dev.156257] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/22/2018] [Indexed: 12/30/2022]
Abstract
Oxygen concentrations vary between tissues of multicellular organisms and change under certain physiological or pathological conditions. Multiple methods have been developed for measuring oxygenation of biological samples in vitro and in vivo However, most require complex equipment, are laborious and have significant limitations. Here we report that oxygen concentration determines the choice between two maturation pathways of DsRed FT (Timer). At high oxygen levels, this DsRed derivate matures predominantly into a red fluorescent isoform. By contrast, a green fluorescent isoform is favored by low oxygen levels. Ratiometric analysis of green and red fluorescence after a pulse of Timer expression in Drosophila larvae provides a record of the history of tissue oxygenation during a subsequent chase period, for the whole animal with single-cell precision. Tissue spreads revealed fine differences in oxygen exposure among different cells of the same organ. We expect that the simplicity and robustness of our approach will greatly impact hypoxia research, especially in small animal models.
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Affiliation(s)
- Peter V Lidsky
- Institute of Molecular Life Sciences (IMLS), University of Zurich, 8057 Zurich, Switzerland .,Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94158, USA
| | - Konstantin A Lukyanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod, 603005, Russia
| | - Tvisha Misra
- Institute of Molecular Life Sciences (IMLS), University of Zurich, 8057 Zurich, Switzerland
| | - Björn Handke
- Institute of Molecular Life Sciences (IMLS), University of Zurich, 8057 Zurich, Switzerland
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod, 603005, Russia
| | - Christian F Lehner
- Institute of Molecular Life Sciences (IMLS), University of Zurich, 8057 Zurich, Switzerland
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31
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Povarova NV, Markina NM, Baranov MS, Barinov NA, Klinov DV, Kozhemyako VB, Lukyanov KA. A water-soluble precursor for efficient silica polymerization by silicateins. Biochem Biophys Res Commun 2018; 495:2066-2070. [PMID: 29253563 DOI: 10.1016/j.bbrc.2017.12.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 12/14/2017] [Indexed: 11/18/2022]
Abstract
Silicateins, the spicule-forming proteins from marine demosponges capable to polymerize silica, are popular objects of biomineralization studies due to their ability to form particles varied in shape and composition under physiological conditions. Despite the occurrence of the many approaches to nanomaterial synthesis using silicateins, biochemical properties of this protein family are poorly characterized. The main reason for this is that tetraethyl orthosilicate (TEOS), the commonly used silica acid precursor, is almost insoluble in water and thus is poorly available for the protein. To solve this problem, we synthesized new water-soluble silica precursor, tetra(glycerol)orthosilicate (TGS), and characterized biochemical properties of the silicatein A1 from marine sponge Latrunculia oparinae. Compared to TEOS, TGS ensured much greater activity of silicatein and was less toxic for the mammalian cell culture. We evaluated optimum conditions for the enzyme - pH range, temperature and TGS concentration. We concluded that TGS is a useful silica acid precursor that can be used for silica particles synthesis and in vivo applications.
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Affiliation(s)
- Natalia V Povarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia.
| | - Nadezda M Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435 Moscow, Russia.
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Malaya Pirogovskaya 1a, 119435 Moscow, Russia.
| | - Valery B Kozhemyako
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, 690022 Vladivostok, Russia.
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; Nizhny Novgorod State Medical Academy, Minin and Pozharsky Sq. 10/1, 603005 Nizhny Novgorod, Russia.
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32
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Pakhomov AA, Martynov VI, Orsa AN, Bondarenko AA, Chertkova RV, Lukyanov KA, Petrenko AG, Deyev IE. Fluorescent protein Dendra2 as a ratiometric genetically encoded pH-sensor. Biochem Biophys Res Commun 2017; 493:1518-1521. [PMID: 28986251 DOI: 10.1016/j.bbrc.2017.09.170] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 09/30/2017] [Indexed: 10/18/2022]
Abstract
Fluorescent protein Dendra2 is a monomeric GFP-like protein that belongs to the group of Kaede-like photoconvertible fluorescent proteins with irreversible photoconversion from a green- to red-emitting state when exposed to violet-blue light. In an acidic environment, photoconverted Dendra2 turns green due to protonation of the phenolic group of the chromophore with pKa of about 7.5. Thus, photoconverted form of Dendra2 can be potentially used as a ratiometric pH-sensor in the physiological pH range. However, incomplete photoconversion makes ratiometric measurements irreproducible when using standard filter sets. Here, we describe the method to detect fluorescence of only photoconverted Dendra2 form, but not nonconverted green Dendra2. We show that the 350 nm excitation light induces solely the fluorescence of photoconverted protein. By measuring the red to green fluorescence ratio, we determined intracellular pH in live CHO and HEK 293 cells. Thus, Dendra2 can be used as a novel ratiometric genetically encoded pH sensor with emission maxima in the green-red spectral region, which is suitable for application in live cells.
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Affiliation(s)
- Alexey A Pakhomov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Vladimir I Martynov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander N Orsa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alena A Bondarenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Rita V Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander G Petrenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Igor E Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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33
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Kost LA, Nikitin ES, Ivanova VO, Sung U, Putintseva EV, Chudakov DM, Balaban PM, Lukyanov KA, Bogdanov AM. Insertion of the voltage-sensitive domain into circularly permuted red fluorescent protein as a design for genetically encoded voltage sensor. PLoS One 2017; 12:e0184225. [PMID: 28863184 PMCID: PMC5580962 DOI: 10.1371/journal.pone.0184225] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/21/2017] [Indexed: 11/19/2022] Open
Abstract
Visualization of electrical activity in living cells represents an important challenge in context of basic neurophysiological studies. Here we report a new voltage sensitive fluorescent indicator which response could be detected by fluorescence monitoring in a single red channel. To the best of our knowledge, this is the first fluorescent protein-based voltage sensor which uses insertion-into-circular permutant topology to provide an efficient interaction between sensitive and reporter domains. Its fluorescent core originates from red fluorescent protein (FP) FusionRed, which has optimal spectral characteristics to be used in whole body imaging techniques. Indicators using the same domain topology could become a new perspective for the FP-based voltage sensors that are traditionally based on Förster resonance energy transfer (FRET).
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Affiliation(s)
- Liubov A. Kost
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Evgeny S. Nikitin
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russian Federation
| | - Violetta O. Ivanova
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russian Federation
| | - Uhna Sung
- Center for Functional Connectomics, Korea Institute of Science & Technology, Seoul, Korea
| | | | - Dmitry M. Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Pavel M. Balaban
- Institute of Higher Nervous Activity and Neurophysiology, Moscow, Russian Federation
| | - Konstantin A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
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34
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Bozhanova NG, Baranov MS, Klementieva NV, Sarkisyan KS, Gavrikov AS, Yampolsky IV, Zagaynova EV, Lukyanov SA, Lukyanov KA, Mishin AS. Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal. Chem Sci 2017; 8:7138-7142. [PMID: 29147545 PMCID: PMC5676496 DOI: 10.1039/c7sc01628j] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/01/2017] [Indexed: 11/21/2022] Open
Abstract
A novel method of protein labeling uses the highly dynamic reversible association of a cell-permeable fluorogenic dye and lipocalin Blc mutants.
We present protein-PAINT – the implementation of the general principles of PAINT (Point Accumulation for Imaging in Nanoscale Topography) for live-cell protein labeling. Our method employs the specific binding of cell-permeable fluorogenic dyes to genetically encoded protein tags. We engineered three mutants of the bacterial lipocalin Blc that possess different affinities to a fluorogenic dye and exhibit a strong increase in fluorescence intensity upon binding. This allows for rapid labeling and washout of intracellular targets on a time scale from seconds to a few minutes. We demonstrate an order of magnitude higher photostability of the fluorescence signal in comparison with spectrally similar fluorescent proteins. Protein-PAINT ensures prolonged super-resolution fluorescence microscopy of living cells in both single molecule detection and stimulated emission depletion regimes.
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Affiliation(s)
- Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia .
| | | | - Karen S Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Centre for Genomic Regulation (CRG) , The Barcelona Institute for Science and Technology , Dr Aiguader 88 , 08003 Barcelona , Spain
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia .
| | - Ilia V Yampolsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Pirogov Russian National Research Medical University , Moscow , Russia
| | | | - Sergey A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia.,Pirogov Russian National Research Medical University , Moscow , Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
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35
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Bozhanova NG, Baranov MS, Sarkisyan KS, Gritcenko R, Mineev KS, Golodukhina SV, Baleeva NS, Lukyanov KA, Mishin AS. Yellow and Orange Fluorescent Proteins with Tryptophan-based Chromophores. ACS Chem Biol 2017; 12:1867-1873. [PMID: 28525263 DOI: 10.1021/acschembio.7b00337] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid development of new microscopy techniques exposed the need for genetically encoded fluorescent tags with special properties. Recent works demonstrated the potential of fluorescent proteins with tryptophan-based chromophores. We applied rational design and random mutagenesis to the monomeric red fluorescent protein FusionRed and found two groups of mutants carrying a tryptophan-based chromophore: with yellow (535 nm) or orange (565 nm) emission. On the basis of the properties of proteins, a model synthetic chromophore, and a computational modeling, we concluded that the presence of a ketone-containing chromophore in different isomeric forms can explain the observed yellow and orange phenotypes.
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Affiliation(s)
- Nina G Bozhanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1, 117997 Moscow, Russia
| | - Karen S Sarkisyan
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Roman Gritcenko
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University , 22100 Lund, Sweden
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology , Institutsky per., 9, 141701 Dolgoprudny, Russia
| | - Svetlana V Golodukhina
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1, 117997 Moscow, Russia
| | - Konstantin A Lukyanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences , Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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36
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Klementieva NV, Pavlikov AI, Moiseev AA, Bozhanova NG, Mishina NM, Lukyanov SA, Zagaynova EV, Lukyanov KA, Mishin AS. Intrinsic blinking of red fluorescent proteins for super-resolution microscopy. Chem Commun (Camb) 2017; 53:949-951. [PMID: 28044165 DOI: 10.1039/c6cc09200d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Single-molecule localization microscopy relies on either controllable photoswitching of fluorescent probes or their robust blinking. We have found that blinking of monomeric red fluorescent proteins TagRFP, TagRFP-T, and FusionRed occurs at moderate illumination power and matches well with camera acquisition speed. It allows for super-resolution image reconstruction of densely labelled structures in live cells using various algorithms.
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Affiliation(s)
| | | | | | - Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - Natalie M Mishina
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - Sergey A Lukyanov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia. and Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Konstantin A Lukyanov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - Alexander S Mishin
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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37
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Sergeeva TF, Shirmanova MV, Zlobovskaya OA, Gavrina AI, Dudenkova VV, Lukina MM, Lukyanov KA, Zagaynova EV. Relationship between intracellular pH, metabolic co-factors and caspase-3 activation in cancer cells during apoptosis. Biochim Biophys Acta Mol Cell Res 2017; 1864:604-611. [PMID: 28063999 DOI: 10.1016/j.bbamcr.2016.12.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/23/2016] [Accepted: 12/30/2016] [Indexed: 12/21/2022]
Abstract
A complex cascade of molecular events occurs in apoptotic cells but cell-to-cell variability significantly complicates determination of the order and interconnections between different processes. For better understanding of the mechanisms of programmed cell death, dynamic simultaneous registration of several parameters is required. In this paper we used multiparameter fluorescence microscopy to analyze energy metabolism, intracellular pH and caspase-3 activation in living cancer cells in vitro during staurosporine-induced apoptosis. We performed metabolic imaging of two co-factors, NAD(P)H and FAD, and used the genetically encoded pH-indicator SypHer1 and the FRET-based sensor for caspase-3 activity, mKate2-DEVD-iRFP, to visualize these parameters by confocal fluorescence microscopy and two-photon fluorescence lifetime imaging microscopy. The correlation between energy metabolism, intracellular pH and caspase-3 activation and their dynamic changes were studied in CT26 cancer cells during apoptosis. Induction of apoptosis was accompanied by a switch to oxidative phosphorylation, cytosol acidification and caspase-3 activation. We showed that alterations in cytosolic pH and the activation of oxidative phosphorylation are relatively early events associated with the induction of apoptosis.
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Affiliation(s)
- Tatiana F Sergeeva
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia.
| | - Marina V Shirmanova
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia.
| | - Olga A Zlobovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia.
| | - Alena I Gavrina
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia; Nizhny Novgorod State University, Gagarin Ave., 23, 603950 Nizhny Novgorod, Russia.
| | - Varvara V Dudenkova
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia; Nizhny Novgorod State University, Gagarin Ave., 23, 603950 Nizhny Novgorod, Russia.
| | - Maria M Lukina
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia; Nizhny Novgorod State University, Gagarin Ave., 23, 603950 Nizhny Novgorod, Russia.
| | - Konstantin A Lukyanov
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia.
| | - Elena V Zagaynova
- Nizhny Novgorod State Medical Academy, 10/1 Minin and Pozharsky Sq., 603005 Nizhny Novgorod, Russia.
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38
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Acharya A, Bogdanov AM, Grigorenko BL, Bravaya KB, Nemukhin AV, Lukyanov KA, Krylov AI. Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing? Chem Rev 2016; 117:758-795. [PMID: 27754659 DOI: 10.1021/acs.chemrev.6b00238] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10-4-10-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.
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Affiliation(s)
- Atanu Acharya
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
| | - Alexey M Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University , Boston, Massachusetts United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow, Russia.,Nizhny Novgorod State Medical Academy , Nizhny Novgorod, Russia
| | - Anna I Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-0482, United States
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39
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Ryumina AP, Serebrovskaya EO, Staroverov DB, Zlobovskaya OA, Shcheglov AS, Lukyanov SA, Lukyanov KA. Lysosome-associated miniSOG as a photosensitizer for mammalian cells. Biotechniques 2016; 61:92-4. [PMID: 27528074 DOI: 10.2144/000114445] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/16/2016] [Indexed: 11/23/2022] Open
Abstract
Genetically encoded photosensitizers represent a promising optogenetic tool for the induction of light-controlled oxidative stress strictly localized to a selected intracellular compartment. Here we tested the phototoxic effects of the flavin-containing phototoxic protein miniSOG targeted to the cytoplasmic surfaces of late endosomes and lysosomes by fusion with Rab7. In HeLa Kyoto cells stably expressing miniSOG-Rab7, we demonstrated a high level of cell death upon blue-light illumination. Pepstatin A completely abolished phototoxicity of miniSOG-Rab7, showing a key role for cathepsin D in this model. Using a far-red fluorescence sensor for caspase-3, we observed caspase-3 activation during miniSOG-Rab7-mediated cell death. We conclude that upon illumination, miniSOG-Rab7 induces lysosomal membrane permeabilization (LMP) and leakage of cathepsins into the cytosol, resulting in caspase-dependent apoptosis.
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Affiliation(s)
- Alina P Ryumina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | | | | | | | - Sergey A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
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40
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Sarkisyan KS, Goryashchenko AS, Lidsky PV, Gorbachev DA, Bozhanova NG, Gorokhovatsky AY, Pereverzeva AR, Ryumina AP, Zherdeva VV, Savitsky AP, Solntsev KM, Bommarius AS, Sharonov GV, Lindquist JR, Drobizhev M, Hughes TE, Rebane A, Lukyanov KA, Mishin AS. Green fluorescent protein with anionic tryptophan-based chromophore and long fluorescence lifetime. Biophys J 2016. [PMID: 26200874 DOI: 10.1016/j.bpj.2015.06.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Spectral diversity of fluorescent proteins, crucial for multiparameter imaging, is based mainly on chemical diversity of their chromophores. Recently we have reported, to our knowledge, a new green fluorescent protein WasCFP-the first fluorescent protein with a tryptophan-based chromophore in the anionic state. However, only a small portion of WasCFP molecules exists in the anionic state at physiological conditions. In this study we report on an improved variant of WasCFP, named NowGFP, with the anionic form dominating at 37°C and neutral pH. It is 30% brighter than enhanced green fluorescent protein (EGFP) and exhibits a fluorescence lifetime of 5.1 ns. We demonstrated that signals of NowGFP and EGFP can be clearly distinguished by fluorescence lifetime in various models, including mammalian cells, mouse tumor xenograft, and Drosophila larvae. NowGFP thus provides an additional channel for multiparameter fluorescence lifetime imaging microscopy of green fluorescent proteins.
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Affiliation(s)
- Karen S Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Peter V Lidsky
- Institute of Gene Biology, Moscow, Russia; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California
| | | | - Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Andrey Yu Gorokhovatsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Pushchino Branch, Pushchino, Russia
| | | | - Alina P Ryumina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Victoria V Zherdeva
- A.N. Bach Institute of Biochemistry, Moscow, Russia; Russian Medical Academy of Postgraduate Education, Moscow, Russia
| | | | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Andreas S Bommarius
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia; Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - George V Sharonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Faculty of Medicine, Moscow State University, Moscow, Russia
| | - Jake R Lindquist
- Department of Physics, Montana State University, Bozeman, Montana
| | | | - Thomas E Hughes
- Department of Cell Biology and Neuroscience, Montana State University, Bozeman, Montana
| | - Aleksander Rebane
- Department of Physics, Montana State University, Bozeman, Montana; National Insitute of Chemical Physics and Biophysics, Tallinn, Estonia
| | | | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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41
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Bogdanov AM, Acharya A, Titelmayer AV, Mamontova AV, Bravaya KB, Kolomeisky AB, Lukyanov KA, Krylov AI. Turning On and Off Photoinduced Electron Transfer in Fluorescent Proteins by π-Stacking, Halide Binding, and Tyr145 Mutations. J Am Chem Soc 2016; 138:4807-17. [DOI: 10.1021/jacs.6b00092] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Alexey M. Bogdanov
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod 603005, Russia
| | - Atanu Acharya
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | | | | | - Ksenia B. Bravaya
- Department
of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | | | - Konstantin A. Lukyanov
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod 603005, Russia
| | - Anna I. Krylov
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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42
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Gurskaya NG, Pereverzev AP, Staroverov DB, Markina NM, Lukyanov KA. Analysis of Nonsense-Mediated mRNA Decay at the Single-Cell Level Using Two Fluorescent Proteins. Methods Enzymol 2016; 572:291-314. [PMID: 27241760 DOI: 10.1016/bs.mie.2016.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved mechanism of specific degradation of transcripts with a premature stop codon. NMD eliminates aberrant mRNAs arising from mutations, alternative splicing, and other events in cells. In addition, many normal transcripts undergo NMD. Recent studies demonstrated that NMD activity is specifically regulated and that NMD can play a role of global regulator of gene expression. Recently, we developed dual-color fluorescent protein-based reporters for quantification of NMD activity using fluorescence microscopy and flow cytometry (Pereverzev, Gurskaya, et al., 2015). Due to ratiometric fluorescence response, these reporters make it possible to assess NMD activity in live cells at the single-cell level and to reveal otherwise hidden heterogeneity of cells in respect of NMD activity. Here we provide a detailed description of applications of the NMD reporters in mammalian cell lines.
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Affiliation(s)
- N G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - A P Pereverzev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - D B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - N M Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - K A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.
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43
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Eroshkin FM, Nesterenko AM, Borodulin AV, Martynova NY, Ermakova GV, Gyoeva FK, Orlov EE, Belogurov AA, Lukyanov KA, Bayramov AV, Zaraisky AG. Noggin4 is a long-range inhibitor of Wnt8 signalling that regulates head development in Xenopus laevis. Sci Rep 2016; 6:23049. [PMID: 26973133 PMCID: PMC4789793 DOI: 10.1038/srep23049] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/25/2016] [Indexed: 12/05/2022] Open
Abstract
Noggin4 is a Noggin family secreted protein whose molecular and physiological functions remain unknown. In this study, we demonstrate that in contrast to other Noggins, Xenopus laevis Noggin4 cannot antagonise BMP signalling; instead, it specifically binds to Wnt8 and inhibits the Wnt/β -catenin pathway. Live imaging demonstrated that Noggin4 diffusivity in embryonic tissues significantly exceeded that of other Noggins. Using the Fluorescence Recovery After Photobleaching (FRAP) assay and mathematical modelling, we directly estimated the affinity of Noggin4 for Wnt8 in living embryos and determined that Noggin4 fine-tune the Wnt8 posterior-to-anterior gradient. Our results suggest a role for Noggin4 as a unique, freely diffusing, long-range inhibitor of canonical Wnt signalling, thus explaining its ability to promote head development.
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Affiliation(s)
- Fedor M Eroshkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexey M Nesterenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gory, 1/40, 119991 Moscow, Russia
| | - Alexander V Borodulin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Natalia Yu Martynova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Galina V Ermakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Fatima K Gyoeva
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russia
| | - Eugeny E Orlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexey A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Andrey V Bayramov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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44
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Gurskaya NG, Staroverov DB, Lukyanov KA. Fluorescent Protein-Based Quantification of Alternative Splicing of a Target Cassette Exon in Mammalian Cells. Methods Enzymol 2016; 572:255-68. [PMID: 27241758 DOI: 10.1016/bs.mie.2016.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Alternative splicing is an important mechanism of regulation of gene expression and expansion of proteome complexity. Recently we developed a new fluorescence reporter for quantitative analysis of alternative splicing of a target cassette exon in live cells (Gurskaya et al., 2012). It consists of a specially designed minigene encoding red and green fluorescent proteins (Katushka and TagGFP2) and a fragment of the target gene between them. Skipping or inclusion of the alternative exon induces a frameshift; ie, alternative exon length must not be a multiple of 3. Finally, red and green fluorescence intensities of cells expressing this reporter are used to estimate the percentage of alternative (exon-skipped) and normal (exon-retained) transcripts. Here, we provide a detailed description of design and application of the fluorescence reporter of a target alternative exon splicing in mammalian cell lines.
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Affiliation(s)
- N G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - D B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - K A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.
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Prudkovsky AA, Ivanenko VN, Nikitin MA, Lukyanov KA, Belousova A, Reimer JD, Berumen ML. Green Fluorescence of Cytaeis Hydroids Living in Association with Nassarius Gastropods in the Red Sea. PLoS One 2016; 11:e0146861. [PMID: 26840497 PMCID: PMC4739711 DOI: 10.1371/journal.pone.0146861] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 12/21/2015] [Indexed: 11/26/2022] Open
Abstract
Green Fluorescent Proteins (GFPs) have been reported from a wide diversity of medusae, but only a few observations of green fluorescence have been reported for hydroid colonies. In this study, we report on fluorescence displayed by hydroid polyps of the genus Cytaeis Eschscholtz, 1829 (Hydrozoa: Anthoathecata: Filifera) found at night time in the southern Red Sea (Saudi Arabia) living on shells of the gastropod Nassarius margaritifer (Dunker, 1847) (Neogastropoda: Buccinoidea: Nassariidae). We examined the fluorescence of these polyps and compare with previously reported data. Intensive green fluorescence with a spectral peak at 518 nm was detected in the hypostome of the Cytaeis polyps, unlike in previous reports that reported fluorescence either in the basal parts of polyps or in other locations on hydroid colonies. These results suggest that fluorescence may be widespread not only in medusae, but also in polyps, and also suggests that the patterns of fluorescence localization can vary in closely related species. The fluorescence of polyps may be potentially useful for field identification of cryptic species and study of geographical distributions of such hydroids and their hosts.
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Affiliation(s)
- Andrey A. Prudkovsky
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Viatcheslav N. Ivanenko
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail A. Nikitin
- A.N. Belozersky Institute of Physico-chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Anna Belousova
- Department of Invertebrate Zoology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - James D. Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Department of Biology, Chemistry, and Marine Sciences, Faculty of Science, University of the Ryukyus, Okinawa, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Michael L. Berumen
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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Zlobovskaya OA, Sergeeva TF, Shirmanova MV, Dudenkova VV, Sharonov GV, Zagaynova EV, Lukyanov KA. Genetically encoded far-red fluorescent sensors for caspase-3 activity. Biotechniques 2016; 60:62-8. [PMID: 26842350 DOI: 10.2144/000114377] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/07/2015] [Indexed: 11/23/2022] Open
Abstract
Caspase-3 is a key effector caspase that is activated in both extrinsic and intrinsic pathways of apoptosis. Available fluorescent sensors for caspase-3 activity operate in relatively short wavelength regions and are nonoptimal for multiparameter microscopy and whole-body imaging. In the present work, we developed new genetically encoded sensors for caspase-3 activity possessing the most red-shifted spectra to date. These consist of Förster resonance energy transfer (FRET) pairs in which a far-red fluorescent protein (mKate2 or eqFP650) is connected to the infrared fluorescent protein iRFP through a linker containing the DEVD caspase-3 cleavage site. During staurosporine-induced apoptosis of mammalian cells (HeLa and CT26), both mKate2-DEVD-iRFP and eqFP650-DEVD-iRFP sensors showed a robust response (1.6-fold increase of the donor fluorescence intensity). However, eqFP650-DEVD-iRFP displayed aggregation in some cells. For stably transfected CT26 mKate2-DEVD-iRFP cells, fluorescence lifetime imaging (FLIM) enabled us to detect caspase-3 activation due to the increase of mKate2 donor fluorescence lifetime from 1.45 to 2.05 ns. We took advantage of the strongly red-shifted spectrum of mKate2-DEVD-iRFP to perform simultaneous imaging of EGFP-Bax translocation during apoptosis. We conclude that mKate2-DEVD-iRFP is well-suited for multiparameter imaging and also potentially beneficial for in vivo imaging in animal tissues.
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Affiliation(s)
| | | | | | - Varvara V Dudenkova
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
- Nizhny Novgorod State University, Nizhny Novgorod, Russia
| | - George V Sharonov
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
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Pereverzev AP, Matlashov ME, Staroverov DB, Lukyanov KA, Gurskaya NG. [Differences of Nonsense-Mediated mRNA Degradation Activity in Mammalian Cell Lines Revealed by a Fluorescence Reporter]. Bioorg Khim 2016; 41:587-91. [PMID: 26762096 DOI: 10.1134/s1068162015050118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Activity of nonsense-mediated mRNA degradation (NMD) was studied in several mammalian cell cultures using recently developed genetically encoded fluorescence sensor [Pereverzev et al., Sci. Rep., 2015, vol. 5, p. 7729]. This NMD reporter enables measurement of NMD activity in single live cells using ratio of green and red fluorescent proteins signals. The following cell lines were analyzed: mouse colon carcinoma CT26, mouse Lewis lung carcinoma LLC, human T-cell leukemia Jurkat, and spontaneously immortalized human keratinocytes HaCaT. These cell lines demonstrated very different NMD activities. In CT26, NMD activity was low, whereas in LLC it was high (8.5-fold higher than in CT26). Jurkat and HaCaT cells possessed strong heterogeneity and consisted of two cell subpopulations with high and low NMD activities. In addition, we detected high NMD activity in primary culture of mouse embryonic hippocampal neurons.
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Pletneva NV, Pletnev VZ, Sarkisyan KS, Gorbachev DA, Egorov ES, Mishin AS, Lukyanov KA, Dauter Z, Pletnev S. Crystal Structure of Phototoxic Orange Fluorescent Proteins with a Tryptophan-Based Chromophore. PLoS One 2015; 10:e0145740. [PMID: 26699366 PMCID: PMC4689385 DOI: 10.1371/journal.pone.0145740] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/08/2015] [Indexed: 01/15/2023] Open
Abstract
Phototoxic fluorescent proteins represent a sparse group of genetically encoded photosensitizers that could be used for precise light-induced inactivation of target proteins, DNA damage, and cell killing. Only two such GFP-based fluorescent proteins (FPs), KillerRed and its monomeric variant SuperNova, were described up to date. Here, we present a crystallographic study of their two orange successors, dimeric KillerOrange and monomeric mKillerOrange, at 1.81 and 1.57 Å resolution, respectively. They are the first orange-emitting protein photosensitizers with a tryptophan-based chromophore (Gln65-Trp66-Gly67). Same as their red progenitors, both orange photosensitizers have a water-filled channel connecting the chromophore to the β-barrel exterior and enabling transport of ROS. In both proteins, Trp66 of the chromophore adopts an unusual trans-cis conformation stabilized by H-bond with the nearby Gln159. This trans-cis conformation along with the water channel was shown to be a key structural feature providing bright orange emission and phototoxicity of both examined orange photosensitizers.
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Affiliation(s)
- Nadya V. Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir Z. Pletnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Karen S. Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Dmitry A. Gorbachev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Faculty of Biology, Moscow State University, Moscow, Russian Federation
| | - Evgeny S. Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russian Federation
| | - Konstantin A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russian Federation
| | - Zbigniew Dauter
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, Illinois, United States of America
| | - Sergei Pletnev
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne, Illinois, United States of America
- Leidos Biomedical Research, Inc., Basic Research Program, Argonne, Illinois, United States of America
- * E-mail: ;
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49
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Sarkisyan KS, Zlobovskaya OA, Gorbachev DA, Bozhanova NG, Sharonov GV, Staroverov DB, Egorov ES, Ryabova AV, Solntsev KM, Mishin AS, Lukyanov KA. KillerOrange, a Genetically Encoded Photosensitizer Activated by Blue and Green Light. PLoS One 2015; 10:e0145287. [PMID: 26679300 PMCID: PMC4683004 DOI: 10.1371/journal.pone.0145287] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 12/02/2015] [Indexed: 11/19/2022] Open
Abstract
Genetically encoded photosensitizers, proteins that produce reactive oxygen species when illuminated with visible light, are increasingly used as optogenetic tools. Their applications range from ablation of specific cell populations to precise optical inactivation of cellular proteins. Here, we report an orange mutant of red fluorescent protein KillerRed that becomes toxic when illuminated with blue or green light. This new protein, KillerOrange, carries a tryptophan-based chromophore that is novel for photosensitizers. We show that KillerOrange can be used simultaneously and independently from KillerRed in both bacterial and mammalian cells offering chromatic orthogonality for light-activated toxicity.
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Affiliation(s)
| | | | - Dmitry A. Gorbachev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Faculty of Biology, Moscow State University, Moscow, Russia
| | - Nina G. Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - George V. Sharonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Faculty of Medicine, Moscow State University, Moscow, Russia
| | | | - Evgeny S. Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anastasia V. Ryabova
- Laser Biospectroscopy Laboratory, Prokhorov General Physics Institute, Moscow, Russia
| | - Kyril M. Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, 30332, United States of America
| | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - Konstantin A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
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50
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Povarova NV, Baranov MS, Kovalchuk SN, Semiletova IV, Lukyanov KA, Kozhemyak VB. [Novel Water-Soluble Substrate for Silicateins]. Bioorg Khim 2015; 41:380-2. [PMID: 26502615 DOI: 10.1134/s1068162015030073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We suggested to use tetrakis(2-hydroxyethyl)orthosilicate (THEOS) as a substrate for silicateins--an enzyme family playing a key role in formation of skeleton in marine sponges. We compared THEOS with tetraethylorthosilicate (TEOS)--a commonly used substrate for silicateins. These substrates were tested in reaction of amorphous silica formation in vitro catalyzed by silicatein Al from sponge Latrunculia oparinae. It was found that reaction with THEOS occurs more efficiently than with TEOS, probably due to high water solubility and higher hydrolysis rate of THEOS.
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