1
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Felčíková K, Hovan A, Polák M, Loginov DS, Holotová V, Díaz C, Kožár T, Lee O, Varhač R, Novák P, Bánó G, Sedlák E. Design of AsLOV2 domain as a carrier of light-induced dissociable FMN photosensitizer. Protein Sci 2024; 33:e4921. [PMID: 38501448 PMCID: PMC10949324 DOI: 10.1002/pro.4921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/09/2024] [Accepted: 01/25/2024] [Indexed: 03/20/2024]
Abstract
Flavin mononucleotide (FMN) is a highly efficient photosensitizer (PS) yielding singlet oxygen (1 O2 ). However, its 1 O2 production efficiency significantly decreases upon isoalloxazine ring encapsulation into the protein matrix in genetically encoded photosensitizers (GEPS). Reducing isoalloxazine ring interactions with surrounding amino acids by protein engineering may increase 1 O2 production efficiency GEPS, but at the same time weakened native FMN-protein interactions may cause undesirable FMN dissociation. Here, in contrast, we intentionally induce the FMN release by light-triggered sulfur oxidation of strategically placed cysteines (oxidation-prone amino acids) in the isoalloxazine-binding site due to significantly increased volume of the cysteinyl side residue(s). As a proof of concept, in three variants of the LOV2 domain of Avena sativa (AsLOV2), namely V416C, T418C, and V416C/T418C, the effective 1 O2 production strongly correlated with the efficiency of irradiation-induced FMN dissociation (wild type (WT) < V416C < T418C < V416C/T418C). This alternative approach enables us: (i) to overcome the low 1 O2 production efficiency of flavin-based GEPSs without affecting native isoalloxazine ring-protein interactions and (ii) to utilize AsLOV2, due to its inherent binding propensity to FMN, as a PS vehicle, which is released at a target by light irradiation.
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Affiliation(s)
- Kristína Felčíková
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Andrej Hovan
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Marek Polák
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Dmitry S. Loginov
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Veronika Holotová
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Carlos Díaz
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - One‐Sun Lee
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
| | - Rastislav Varhač
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Petr Novák
- Institute of Microbiology ‐ BioCeV, Academy of Sciences of the Czech RepublicPragueCzech Republic
| | - Gregor Bánó
- Department of Biophysics, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation ParkP.J. Šafárik UniversityKošiceSlovakia
- Department of Biochemistry, Faculty of ScienceP.J. Šafárik UniversityKošiceSlovakia
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2
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Grigorenko BL, Khrenova MG, Jones DD, Nemukhin AV. Histidine-assisted reduction of arylnitrenes upon photo-activation of phenyl azide chromophores in GFP-like fluorescent proteins. Org Biomol Chem 2024; 22:337-347. [PMID: 38063860 DOI: 10.1039/d3ob01450a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The photochemically active sites of the proteins sfGFP66azF and Venus66azF, members of the green fluorescent protein (GFP) family, contain a non-canonical amino acid residue p-azidophenylalanine (azF) instead of Tyr66. The light-induced decomposition of azF at these sites leads to the formation of reactive arylnitrene (nF) intermediates followed by the formation of phenylamine-containing chromophores. We report the first study of the reaction mechanism of the reduction of the arylnitrene intermediates in sfGFP66nF and Venus66nF using molecular modeling methods. The Gibbs energy profiles for the elementary steps of the chemical reaction in sfGFP66nF are computed using molecular dynamics simulations with quantum mechanics/molecular mechanics (QM/MM) potentials. Structures and energies along the reaction pathway in Venus66nF are evaluated using a QM/MM approach. According to the results of the simulations, arylnitrene reduction is coupled with oxidation of the histidine side chain on the His148 residue located near the chromophore.
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Affiliation(s)
- Bella L Grigorenko
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation.
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria G Khrenova
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation.
- Bach Institute of Biochemistry, Moscow, Russian Federation
| | - D Dafydd Jones
- School of Biosciences, Molecular Biosciences Division, Cardiff University, Cardiff, UK
| | - Alexander V Nemukhin
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation.
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russian Federation
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3
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Tong Y, Kaya SG, Russo S, Rozeboom HJ, Wijma HJ, Fraaije MW. Fixing Flavins: Hijacking a Flavin Transferase for Equipping Flavoproteins with a Covalent Flavin Cofactor. J Am Chem Soc 2023; 145:27140-27148. [PMID: 38048072 PMCID: PMC10722498 DOI: 10.1021/jacs.3c12009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/05/2023]
Abstract
Most flavin-dependent enzymes contain a dissociable flavin cofactor. We present a new approach for installing in vivo a covalent bond between a flavin cofactor and its host protein. By using a flavin transferase and carving a flavinylation motif in target proteins, we demonstrate that "dissociable" flavoproteins can be turned into covalent flavoproteins. Specifically, four different flavin mononucleotide-containing proteins were engineered to undergo covalent flavinylation: a light-oxygen-voltage domain protein, a mini singlet oxygen generator, a nitroreductase, and an old yellow enzyme-type ene reductase. Optimizing the flavinylation motif and expression conditions led to the covalent flavinylation of all four flavoproteins. The engineered covalent flavoproteins retained function and often exhibited improved performance, such as higher thermostability or catalytic performance. The crystal structures of the designed covalent flavoproteins confirmed the designed threonyl-phosphate linkage. The targeted flavoproteins differ in fold and function, indicating that this method of introducing a covalent flavin-protein bond is a powerful new method to create flavoproteins that cannot lose their cofactor, boosting their performance.
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Affiliation(s)
- Yapei Tong
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Saniye G. Kaya
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Sara Russo
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Henriette J. Rozeboom
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Hein J. Wijma
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Marco W. Fraaije
- Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
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4
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Polyakov I, Kulakova A, Nemukhin A. Computational Modeling of the Interaction of Molecular Oxygen with the miniSOG Protein—A Light Induced Source of Singlet Oxygen. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3020016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Interaction of molecular oxygen 3O2 with the flavin-dependent protein miniSOG after light illumination results in creation of singlet oxygen 1O2 and superoxide O2●−. Despite the recently resolved crystal structures of miniSOG variants, oxygen-binding sites near the flavin chromophore are poorly characterized. We report the results of computational studies of the protein−oxygen systems using molecular dynamics (MD) simulations with force-field interaction potentials and quantum mechanics/molecular mechanics (QM/MM) potentials for the original miniSOG and the mutated protein. We found several oxygen-binding pockets and pointed out possible tunnels bridging the bulk solvent and the isoalloxazine ring of the chromophore. These findings provide an essential step toward understanding photophysical properties of miniSOG—an important singlet oxygen photosensitizer.
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Affiliation(s)
- Igor Polyakov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Anna Kulakova
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Nemukhin
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
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5
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Chernov KG, Manoilov KY, Oliinyk OS, Shcherbakova DM, Verkhusha VV. Photodegradable by Yellow-Orange Light degFusionRed Optogenetic Module with Autocatalytically Formed Chromophore. Int J Mol Sci 2023; 24:6526. [PMID: 37047499 PMCID: PMC10095432 DOI: 10.3390/ijms24076526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Optogenetic systems driven by yellow-orange light are required for the simultaneous regulation of several cellular processes. We have engineered the red fluorescent protein FusionRed into a 26 kDa monomeric optogenetic module, called degFusionRed. Unlike other fluorescent protein-based optogenetic domains, which exhibit light-induced self-inactivation by generating reactive oxygen species, degFusionRed undergoes proteasomal degradation upon illumination with 567 nm light. Similarly to the parent protein, degFusionRed has minimal absorbance at 450 nm and above 650 nm, making it spectrally compatible with blue and near-infrared-light-controlled optogenetic tools. The autocatalytically formed chromophore provides degFusionRed with an additional advantage over most optogenetic tools that require the binding of the exogenous chromophores, the amount of which varies in different cells. The degFusionRed efficiently performed in the engineered light-controlled transcription factor and in the targeted photodegradation of the protein of interest, demonstrating its versatility as the optogenetic module of choice for spectral multiplexed interrogation of various cellular processes.
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Affiliation(s)
| | - Kyrylo Yu. Manoilov
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olena S. Oliinyk
- Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Daria M. Shcherbakova
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Vladislav V. Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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6
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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7
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Obozina AS, Komedchikova EN, Kolesnikova OA, Iureva AM, Kovalenko VL, Zavalko FA, Rozhnikova TV, Tereshina ED, Mochalova EN, Shipunova VO. Genetically Encoded Self-Assembling Protein Nanoparticles for the Targeted Delivery In Vitro and In Vivo. Pharmaceutics 2023; 15:pharmaceutics15010231. [PMID: 36678860 PMCID: PMC9861179 DOI: 10.3390/pharmaceutics15010231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Targeted nanoparticles of different origins are considered as new-generation diagnostic and therapeutic tools. However, there are no targeted drug formulations within the composition of nanoparticles approved by the FDA for use in the clinic, which is associated with the insufficient effectiveness of the developed candidates, the difficulties of their biotechnological production, and inadequate batch-to-batch reproducibility. Targeted protein self-assembling nanoparticles circumvent this problem since proteins are encoded in DNA and the final protein product is produced in only one possible way. We believe that the combination of the endless biomedical potential of protein carriers as nanoparticles and the standardized protein purification protocols will make significant progress in "magic bullet" creation possible, bringing modern biomedicine to a new level. In this review, we are focused on the currently existing platforms for targeted self-assembling protein nanoparticles based on transferrin, lactoferrin, casein, lumazine synthase, albumin, ferritin, and encapsulin proteins, as well as on proteins from magnetosomes and virus-like particles. The applications of these self-assembling proteins for targeted delivery in vitro and in vivo are thoroughly discussed, including bioimaging applications and different therapeutic approaches, such as chemotherapy, gene delivery, and photodynamic and photothermal therapy. A critical assessment of these protein platforms' efficacy in biomedicine is provided and possible problems associated with their further development are described.
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Affiliation(s)
| | | | | | - Anna M. Iureva
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Vera L. Kovalenko
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Fedor A. Zavalko
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | | | | | - Elizaveta N. Mochalova
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Nanobiomedicine Division, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Victoria O. Shipunova
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Nanobiomedicine Division, Sirius University of Science and Technology, 354340 Sochi, Russia
- Correspondence:
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8
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Bitzenhofer NL, Hilgers F, Bosio GN, Torra J, Casini G, Beinlich FRM, Knieps-Grünhagen E, Gordeliy V, Jaeger KE, Nonell S, Krauss U, Gensch T, Drepper T. Development and Characterization of Flavin-Binding Fluorescent Proteins, Part II: Advanced Characterization. Methods Mol Biol 2023; 2564:143-183. [PMID: 36107341 DOI: 10.1007/978-1-0716-2667-2_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Flavin-based fluorescent proteins (FbFPs), a class of small fluorescent proteins derived from light-oxygen-voltage (LOV) domains, bind ubiquitous endogenous flavins as chromophores. Due to their unique properties, they can be used as versatile in vivo reporter proteins under aerobic and anaerobic conditions. This chapter presents methodologies for in-depth characterization of the biochemical, spectroscopic, photophysical, and photochemical properties of FbFPs.
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Affiliation(s)
- Nora Lisa Bitzenhofer
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Gabriela N Bosio
- Institute of Biological Information Processing IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Joaquim Torra
- Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
| | - Giorgia Casini
- Institute of Biological Information Processing IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Felix R M Beinlich
- Institute of Biological Information Processing IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Esther Knieps-Grünhagen
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Valentin Gordeliy
- Institute of Bio-and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Institute of Biological Information Processing IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain.
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Thomas Gensch
- Institute of Biological Information Processing IBI-1: Molecular and Cellular Physiology, Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.
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9
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Zhuang B, Liebl U, Vos MH. Flavoprotein Photochemistry: Fundamental Processes and Photocatalytic Perspectives. J Phys Chem B 2022; 126:3199-3207. [PMID: 35442696 DOI: 10.1021/acs.jpcb.2c00969] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Flavins are highly versatile redox-active and colored cofactors in a large variety of proteins. These do include photoenzymes and photoreceptors, although the vast majority performs non-light-driven physiological functions. Nevertheless, electron transfer between flavins and specific nearby amino acid residues (in particular tyrosine, tryptophan, and presumably histidine and arginine) takes place upon excitation of flavin in many flavoproteins. For oxidized flavoproteins these reactions potentially have a photoprotective role. In this Perspective, we outline work on the characterization of early reaction intermediates not only in the relatively well-studied resting oxidized forms but also in the fully reduced and the intrinsically unstable semireduced forms, where ultrafast photooxidation of flavin was recently demonstrated. Along different lines, flavoprotein-based novel photocatalysts for biotechnological applications are presently emerging, employing both substrate photooxidation and photoreduction strategies. Deep insight into the fundamental flavin photochemical reactions may help in guiding and optimizing their development and in the exploration of novel photocatalytic approaches.
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Affiliation(s)
- Bo Zhuang
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Ursula Liebl
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
| | - Marten H Vos
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau Cedex, France
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10
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Zerlotti R, Losi A, Polverini E. Oxygen diffusion pathways in mutated forms of a LOV photoreceptor from Methylobacterium radiotolerans: A molecular dynamics study. Biomol Concepts 2022; 13:164-174. [DOI: 10.1515/bmc-2022-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/08/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Mr4511 from Methylobacterium radiotolerans is a photoreceptor of the light, oxygen voltage (LOV) family, binding flavin mononucleotide (FMN) as a chromophore. It exhibits the prototypical LOV photocycle, with the reversible formation of an FMN-Cys71 adduct via fast decay of the FMN triplet state. Mr4511 has high potential as a photosensitiser for singlet oxygen (SO) upon mutation of C71. Mr4511-C71S shows a triplet lifetime (τ
T) of several hundreds of microseconds, ensuring efficient energy transfer to dioxygen to form SO. In this work, we have explored the potential diffusion pathways for dioxygen within Mr4511 using molecular dynamics (MD) simulations. The structural model of wild-type (wt) Mr4511 showed a dimeric structure stabilised by a strong leucine zipper at the two C-terminal helical ends. We then introduced in silico the C71S mutation and analysed transient and persistent oxygen channels. MD simulations indicate that the chromophore binding site is highly accessible to dioxygen. Mutations that might favour SO generation were designed based on their position with respect to FMN and the oxygen channels. In particular, the C71S-Y61T and C71S-Y61S variants showed an increased diffusion and persistence of oxygen molecules inside the binding cavity.
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Affiliation(s)
- Rocco Zerlotti
- NeuroTrans ETN Network c/o Nanion Technologies GmbH, Ganghoferstraße 70/a , 80339 München , Bayern , Germany
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A , 43124 Parma , Italy
| | - Aba Losi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A , 43124 Parma , Italy
| | - Eugenia Polverini
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A , 43124 Parma , Italy
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11
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Lafaye C, Aumonier S, Torra J, Signor L, von Stetten D, Noirclerc-Savoye M, Shu X, Ruiz-González R, Gotthard G, Royant A, Nonell S. Riboflavin-binding proteins for singlet oxygen production. Photochem Photobiol Sci 2022; 21:1545-1555. [PMID: 35041199 DOI: 10.1007/s43630-021-00156-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022]
Abstract
miniSOG, developed as the first fully genetically encoded singlet oxygen photosensitiser, has found various applications in cell imaging and functional studies. Yet, miniSOG has suboptimal properties, including a low yield of singlet oxygen generation, which can nevertheless be improved tenfold upon blue light irradiation. In a previous study, we showed that this improvement was due to the photolysis of the miniSOG chromophore, flavin mononucleotide (FMN), into lumichrome, with concomitant removal of the phosphoribityl tail, thereby improving oxygen access to the alloxazine ring. We thus reasoned that a chromophore with a shorter tail would readily improve the photosensitizing properties of miniSOG. In this work, we show that the replacement of FMN by riboflavin (RF), which lacks the bulky phosphate group, significantly improves the singlet oxygen quantum yield (ΦΔ). We then proceeded to mutagenize the residues stabilizing the phosphate group of FMN to alter the chromophore specificity. We identified miniSOG-R57Q as a flavoprotein that selectively binds RF in cellulo, with a modestly improved ΦΔ. Our results show that it is possible to modify the flavin specificity of a given flavoprotein, thus providing a new option to tune its photophysical properties, including those leading to photosensitization. We also determined the structure of miniSOG-Q103L, a mutant with a much increased ΦΔ, which allowed us to postulate the existence of another access channel to FMN for molecular oxygen.
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Affiliation(s)
- Céline Lafaye
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
| | - Sylvain Aumonier
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France
| | - Joaquim Torra
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Luca Signor
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
| | - David von Stetten
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France
| | - Marjolaine Noirclerc-Savoye
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, 94158-9001, USA.,Cardiovascular Research Institute, University of California-San Francisco, San Francisco, CA, 94158-9001, USA
| | - Rubén Ruiz-González
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain
| | - Guillaume Gotthard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France
| | - Antoine Royant
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044, Grenoble Cedex 9, France. .,European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043, Grenoble Cedex 9, France.
| | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017, Barcelona, Spain.
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12
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Delcanale P, Abbruzzetti S, Viappiani C. Photodynamic treatment of pathogens. LA RIVISTA DEL NUOVO CIMENTO 2022; 45:407-459. [PMCID: PMC8921710 DOI: 10.1007/s40766-022-00031-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/10/2022] [Indexed: 06/01/2023]
Abstract
The current viral pandemic has highlighted the compelling need for effective and versatile treatments, that can be quickly tuned to tackle new threats, and are robust against mutations. Development of such treatments is made even more urgent in view of the decreasing effectiveness of current antibiotics, that makes microbial infections the next emerging global threat. Photodynamic effect is one such method. It relies on physical processes proceeding from excited states of particular organic molecules, called photosensitizers, generated upon absorption of visible or near infrared light. The excited states of these molecules, tailored to undergo efficient intersystem crossing, interact with molecular oxygen and generate short lived reactive oxygen species (ROS), mostly singlet oxygen. These species are highly cytotoxic through non-specific oxidation reactions and constitute the basis of the treatment. In spite of the apparent simplicity of the principle, the method still has to face important challenges. For instance, the short lifetime of ROS means that the photosensitizer must reach the target within a few tens nanometers, which requires proper molecular engineering at the nanoscale level. Photoactive nanostructures thus engineered should ideally comprise a functionality that turns the system into a theranostic means, for instance, through introduction of fluorophores suitable for nanoscopy. We discuss the principles of the method and the current molecular strategies that have been and still are being explored in antimicrobial and antiviral photodynamic treatment.
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Affiliation(s)
- Pietro Delcanale
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
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13
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Engel KL, Lo HYG, Goering R, Li Y, Spitale RC, Taliaferro JM. Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq. Nucleic Acids Res 2021; 50:e24. [PMID: 34875090 PMCID: PMC8887463 DOI: 10.1093/nar/gkab1185] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/26/2021] [Accepted: 11/16/2021] [Indexed: 12/22/2022] Open
Abstract
Thousands of RNA species display nonuniform distribution within cells. However, quantification of the spatial patterns adopted by individual RNAs remains difficult, in part by a lack of quantitative tools for subcellular transcriptome analysis. In this study, we describe an RNA proximity labeling method that facilitates the quantification of subcellular RNA populations with high spatial specificity. This method, termed Halo-seq, pairs a light-activatable, radical generating small molecule with highly efficient Click chemistry to efficiently label and purify spatially defined RNA samples. We compared Halo-seq with previously reported similar methods and found that Halo-seq displayed a higher efficiency of RNA labeling, indicating that it is well suited to the investigation of small, precisely localized RNA populations. We then used Halo-seq to quantify nuclear, nucleolar and cytoplasmic transcriptomes, characterize their dynamic nature following perturbation, and identify RNA sequence features associated with their composition. Specifically, we found that RNAs containing AU-rich elements are relatively enriched in the nucleus. This enrichment becomes stronger upon treatment with the nuclear export inhibitor leptomycin B, both expanding the role of HuR in RNA export and generating a comprehensive set of transcripts whose export from the nucleus depends on HuR.
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Affiliation(s)
- Krysta L Engel
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hei-Yong G Lo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ying Li
- Department of Chemistry, Hong Kong University
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA.,Department of Chemistry, University of California Irvine, Irvine, CA, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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14
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Smolentseva A, Goncharov IM, Yudenko A, Bogorodskiy A, Semenov O, Nazarenko VV, Borshchevskiy V, Fonin AV, Remeeva A, Jaeger KE, Krauss U, Gordeliy V, Gushchin I. Extreme dependence of Chloroflexus aggregans LOV domain thermo- and photostability on the bound flavin species. Photochem Photobiol Sci 2021; 20:1645-1656. [PMID: 34796467 DOI: 10.1007/s43630-021-00138-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/08/2021] [Indexed: 01/10/2023]
Abstract
Light-oxygen-voltage (LOV) domains are common photosensory modules that found many applications in fluorescence microscopy and optogenetics. Here, we show that the Chloroflexus aggregans LOV domain can bind different flavin species (lumichrome, LC; riboflavin, RF; flavin mononucleotide, FMN; flavin adenine dinucleotide, FAD) during heterologous expression and that its physicochemical properties depend strongly on the nature of the bound flavin. We show that whereas the dissociation constants for different chromophores are similar, the melting temperature of the protein reconstituted with single flavin species varies from ~ 60 °C for LC to ~ 81 °C for FMN, and photobleaching half-times vary almost 100-fold. These observations serve as a caution for future studies of LOV domains in non-native conditions yet raise the possibility of fine-tuning various properties of LOV-based fluorescent probes and optogenetic tools by manipulating the chromophore composition.
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Affiliation(s)
- Anastasia Smolentseva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan M Goncharov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vera V Nazarenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Biological Information Processing IBI-7: Structural Biochemistry, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alexander V Fonin
- Institute of Cytology, Russian Academy of Sciences, 194064, Saint Petersburg, Russia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ulrich Krauss
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, 38000, Grenoble, France.,Institute of Biological Information Processing IBI-7: Structural Biochemistry, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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15
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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] [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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16
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Van de Steen A, Khalife R, Colant N, Mustafa Khan H, Deveikis M, Charalambous S, Robinson CM, Dabas R, Esteban Serna S, Catana DA, Pildish K, Kalinovskiy V, Gustafsson K, Frank S. Bioengineering bacterial encapsulin nanocompartments as targeted drug delivery system. Synth Syst Biotechnol 2021; 6:231-241. [PMID: 34541345 PMCID: PMC8435816 DOI: 10.1016/j.synbio.2021.09.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 11/21/2022] Open
Abstract
The development of Drug Delivery Systems (DDS) has led to increasingly efficient therapies for the treatment and detection of various diseases. DDS use a range of nanoscale delivery platforms produced from polymeric of inorganic materials, such as micelles, and metal and polymeric nanoparticles, but their variant chemical composition make alterations to their size, shape, or structures inherently complex. Genetically encoded protein nanocages are highly promising DDS candidates because of their modular composition, ease of recombinant production in a range of hosts, control over assembly and loading of cargo molecules and biodegradability. One example of naturally occurring nanocompartments are encapsulins, recently discovered bacterial organelles that have been shown to be reprogrammable as nanobioreactors and vaccine candidates. Here we report the design and application of a targeted DDS platform based on the Thermotoga maritima encapsulin reprogrammed to display an antibody mimic protein called Designed Ankyrin repeat protein (DARPin) on the outer surface and to encapsulate a cytotoxic payload. The DARPin9.29 chosen in this study specifically binds to human epidermal growth factor receptor 2 (HER2) on breast cancer cells, as demonstrated in an in vitro cell culture model. The encapsulin-based DDS is assembled in one step in vivo by co-expressing the encapsulin-DARPin9.29 fusion protein with an engineered flavin-binding protein mini-singlet oxygen generator (MiniSOG), from a single plasmid in Escherichia coli. Purified encapsulin-DARPin_miniSOG nanocompartments bind specifically to HER2 positive breast cancer cells and trigger apoptosis, indicating that the system is functional and specific. The DDS is modular and has the potential to form the basis of a multi-receptor targeted system by utilising the DARPin screening libraries, allowing use of new DARPins of known specificities, and through the proven flexibility of the encapsulin cargo loading mechanism, allowing selection of cargo proteins of choice.
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Key Words
- Annexin V-FITC, Annexin V-Fluorescein IsoThiocyanate Conjugate
- Cytotoxic protein
- DARPin
- DARPin9.29, Designed Ankyrin Repeat Protein 9.29
- DDS, Drug Delivery System
- Drug delivery system
- EPR, Enhanced Permeability and Retention effect
- Encapsulin
- HER2, Human Epidermal growth factor Receptor 2
- His6, Hexahistidine
- MSCs, Mesenchymal Stem Cells
- NPs, NanoParticles
- SK-BR-3, Sloan-Kettering Breast cancer cell line/HER2-overexpressing human breast cancer cell line
- STII, StrepII-tag, an eight-residue peptide sequence (Trp-Ser-His-Pro-Gln-Phe-Glu-Lys) with intrinsic affinity toward streptavidin that can be fused to recombinant protein in various fashions
- T. maritima, Thermotoga maritima
- VLPs, Virus-Like Particle
- iGEM, international Genetically Engineered Machine
- iLOV, improved Light, Oxygen or Voltage-sensing flavoprotein
- mScarlet, a bright monomeric red fluorescent protein
- miniSOG, mini-Singlet Oxygen Generator
- rTurboGFP, recombinant Turbo Green Fluorescent Protein
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Affiliation(s)
| | - Rana Khalife
- Department of Biochemical Engineering, University College London, UK
| | - Noelle Colant
- Department of Biochemical Engineering, University College London, UK
| | | | - Matas Deveikis
- Department of Biochemical Engineering, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Saverio Charalambous
- Department of Biochemical Engineering, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Clare M. Robinson
- Natural Sciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Rupali Dabas
- Natural Sciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Sofia Esteban Serna
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Diana A. Catana
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Konstantin Pildish
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Vladimir Kalinovskiy
- Division of Biosciences, University College London, UK
- UCL iGEM Student Team 2019, UK
| | - Kenth Gustafsson
- Department of Biochemical Engineering, University College London, UK
| | - Stefanie Frank
- Department of Biochemical Engineering, University College London, UK
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17
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Ding Y, Zhao Z, Matysik J, Gärtner W, Losi A. Mapping the role of aromatic amino acids within a blue-light sensing LOV domain. Phys Chem Chem Phys 2021; 23:16767-16775. [PMID: 34319324 DOI: 10.1039/d1cp02217b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Photosensing LOV (Light, Oxygen, Voltage) domains detect and respond to UVA/Blue (BL) light by forming a covalent adduct between the flavin chromophore and a nearby cysteine, via the decay of the flavin triplet excited state. LOV domains where the reactive cysteine has been mutated are valuable fluorescent tools for microscopy and as genetically encoded photosensitisers for reactive oxygen species. Besides being convenient tools for applications, LOV domains without the reactive cysteine (naturally occurring or engineered) can still be functionally photoactivated via formation of a neutral flavin radical. Tryptophans and tyrosines are held as the main partners as potential electron donors to the flavin excited states. In this work, we explore the relevance of aromatic amino acids in determining the photophysical features of the LOV protein Mr4511 from Methylobacterium radiotolerans by introducing point mutations into the C71S variant that does not form the covalent adduct. By using an array of spectroscopic techniques we measured the fluorescence quantum yields and lifetimes, the triplet yields and lifetimes, and the efficiency of singlet oxygen (SO) formation for eleven Mr4511 variants. Insertion of Trp residues at distances between 0.6 and 1.5 nm from the flavin chromophore results in strong quenching of the flavin excited triplet state and, at the shorter distances even of the singlet excited state. The mutation F130W (ca. 0.6 nm) completely quenches the singlet excited state, preventing triplet formation: in this case, even if the cysteine is present, the photo-adduct is not formed. Tyrosines are also quenchers for the flavin excited states, although not as efficient as Trp residues, as demonstrated with their substitution with the inert phenylalanine. For one of these variants, C71S/Y116F, we found that the quantum yield of formation for singlet oxygen is 0.44 in aqueous aerobic solution, vs 0.17 for C71S. Based on our study with Mr4511 and on literature data for other LOV domains we suggest that Trp and Tyr residues too close to the flavin chromophore (at distances less than 0.9 nm) reduce the yield of photoproduct formation and that introduction of inert Phe residues in key positions can help in developing efficient, LOV-based photosensitisers.
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Affiliation(s)
- Yonghong Ding
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany
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18
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Hovan A, Berta M, Sedláková D, Miskovsky P, Bánó G, Sedlák E. Heme is responsible for enhanced singlet oxygen deactivation in cytochrome c. Phys Chem Chem Phys 2021; 23:15557-15563. [PMID: 34259248 DOI: 10.1039/d1cp01517f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The deactivation of singlet oxygen, the lowest electronic excited state of molecular oxygen, by proteins is usually described through the interaction of singlet oxygen with certain amino acids. Changes in accessibility of these amino acids influence the quenching rate and the phosphorescence kinetics of singlet oxygen. In the cellular environment, however, numerous proteins with covalently bound or encapsulated cofactors are present. These cofactors could also influence the deactivation of singlet oxygen, and these have received little attention. To confront this issue, we used cytochrome c (cyt c) and apocytochrome c (apocyt c) to illustrate how the heme prosthetic group influences the rate constant of singlet oxygen deactivation upon acidic pH-induced conformational change of cyt c. Photo-excited flavin mononucleotide (FMN) was used to produce singlet oxygen. Our data show that the heme group has a significant and measurable effect on singlet oxygen quenching when the heme is exposed to solvents and is therefore more accessible to singlet oxygen. The effect of amino acids and heme accessibility on the FMN triplet state deactivation was also investigated.
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Affiliation(s)
- Andrej Hovan
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia.
| | - Martin Berta
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia.
| | - Dagmar Sedláková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - Pavol Miskovsky
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia. and SAFTRA Photonics Ltd., Moldavská cesta 51, 040 11 Košice, Slovakia
| | - Gregor Bánó
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia.
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia.
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19
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Gabarre S, Vernaillen F, Baatsen P, Vints K, Cawthorne C, Boeynaems S, Michiels E, Vandael D, Gounko NV, Munck S. A workflow for streamlined acquisition and correlation of serial regions of interest in array tomography. BMC Biol 2021; 19:152. [PMID: 34330271 PMCID: PMC8323292 DOI: 10.1186/s12915-021-01072-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 06/14/2021] [Indexed: 11/20/2022] Open
Abstract
Background Array tomography (AT) is a high-resolution imaging method to resolve fine details at the organelle level and has the advantage that it can provide 3D volumes to show the tissue context. AT can be carried out in a correlative way, combing light and electron microscopy (LM, EM) techniques. However, the correlation between modalities can be a challenge and delineating specific regions of interest in consecutive sections can be time-consuming. Integrated light and electron microscopes (iLEMs) offer the possibility to provide well-correlated images and may pose an ideal solution for correlative AT. Here, we report a workflow to automate navigation between regions of interest. Results We use a targeted approach that allows imaging specific tissue features, like organelles, cell processes, and nuclei at different scales to enable fast, directly correlated in situ AT using an integrated light and electron microscope (iLEM-AT). Our workflow is based on the detection of section boundaries on an initial transmitted light acquisition that serves as a reference space to compensate for changes in shape between sections, and we apply a stepwise refinement of localizations as the magnification increases from LM to EM. With minimal user interaction, this enables autonomous and speedy acquisition of regions containing cells and cellular organelles of interest correlated across different magnifications for LM and EM modalities, providing a more efficient way to obtain 3D images. We provide a proof of concept of our approach and the developed software tools using both Golgi neuronal impregnation staining and fluorescently labeled protein condensates in cells. Conclusions Our method facilitates tracing and reconstructing cellular structures over multiple sections, is targeted at high resolution ILEMs, and can be integrated into existing devices, both commercial and custom-built systems. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01072-7.
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Affiliation(s)
- Sergio Gabarre
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Frank Vernaillen
- VIB BioInformatics Core, Technologiepark 75, 9052, Ghent, Belgium
| | - Pieter Baatsen
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | | | - Steven Boeynaems
- Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Emiel Michiels
- VIB Center for Brain and Disease Research, 3000, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, 3000, Leuven, Belgium
| | - Dorien Vandael
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium
| | - Natalia V Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium. .,KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.
| | - Sebastian Munck
- KU Leuven Department of Neurosciences, Leuven Brain Institute, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium. .,VIB-KU Leuven Center for Brain & Disease Research, Light Microscopy Expertise Unit & VIB BioImaging Core, O&N5 Herestraat 49 box 602, 3000, Leuven, Belgium.
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20
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Rodríguez JM, Allende-Ballestero C, Cornelissen JJLM, Castón JR. Nanotechnological Applications Based on Bacterial Encapsulins. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1467. [PMID: 34206092 PMCID: PMC8229669 DOI: 10.3390/nano11061467] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/23/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023]
Abstract
Encapsulins are proteinaceous nanocontainers, constructed by a single species of shell protein that self-assemble into 20-40 nm icosahedral particles. Encapsulins are structurally similar to the capsids of viruses of the HK97-like lineage, to which they are evolutionarily related. Nearly all these nanocontainers encase a single oligomeric protein that defines the physiological role of the complex, although a few encapsulate several activities within a single particle. Encapsulins are abundant in bacteria and archaea, in which they participate in regulation of oxidative stress, detoxification, and homeostasis of key chemical elements. These nanocontainers are physically robust, contain numerous pores that permit metabolite flux through the shell, and are very tolerant of genetic manipulation. There are natural mechanisms for efficient functionalization of the outer and inner shell surfaces, and for the in vivo and in vitro internalization of heterologous proteins. These characteristics render encapsulin an excellent platform for the development of biotechnological applications. Here we provide an overview of current knowledge of encapsulin systems, summarize the remarkable toolbox developed by researchers in this field, and discuss recent advances in the biomedical and bioengineering applications of encapsulins.
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Affiliation(s)
- Javier M. Rodríguez
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
| | - Carolina Allende-Ballestero
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
| | - Jeroen J. L. M. Cornelissen
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands;
| | - José R. Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049 Madrid, Spain; (J.M.R.); (C.A.-B.)
- Nanobiotechnology Associated Unit CNB-CSIC-IMDEA, Campus Cantoblanco, 28049 Madrid, Spain
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21
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Gurruchaga-Pereda J, Martínez-Martínez V, Formoso E, Azpitarte O, Rezabal E, Lopez X, Cortajarena AL, Salassa L. Enhancing the Photocatalytic Conversion of Pt(IV) Substrates by Flavoprotein Engineering. J Phys Chem Lett 2021; 12:4504-4508. [PMID: 33960797 DOI: 10.1021/acs.jpclett.1c00802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Our recent work demonstrates that certain flavoproteins can catalyze the redox activation of Pt(IV) prodrug complexes under light irradiation. Herein, we used site-directed mutagenesis on the mini singlet oxygen generator (mSOG) to modulate the photocatalytic activity of this flavoprotein toward two model Pt(IV) substrates. Among the prepared mutants, Q103V mSOG displayed enhanced catalytic efficiency as a result of its longer triplet excited-state lifetime. This study shows, for the first time, that protein engineering can improve the catalytic capacity of a protein toward metal-containing substrates.
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Affiliation(s)
- Juan Gurruchaga-Pereda
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia 20018, Spain
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia, San Sebastián 20014, Spain
| | | | - Elena Formoso
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia 20018, Spain
- Kimika Fisikoa, Farmazia Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Paseo de la Universidad 7, Vitoria-Gasteiz 01006, Spain
| | - Oksana Azpitarte
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia 20018, Spain
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Paseo Manuel de Lardizabal 3, Donostia 20018, Spain
| | - Elixabete Rezabal
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia 20018, Spain
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Paseo Manuel de Lardizabal 3, Donostia 20018, Spain
| | - Xabier Lopez
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia 20018, Spain
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Paseo Manuel de Lardizabal 3, Donostia 20018, Spain
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia, San Sebastián 20014, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao 48011, Spain
| | - Luca Salassa
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia 20018, Spain
- Polimero eta Material Aurreratuak: Fisika, Kimika eta Teknologia, Kimika Fakultatea, Euskal Herriko Unibertsitatea UPV/EHU, Paseo Manuel de Lardizabal 3, Donostia 20018, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao 48011, Spain
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22
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Mogensen DJ, Westberg M, Breitenbach T, Etzerodt M, Ogilby PR. Stable Transfection of the Singlet Oxygen Photosensitizing Protein SOPP3: Examining Aspects of Intracellular Behavior †. Photochem Photobiol 2021; 97:1417-1430. [PMID: 33934354 DOI: 10.1111/php.13440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/26/2021] [Indexed: 01/28/2023]
Abstract
Protein-encased chromophores that photosensitize the production of reactive oxygen species, ROS, have been the center of recent activity in studies of oxidative stress. One potential attribute of such systems is that the local environment surrounding the chromophore, and that determines the chromophore's photophysics, ideally remains constant and independent of the global environment into which the system is placed. Therefore, a protein-encased sensitizer localized in the mitochondria would arguably have the same photophysics as that protein-encased sensitizer at the plasma membrane, for example. One thus obtains a useful tool to study processes modulated by spatially localized ROS. One ROS of interest is singlet oxygen, O2 (a1 Δg ). We recently developed a singlet oxygen photosensitizing protein, SOPP, in which flavin mononucleotide, FMN, is encased in a re-engineered light-oxygen-voltage protein. One goal was to ascertain how a version of this system, SOPP3, which selectively makes O2 (a1 Δg ), in vitro, behaves in a cell. We now demonstrate that SOPP3 undergoes exacerbated irradiation-mediated bleaching when expressed at either the plasma membrane or mitochondria in stable cell lines. We find that the environment around the SOPP3 system affects the bleaching rate, which argues against one of the key suppositions in support of a protein-encased chromophore.
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Affiliation(s)
| | | | | | - Michael Etzerodt
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Peter R Ogilby
- Department of Chemistry, Aarhus University, Aarhus, Denmark
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23
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Dichmann L, Bregnhøj M, Liu H, Westberg M, Poulsen TB, Etzerodt M, Ogilby PR. Photophysics of a protein-bound derivative of malachite green that sensitizes the production of singlet oxygen. Photochem Photobiol Sci 2021; 20:435-449. [DOI: 10.1007/s43630-021-00032-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/23/2021] [Indexed: 12/25/2022]
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24
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van Galen C, Barnard DT, Stanley RJ. Stark Spectroscopy of Lumichrome: A Possible Candidate for Stand-Off Detection of Bacterial Quorum Sensing. J Phys Chem B 2020; 124:11835-11842. [PMID: 33325706 DOI: 10.1021/acs.jpcb.0c09498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Lumichrome (7,8-dimethylalloxazine, LC) is a natural photodegradation product and catabolite of flavin coenzymes. Although not a coenzyme itself, LC is used for biosignaling in plants and single-celled organisms, including quorum sensing in the formation of biofilms. The noninvasive detection of in vivo lumichrome would be useful for monitoring this signaling event. For molecules that undergo significant charge redistribution upon light excitation (e.g., intramolecular charge transfer), there are optical detection methods (e.g., second-harmonic generation) that would be well suited to this task. Here, we have used Stark spectroscopy to measure the extent and direction of charge redistribution in photoexcited LC. Stark and low-temperature absorption spectra were obtained at 77 K on LC in ethanol glasses and analyzed using the Liptay analysis to obtain the difference dipole moments and polarizabilities. These data were complemented by a computational analysis of the excited states using density functional theory (DFT) at the TD-B3LYP/6-311+G(2d,p) level of theory.
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Affiliation(s)
- Cornelius van Galen
- Department of Chemistry, Temple University, 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - David T Barnard
- Department of Chemistry, Temple University, 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University, 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
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25
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Das S, Tiwari M, Mondal D, Sahoo BR, Tiwari DK. Growing tool-kit of photosensitizers for clinical and non-clinical applications. J Mater Chem B 2020; 8:10897-10940. [PMID: 33165483 DOI: 10.1039/d0tb02085k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photosensitizers are photosensitive molecules utilized in clinical and non-clinical applications by taking advantage of light-mediated reactive oxygen generation, which triggers local and systemic cellular toxicity. Photosensitizers are used for diverse biological applications such as spatio-temporal inactivation of a protein in a living system by chromophore-assisted light inactivation, localized cell photoablation, photodynamic and immuno-photodynamic therapy, and correlative light-electron microscopy imaging. Substantial efforts have been made to develop several genetically encoded, chemically synthesized, and nanotechnologically driven photosensitizers for successful implementation in redox biology applications. Genetically encoded photosensitizers (GEPS) or reactive oxygen species (ROS) generating proteins have the advantage of using them in the living system since they can be manipulated by genetic engineering with a variety of target-specific genes for the precise spatio-temporal control of ROS generation. The GEPS variety is limited but is expanding with a variety of newly emerging GEPS proteins. Apart from GEPS, a large variety of chemically- and nanotechnologically-empowered photosensitizers have been developed with a major focus on photodynamic therapy-based cancer treatment alone or in combination with pre-existing treatment methods. Recently, immuno-photodynamic therapy has emerged as an effective cancer treatment method using smartly designed photosensitizers to initiate and engage the patient's immune system so as to empower the photosensitizing effect. In this review, we have discussed various types of photosensitizers, their clinical and non-clinical applications, and implementation toward intelligent efficacy, ROS efficiency, and target specificity in biological systems.
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Affiliation(s)
- Suman Das
- Department of Biotechnology, Faculty of Life Sciences and Environment, Goa University, Taleigao Plateau, Goa 403206, India.
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26
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Li Y, Cui ZJ. Photodynamic Activation of Cholecystokinin 1 Receptor with Different Genetically Encoded Protein Photosensitizers and from Varied Subcellular Sites. Biomolecules 2020; 10:biom10101423. [PMID: 33050050 PMCID: PMC7601527 DOI: 10.3390/biom10101423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
Cholecystokinin 1 receptor (CCK1R) is activated by singlet oxygen (1O2) generated in photodynamic action with sulphonated aluminum phthalocyanine (SALPC) or genetically encoded protein photosensitizer (GEPP) KillerRed or mini singlet oxygen generator (miniSOG). A large number of GEPP with varied 1O2 quantum yields have appeared recently; therefore, in the present work, the efficacy of different GEPP to photodynamically activate CCK1R was examined, as monitored by Fura-2 calcium imaging. KillerRed, miniSOG, miniSOG2, singlet oxygen protein photosensitizer (SOPP), flavin-binding fluorescent protein from Methylobacterium radiotolerans with point mutation C71G (Mr4511C71G), and flavin-binding fluorescent protein from Dinoroseobacter shibae (DsFbFP) were expressed at the plasma membrane (PM) in AR4-2J cells, which express endogenous CCK1R. Light irradiation (KillerRed: white light 85.3 mW‧cm-2, 4' and all others: LED 450 nm, 85 mW·cm-2, 1.5') of GEPPPM-expressing AR4-2J was found to all trigger persistent calcium oscillations, a hallmark of permanent photodynamic CCK1R activation; DsFbFP was the least effective, due to poor expression. miniSOG was targeted to PM, mitochondria (MT) or lysosomes (LS) in AR4-2J in parallel experiments; LED light irradiation was found to all induce persistent calcium oscillations. In miniSOGPM-AR4-2J cells, light emitting diode (LED) light irradiation-induced calcium oscillations were readily inhibited by CCK1R antagonist devazepide 2 nM; miniSOGMT-AR4-2J cells were less susceptible, but miniSOGLS-AR4-2J cells were not inhibited. In conclusion, different GEPPPM could all photodynamically activate CCK1R. Intracellular GEPP photodynamic action may prove particularly suited to study intracellular GPCR.
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27
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Aissa HB, Gautier A. Engineering Glowing Chemogenetic Hybrids for Spying on Cells. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hela Ben Aissa
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
| | - Arnaud Gautier
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
- Institut Universitaire de France Paris France
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28
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Binns TC, Ayala AX, Grimm JB, Tkachuk AN, Castillon GA, Phan S, Zhang L, Brown TA, Liu Z, Adams SR, Ellisman MH, Koyama M, Lavis LD. Rational Design of Bioavailable Photosensitizers for Manipulation and Imaging of Biological Systems. Cell Chem Biol 2020; 27:1063-1072.e7. [PMID: 32698018 PMCID: PMC7483975 DOI: 10.1016/j.chembiol.2020.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/04/2020] [Accepted: 06/29/2020] [Indexed: 01/14/2023]
Abstract
Light-mediated chemical reactions are powerful methods for manipulating and interrogating biological systems. Photosensitizers, compounds that generate reactive oxygen species upon excitation with light, can be utilized for numerous biological experiments, but the repertoire of bioavailable photosensitizers is limited. Here, we describe the synthesis, characterization, and utility of two photosensitizers based upon the widely used rhodamine scaffold and demonstrate their efficacy for chromophore-assisted light inactivation, cell ablation in culture and in vivo, and photopolymerization of diaminobenzidine for electron microscopy. These chemical tools will facilitate a broad range of applications spanning from targeted destruction of proteins to high-resolution imaging.
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Affiliation(s)
- Thomas C Binns
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Graduate School, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Anthony X Ayala
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ariana N Tkachuk
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Guillaume A Castillon
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sebastien Phan
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Lixia Zhang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Timothy A Brown
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Stephen R Adams
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Mark H Ellisman
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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29
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Li Y, Cui ZJ. NanoLuc Bioluminescence-Driven Photodynamic Activation of Cholecystokinin 1 Receptor with Genetically-Encoded Protein Photosensitizer MiniSOG. Int J Mol Sci 2020; 21:ijms21113763. [PMID: 32466589 PMCID: PMC7313028 DOI: 10.3390/ijms21113763] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 02/07/2023] Open
Abstract
In contrast to reversible activation by agonist, cholecystokinin 1 receptor (CCK1R) is permanently activated by singlet oxygen generated in photodynamic action, with sulphonated aluminium phthalocyanine or genetically encoded mini singlet oxygen generator (miniSOG) as photosensitizer. In these works, a halogen light source was used to power photodynamic action. For possible in vivo application of photodynamic CCK1R physiology, bearing a cumbersome light-delivery device connected to an external light source by experimental animals might interfere with their behavior. Therefore, in the present work, the possibility of bioluminescence-driven miniSOG photodynamic CCK1R activation was examined, as monitored by Fura-2 calcium imaging. In parallel experiments, it was found that, after plasma membrane (PM)-localized expression of miniSOGPM in AR4-2J cells, light irradiation with blue light-emitting diode (LED) (450 nm, 85 mW·cm-2, 1.5 min) induced persistent calcium oscillations that were blocked by CCK1R antagonist devazepide 2 nM. NanoLuc was expressed bicistronically with miniSOGPM via an internal ribosome entry site (IRES) sequence (pminiSOGPM-IRES-NanoLuc). The resultant miniSOGPM-IRES-NanoLuc-AR4-2J cells were found to generate strong bioluminescence upon addition of NanoLuc substrate coelenterazine. Strikingly, coelenterazine 5 microM was found to trigger long-lasting calcium oscillations (a hallmark for permanent CCK1R activation) in perifused miniSOGPM-IRES-NanoLuc-AR4-2J cells. These data indicate that NanoLuc bioluminescence can drive miniSOGPM photodynamic CCK1R activation, laying the foundation for its future in vivo applications.
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30
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Photoinduced damage of AsLOV2 domain is accompanied by increased singlet oxygen production due to flavin dissociation. Sci Rep 2020; 10:4119. [PMID: 32139757 PMCID: PMC7058016 DOI: 10.1038/s41598-020-60861-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 02/13/2020] [Indexed: 01/05/2023] Open
Abstract
Flavin mononucleotide (FMN) belongs to the group of very efficient endogenous photosensitizers producing singlet oxygen, 1O2, but with limited ability to be targeted. On the other hand, in genetically-encoded photosensitizers, which can be targeted by means of various tags, the efficiency of FMN to produce 1O2 is significantly diminished due to its interactions with surrounding amino acid residues. Recently, an increase of 1O2 production yield by FMN buried in a protein matrix was achieved by a decrease of quenching of the cofactor excited states by weakening of the protein-FMN interactions while still forming a complex. Here, we suggest an alternative approach which relies on the blue light irradiation-induced dissociation of FMN to solvent. This dissociation unlocks the full capacity of FMN as 1O2 producer. Our suggestion is based on the study of an irradiation effect on two variants of the LOV2 domain from Avena sativa; wild type, AsLOV2 wt, and the variant with a replaced cysteine residue, AsLOV2 C450A. We detected irradiation-induced conformational changes as well as oxidation of several amino acids in both AsLOV2 variants. Detailed analysis of these observations indicates that irradiation-induced increase in 1O2 production is caused by a release of FMN from the protein. Moreover, an increased FMN dissociation from AsLOV2 wt in comparison with AsLOV2 C450A points to a role of C450 oxidation in repelling the cofactor from the protein.
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31
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Hally C, Delcanale P, Nonell S, Viappiani C, Abbruzzetti S. Photosensitizing proteins for antibacterial photodynamic inactivation. TRANSLATIONAL BIOPHOTONICS 2020. [DOI: 10.1002/tbio.201900031] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Cormac Hally
- Institut Quimic de Sarrià, Universitat Ramon Llull Barcelona Spain
- Dipartimento di Scienze Matematiche, Fisiche e InformaticheUniversità di Parma Parma Italy
| | - Pietro Delcanale
- Institute for Bioengineering of Catalonia (IBEC), the Barcelona Institute of Science and Technology (BIST) Barcelona Spain
| | - Santi Nonell
- Institut Quimic de Sarrià, Universitat Ramon Llull Barcelona Spain
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e InformaticheUniversità di Parma Parma Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e InformaticheUniversità di Parma Parma Italy
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32
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Tang WZ, Cui ZJ. Permanent Photodynamic Activation of the Cholecystokinin 2 Receptor. Biomolecules 2020; 10:biom10020236. [PMID: 32033232 PMCID: PMC7072308 DOI: 10.3390/biom10020236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 02/07/2023] Open
Abstract
The cholecystokinin 2 receptor (CCK2R) is expressed in the central nervous system and peripheral tissues, playing an important role in higher nervous and gastrointestinal functions, pain sensation, and cancer growth. CCK2R is reversibly activated by cholecystokinin or gastrin, but whether it can be activated permanently is not known. In this work, we found that CCK2R expressed ectopically in CHO-K1 cells was permanently activated in the dark by sulfonated aluminum phthalocyanine (SALPC / AlPcS4, 10-1,000 nM), as monitored by Fura-2 fluorescent calcium imaging. Permanent CCK2R activation was also observed with AlPcS2, but not PcS4. CCK2R previously exposed to SALPC (3 and 10 nM) was sensitized by subsequent light irradiation (> 580 nm, 31.5 mW·cm-2). After the genetically encoded protein photosensitizer mini singlet oxygen generator (miniSOG) was fused to the N-terminus of CCK2R and expressed in CHO-K1 cells, light irradiation (450 nm, 85 mW·cm-2) activated in-frame CCK2R (miniSOG-CCK2R), permanently triggering persistent calcium oscillations blocked by the CCK2R antagonist YM 022 (30 nM). From these data, it is concluded that SALPC is a long-lasting CCK2R agonist in the dark, and CCK2R is photogenetically activated permanently with miniSOG as photosensitizer. These properties of SALPC and CCK2R could be used to study CCK2R physiology and possibly for pain and cancer therapies.
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33
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Gurruchaga-Pereda J, Martínez-Martínez V, Rezabal E, Lopez X, Garino C, Mancin F, Cortajarena AL, Salassa L. Flavin Bioorthogonal Photocatalysis Toward Platinum Substrates. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02863] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Juan Gurruchaga-Pereda
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain
- CIC biomaGUNE, Paseo de Miramón 182, Donostia, 20014, Spain
| | | | - Elixabete Rezabal
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, Donostia, 20080, Spain
| | - Xabier Lopez
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, UPV/EHU, Donostia, 20080, Spain
| | - Claudio Garino
- Department of Chemistry, University of Turin, via Pietro Giuria 7, Turin, 10125, Italy
| | - Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, Padova, 35131, Italy
| | - Aitziber L. Cortajarena
- CIC biomaGUNE, Paseo de Miramón 182, Donostia, 20014, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48011, Spain
| | - Luca Salassa
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, Donostia, 20018, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, 48011, Spain
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34
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Consiglieri E, Xu Q, Bregnhøj M, Westberg M, Ogilby PR, Losi A. Single mutation in a novel bacterial LOV protein yields a singlet oxygen generator. Photochem Photobiol Sci 2019; 18:2657-2660. [PMID: 31624823 DOI: 10.1039/c9pp00328b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mr4511 from Methylobacterium radiotolerans is a 164 amino acid protein built of a flavin mononucleotide (FMN) binding, blue-light responsive LOV (Light, Oxygen, Voltage) core domain plus flanking regions. In contrast to the majority of LOV domains, Mr4511 lacks a tryptophan residue that was previously identified as a major quencher for the FMN triplet state in photosensitizers for singlet oxygen (SO) engineered from these photoreceptors. Here we show that for Mr4511 it is sufficient to only mutate the reactive cysteine responsible for the photocycle (Cys71) in the native protein to generate an efficient SO photosensitizer: both C71S and C71G variants exhibit SO quantum yields of formation, ΦΔ, around 0.2 in air-saturated solutions. Under oxygen saturated conditions, ΦΔ reaches ∼0.5 in deuterated buffer. The introduction of Trp112 in the canonical position for LOV domains dramatically lowers ΦΔ to values comparable to miniSOG, one of the early FMN binding proteins touted as a SO sensitizer. Besides its SO properties, Mr4511 is also exceedingly robust against denaturation with urea and is more photostable than free FMN.
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Affiliation(s)
- Eleonora Consiglieri
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.
| | - Qianzhao Xu
- Institute for Analytical Chemistry, University of Leipzig, Linnéstrasse 3, 04103 Leipzig, Germany and State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mikkel Bregnhøj
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Michael Westberg
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Peter R Ogilby
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Aba Losi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.
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35
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Nazarenko VV, Remeeva A, Yudenko A, Kovalev K, Dubenko A, Goncharov IM, Kuzmichev P, Rogachev AV, Buslaev P, Borshchevskiy V, Mishin A, Dhoke GV, Schwaneberg U, Davari MD, Jaeger KE, Krauss U, Gordeliy V, Gushchin I. A thermostable flavin-based fluorescent protein from Chloroflexus aggregans: a framework for ultra-high resolution structural studies. Photochem Photobiol Sci 2019; 18:1793-1805. [DOI: 10.1039/c9pp00067d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A new thermostable fluorescent protein is shown to be a promising model for ultra-high resolution structural studies of LOV domains and for application as a fluorescent reporter.
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