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Nikolaev A, Tropina EV, Boldyrev KN, Maksimov EG, Borshchevskiy V, Mishin A, Yudenko A, Kuzmin A, Kuznetsova E, Semenov O, Remeeva A, Gushchin I. Two distinct mechanisms of flavoprotein spectral tuning revealed by low-temperature and time-dependent spectroscopy. Protein Sci 2024; 33:e4851. [PMID: 38038877 PMCID: PMC10731561 DOI: 10.1002/pro.4851] [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: 07/22/2023] [Revised: 10/22/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Flavins such as flavin mononucleotide or flavin adenine dinucleotide are bound by diverse proteins, yet have very similar spectra when in the oxidized state. Recently, we developed new variants of flavin-binding protein CagFbFP exhibiting notable blue (Q148V) or red (I52V A85Q) shifts of fluorescence emission maxima. Here, we use time-resolved and low-temperature spectroscopy to show that whereas the chromophore environment is static in Q148V, an additional protein-flavin hydrogen bond is formed upon photoexcitation in the I52V A85Q variant. Consequently, in Q148V, excitation, emission, and phosphorescence spectra are shifted, whereas in I52V A85Q, excitation and low-temperature phosphorescence spectra are relatively unchanged, while emission spectrum is altered. We also determine the x-ray structures of the two variants to reveal the flavin environment and complement the spectroscopy data. Our findings illustrate two distinct color-tuning mechanisms of flavin-binding proteins and could be helpful for the engineering of new variants with improved optical properties.
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Affiliation(s)
- Andrey Nikolaev
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elena V. Tropina
- Institute of Spectroscopy RASTroitskMoscowRussia
- National Research University Higher School of EconomicsMoscowRussia
| | | | | | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Anna Yudenko
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alexander Kuzmin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Elizaveta Kuznetsova
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Oleg Semenov
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Alina Remeeva
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age‐Related DiseasesMoscow Institute of Physics and TechnologyDolgoprudnyRussia
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Saady A, Wojtyniak M, Varon E, Böttner V, Kinor N, Shav-Tal Y, Ducho C, Fischer B. Specific, Sensitive, and Quantitative Detection of HER-2 mRNA Breast Cancer Marker by Fluorescent Light-Up Hybridization Probes. Bioconjug Chem 2020; 31:1188-1198. [DOI: 10.1021/acs.bioconjchem.0c00130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Abed Saady
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Melissa Wojtyniak
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Eli Varon
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Verena Böttner
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Noa Kinor
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Yaron Shav-Tal
- Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Christian Ducho
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Bilha Fischer
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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Mérola F, Erard M, Fredj A, Pasquier H. Engineering fluorescent proteins towards ultimate performances: lessons from the newly developed cyan variants. Methods Appl Fluoresc 2016. [DOI: 10.1088/2050-6120/4/1/012001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kyrychenko A. Using fluorescence for studies of biological membranes: a review. Methods Appl Fluoresc 2015; 3:042003. [DOI: 10.1088/2050-6120/3/4/042003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Pachón LA, Brumer P. Direct experimental determination of spectral densities of molecular complexes. J Chem Phys 2014; 141:174102. [DOI: 10.1063/1.4900512] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Leonardo A. Pachón
- Grupo de Física Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
- Chemical Physics Theory Group, Department of Chemistry and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Paul Brumer
- Chemical Physics Theory Group, Department of Chemistry and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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Mérola F, Fredj A, Betolngar DB, Ziegler C, Erard M, Pasquier H. Newly engineered cyan fluorescent proteins with enhanced performances for live cell FRET imaging. Biotechnol J 2013; 9:180-91. [DOI: 10.1002/biot.201300198] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/17/2013] [Accepted: 10/31/2013] [Indexed: 11/06/2022]
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Gaytán P, Roldán-Salgado A. Elimination of redundant and stop codons during the chemical synthesis of degenerate oligonucleotides. Combinatorial testing on the chromophore region of the red fluorescent protein mKate. ACS Synth Biol 2013; 2:453-62. [PMID: 23654278 DOI: 10.1021/sb3001326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although some strategies have been reported for the elimination of stop and redundant codons during the chemical synthesis of degenerate oligonucleotides, incorporating an expensive cocktail of 20 trimer-phosphoramidites is currently a commonly employed and straightforward approach. As an alternative option, we describe here a cheaper strategy based on standard monomer-phosphoramidites and a simplified resin-splitting procedure. The accurate division of the resin, containing the growing oligonucleotide, into four columns represents the key step in this approach. The synthesis of the degenerate codon NDT in column 1, loaded with 60% of the resin, produces 12 codons, while a degenerate codon VMA in column 2, loaded with 30% of the resin, produces 6 codons. Codons ATG and TGG, independently synthesized in columns 3 and 4, respectively, and loaded with 5% each, completes the 20 different codons. The experimental frequency of each mutant codon in the library was assessed by randomizing 12 contiguous codons that encode for amino acids located in the chromophore region of the enhanced red fluorescent protein mKate-S158A. Furthermore, randomization of three contiguous codons that encode for the amino acids Phe62, Met63, and Tyr64, which are equivalent to Phe64, Ser65, and Tyr66 in GFP, gave rise to some red and golden yellow fluorescent mutants displaying interesting phenotypes and spectroscopic properties. The absorption and emission spectra of two of these mutants also suggested that the complete maturation of the red and golden yellow chromophores in mKate proceeds via the formation of a green-type chromophore and a cyan-type chromophore, respectively.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología-Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México.
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The single T65S mutation generates brighter cyan fluorescent proteins with increased photostability and pH insensitivity. PLoS One 2012; 7:e49149. [PMID: 23133673 PMCID: PMC3487735 DOI: 10.1371/journal.pone.0049149] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 10/04/2012] [Indexed: 02/03/2023] Open
Abstract
Cyan fluorescent proteins (CFP) derived from Aequorea victoria GFP, carrying a tryptophan-based chromophore, are widely used as FRET donors in live cell fluorescence imaging experiments. Recently, several CFP variants with near-ultimate photophysical performances were obtained through a mix of site-directed and large scale random mutagenesis. To understand the structural bases of these improvements, we have studied more specifically the consequences of the single-site T65S mutation. We find that all CFP variants carrying the T65S mutation not only display an increased fluorescence quantum yield and a simpler fluorescence emission decay, but also show an improved pH stability and strongly reduced reversible photoswitching reactions. Most prominently, the Cerulean-T65S variant reaches performances nearly equivalent to those of mTurquoise, with QY = 0.84, an almost pure single exponential fluorescence decay and an outstanding stability in the acid pH range (pK1/2 = 3.6). From the detailed examination of crystallographic structures of different CFPs and GFPs, we conclude that these improvements stem from a shift in the thermodynamic balance between two well defined configurations of the residue 65 hydroxyl. These two configurations differ in their relative stabilization of a rigid chromophore, as well as in relaying the effects of Glu222 protonation at acid pHs. Our results suggest a simple method to greatly improve numerous FRET reporters used in cell imaging, and bring novel insights into the general structure-photophysics relationships of fluorescent proteins.
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Olsen S, McKenzie RH. A two-state model of twisted intramolecular charge-transfer in monomethine dyes. J Chem Phys 2012; 137:164319. [DOI: 10.1063/1.4762561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Jonasson G, Teuler JM, Vallverdu G, Mérola F, Ridard J, Lévy B, Demachy I. Excited State Dynamics of the Green Fluorescent Protein on the Nanosecond Time Scale. J Chem Theory Comput 2011; 7:1990-7. [DOI: 10.1021/ct200150r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Gabriella Jonasson
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Jean-Marie Teuler
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Germain Vallverdu
- Equipe de Chimie-Physique, IPREM, UMR5254, Université de Pau et des Pays de l′Adour, 64000 Pau, France
| | - Fabienne Mérola
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Jacqueline Ridard
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Bernard Lévy
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
| | - Isabelle Demachy
- Laboratoire de Chimie-Physique, UMR8000, CNRS, Université Paris-Sud 11, 91405 Orsay Cedex, France
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Organic Dyes with Excited-State Transformations (Electron, Charge, and Proton Transfers). SPRINGER SERIES ON FLUORESCENCE 2010. [DOI: 10.1007/978-3-642-04702-2_7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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