11 results on '"Baranov MS"'
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2. Total Synthesis of Racemic Thieno[3,2- f ]thiochromene Tricarboxylate, a Luciferin from Marine Polychaeta Odontosyllis undecimdonta .
- Author
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Bolt YV, Dubinnyi MA, Litvinenko VV, Kotlobay AA, Belozerova OA, Zagitova RI, Shmygarev VI, Yatskin ON, Guglya EB, Kublitski VS, Baranov MS, Yampolsky IV, Kaskova ZM, and Tsarkova AS
- Abstract
We report the first total synthesis of racemic Odontosyllis undecimdonta luciferin, a thieno[3,2- f ]thiochromene tricarboxylate comprising a 6-6-5-fused tricyclic skeleton with three sulfur atoms in different electronic states. The key transformation is based on tandem condensation of bifunctional thiol-phosphonate, obtained from dimethyl acetylene dicarboxylate, with benzothiophene-6,7-quinone. The presented convergent approach provides the synthesis of the target compound with a previously unreported fused heterocyclic core in 11 steps, thus allowing for unambiguous confirmation of the chemical structure of Odontosyllis luciferin by 2D-NMR spectroscopy.
- Published
- 2023
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3. Fluorescence Modulation of ortho -Green Fluorescent Protein Chromophores Following Ultrafast Proton Transfer in Solution.
- Author
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Boulanger SA, Chen C, Myasnyanko IN, Baranov MS, and Fang C
- Subjects
- Green Fluorescent Proteins chemistry, Hydrogen Bonding, Solvents, Spectrometry, Fluorescence, Protons, Spectrum Analysis, Raman
- Abstract
Photophysical and photochemical properties of the green fluorescent protein (GFP) chromophore and derivatives underlie their bioimaging applications. To date, ultrafast spectroscopic tools represent the key for unraveling fluorescence mechanisms toward rational design of this powerful biomimetic framework. To correlate the excited-state intramolecular proton transfer (ESIPT) with chromophore emission properties, we implement experimental and computational tool sets to elucidate real-time electronic and structural dynamics of two archetypal ortho -GFP chromophores ( o -HBDI and o -LHBDI) possessing an intramolecular hydrogen bond to undergo efficient ESIPT, only differing in a bridge-bond constraint. Using excited-state femtosecond stimulated Raman spectroscopy (FSRS), a low-frequency phenolic (P)-ring-deformation mode (∼562 cm
-1 ) was uncovered to accompany ESIPT. The tautomerized chromophore undergoes either rapid P-ring isomerization to reach the ground state with essentially no fluorescence for o -HBDI or enhanced (up to an impressive 180-fold in acetonitrile) and solvent-polarity-dependent fluorescence by P-ring locking in o -LHBDI. The significant dependence of the fluorescence enhancement ratio on solvent viscosity confirms P-ring isomerization as the dominant nonradiative decay pathway for o -HBDI. This work provides crucial insights into the dynamic solute-solvent electrostatic and steric interactions, enabling the application-specific improvement of ESIPT-capable molecules as versatile fluorescence-based sensors and imaging agents from large Stokes shift emission to brighter probes in physiological environments.- Published
- 2022
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4. Structure-Based Rational Design of Two Enhanced Bacterial Lipocalin Blc Tags for Protein-PAINT Super-resolution Microscopy.
- Author
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Muslinkina L, Gavrikov AS, Bozhanova NG, Mishin AS, Baranov MS, Meiler J, Pletneva NV, Pletnev VZ, and Pletnev S
- Subjects
- Amino Acid Sequence, Boron Compounds chemistry, Fluorescence, Fluorescent Dyes chemistry, HEK293 Cells, HeLa Cells, Humans, Lipocalins genetics, Microscopy, Fluorescence methods, Mutation, Protein Binding, Boron Compounds metabolism, Fluorescent Dyes metabolism, Keratins metabolism, Lipocalins metabolism, Vimentin metabolism
- Abstract
Super-resolution fluorescent imaging in living cells remains technically challenging, largely due to the photodecomposition of fluorescent tags. The recently suggested protein-PAINT is the only super-resolution technique available for prolonged imaging of proteins in living cells. It is realized with complexes of fluorogen-activating proteins, expressed as fusions, and solvatochromic synthetic dyes. Once photobleached, the dye in the complex is replaced with a fresh fluorogen available in the sample. With suitable kinetics, this replacement creates fluorescence blinking required for attaining super-resolution and overcomes photobleaching associated with the loss of an irreplaceable fluorophore. Here we report on the rational design of two protein-PAINT tags based on the 1.58 Å crystal structure of the DiB1:M739 complex, an improved green-emitting DiB3/F74V:M739 and a new orange-emitting DiB3/F53L:M739. They outperform previously reported DiB-based tags to become best in class biomarkers for protein-PAINT. The new tags advance protein-PAINT from the proof-of-concept to a reliable tool suitable for prolonged super-resolution imaging of intracellular proteins in fixed and living cells and two-color PAINT-like nanoscopy with a single fluorogen.
- Published
- 2020
- Full Text
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5. Imidazol-5-one as an Acceptor in Donor-Acceptor Cyclopropanes: Cycloaddition with Aldehydes.
- Author
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Mikhaylov AA, Kuleshov AV, Solyev PN, Korlyukov AA, Dorovatovskii PV, Mineev KS, and Baranov MS
- Abstract
Spiro[imidazol-5-one-4,1'-cyclopropanes] behave as donor-acceptor (D-A) cyclopropanes in a formal cycloaddition reaction with aldehydes. The activation of such type of cyclopropanes is achieved with an equivalent of Brønsted acid. The reaction proceeds in high yields of 51-92% and demonstrates moderate diastereoselectivity at the quaternary stereocenter, which is determined by the electron-donating nature of the aldehyde partner. The ease of separation of stereoisomers allowed the creation of a library of 44 spiroannulated tetrahydrofurans with various substitution patterns.
- Published
- 2020
- Full Text
- View/download PDF
6. Nitroacetic Esters in the Regioselective Synthesis of Isoxazole-3,5-dicarboxylic Acid Derivatives.
- Author
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Smirnov AY, Zaitseva ER, Belozerova OA, Alekseyev RS, Baleeva NS, Zagudaylova MB, Mikhaylov AA, and Baranov MS
- Abstract
An efficient and high-yielding strategy to prepare "unsymmetrical" 4-aryl-isoxazol-3,5-dicarboxylic acid derivatives from nitroacetic esters and aromatic aldehydes has been developed. The strategy is based on the isolation and usage of the previously missed intermediate of the Dornow reaction-5-hydroxy-6-oxo-4-aryl-6 H -1,2-oxazine-3-carboxylates. In addition, the mechanism of the Dornow reaction was partially revised.
- Published
- 2019
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7. Photoinduced Proton Transfer of GFP-Inspired Fluorescent Superphotoacids: Principles and Design.
- Author
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Chen C, Zhu L, Baranov MS, Tang L, Baleeva NS, Smirnov AY, Yampolsky IV, Solntsev KM, and Fang C
- Abstract
Proton transfer remains one of the most fundamental processes in chemistry and biology. Superphotoacids provide an excellent platform to delineate the excited-state proton transfer (ESPT) mechanism on ultrafast time scales and enable one to precisely control photoacidity and other pertinent functionalities such as fluorescence. We modified the GFP core ( p-HBDI chromophore) into two series of highly fluorescent photoacids by fluorinating the phenolic ring and conformationally locking the backbone (i.e., biomimetics). The trifluorinated derivatives, M3F and P3F, represent two of the strongest superphotoacids with p K
a * values of -5.0 and -5.5, respectively, and they can efficiently transfer a proton to organic solvents like methanol. Tunable femtosecond stimulated Raman spectroscopy (FSRS) and femtosecond transient absorption (fs-TA) were employed to dissect the ESPT of M3F and P3F in methanol, particularly with structural dynamics information. By virtue of resonantly enhanced FSRS signal and global analysis of fs-TA spectra, we revealed an inhomogeneous ESPT mechanism consisting of three parallel routes following the initial small-scale proton motion and contact ion-pair formation within ∼300 fs: The first route consists of ultrafast protolytic dissociation facilitated by the pre-existing, largely optimized H-bonding chain; the second route is limited by solvent reorientation that establishes a suitable H-bonding wire for proton separation; the third route is controlled by rotational diffusion that requires rotation of the anisotropically reactive photoacid in a bulky solvent with a complex H-bonding structure over larger distances. Furthermore, we provided new design principles of enhancing photoacidity in a synergistic manner: incorporating electron-withdrawing groups into proximal (often as "donor") and distal (often as "acceptor") ring moieties of the dissociative hydroxyl group to lower the ground-state p Ka and increase the Δp Ka , respectively.- Published
- 2019
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8. Pyridinium Analogues of Green Fluorescent Protein Chromophore: Fluorogenic Dyes with Large Solvent-Dependent Stokes Shift.
- Author
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Ermakova YG, Sen T, Bogdanova YA, Smirnov AY, Baleeva NS, Krylov AI, and Baranov MS
- Subjects
- Animals, HeLa Cells, Humans, Mice, Molecular Structure, NIH 3T3 Cells, Quantum Theory, Solvents chemistry, Fluorescent Dyes chemistry, Green Fluorescent Proteins chemistry, Pyridinium Compounds chemistry
- Abstract
Novel fluorogenic dyes based on the GFP chromophore are developed. The compounds contain a pyridinium ring instead of phenolate and feature large Stokes shifts and solvent-dependent variations in the fluorescence quantum yield. Electronic structure calculations explain the trends in solvatochromic behavior in terms of the increase of the dipole moment upon excited-state relaxation in polar solvents associated with the changes in bonding pattern in the excited state. A unique combination of such optical characteristics and lipophilic properties enables using one of the new dyes for imaging the membrane structure of endoplasmic reticulum. An extremely high photostability (due to a dynamic exchange between the free and absorbed states) and selectivity make this compound a promising label for this type of cellular organelles.
- Published
- 2018
- Full Text
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9. Unveiling Structural Motions of a Highly Fluorescent Superphotoacid by Locking and Fluorinating the GFP Chromophore in Solution.
- Author
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Chen C, Liu W, Baranov MS, Baleeva NS, Yampolsky IV, Zhu L, Wang Y, Shamir A, Solntsev KM, and Fang C
- Abstract
Superphotoacidity involves ultrafast proton motions implicated in numerous chemical and biological processes. We used conformational locking and strategic addition of electron-withdrawing substituents to synthesize a new GFP chromophore analogue: p-HO-3,5-diF-BDI:BF
2 (diF). It is highly fluorescent and exhibits excited-state proton transfer (ESPT) in various solvents, placing it among the strongest photoacids. Tunable femtosecond stimulated Raman spectroscopy with unique resonance conditions and transient absorption are complementarily employed to elucidate the structural basis for superphotoacidity. We reveal a multistep ESPT reaction from diF to methanol with an initial proton dissociation on the ∼600 fs time scale that forms a charge-separated state, stabilized by solvation, and followed by a diffusion-controlled proton transfer on the ∼350 ps time scale. A ∼1580 cm-1 phenolic ring motion is uncovered to accompany ESPT before 1 ps. This study provides a vivid movie of the photoinduced proton dissociation of a superphotoacid with bright fluorescence, effectively bridging fundamental mechanistic insights to precise control of macroscopic functions.- Published
- 2017
- Full Text
- View/download PDF
10. Yellow and Orange Fluorescent Proteins with Tryptophan-based Chromophores.
- Author
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Bozhanova NG, Baranov MS, Sarkisyan KS, Gritcenko R, Mineev KS, Golodukhina SV, Baleeva NS, Lukyanov KA, and Mishin AS
- Subjects
- Color, Computer Simulation, Fluorescent Dyes chemical synthesis, Hydrogen-Ion Concentration, Ketones chemistry, Molecular Structure, Protein Isoforms chemistry, Red Fluorescent Protein, Fluorescent Dyes chemistry, Luminescent Proteins chemistry, Luminescent Proteins genetics, Staining and Labeling methods, Tryptophan chemistry
- Abstract
Rapid development of new microscopy techniques exposed the need for genetically encoded fluorescent tags with special properties. Recent works demonstrated the potential of fluorescent proteins with tryptophan-based chromophores. We applied rational design and random mutagenesis to the monomeric red fluorescent protein FusionRed and found two groups of mutants carrying a tryptophan-based chromophore: with yellow (535 nm) or orange (565 nm) emission. On the basis of the properties of proteins, a model synthetic chromophore, and a computational modeling, we concluded that the presence of a ketone-containing chromophore in different isomeric forms can explain the observed yellow and orange phenotypes.
- Published
- 2017
- Full Text
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11. Conformationally locked chromophores as models of excited-state proton transfer in fluorescent proteins.
- Author
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Baranov MS, Lukyanov KA, Borissova AO, Shamir J, Kosenkov D, Slipchenko LV, Tolbert LM, Yampolsky IV, and Solntsev KM
- Subjects
- Color, Imidazoles chemistry, Protein Conformation, Spectrometry, Fluorescence, Zinc chemistry, Green Fluorescent Proteins chemistry, Protons
- Abstract
Members of the green fluorescent protein (GFP) family form chromophores by modifications of three internal amino acid residues. Previously, many key characteristics of chromophores were studied using model compounds. However, no studies of intermolecular excited-state proton transfer (ESPT) with GFP-like synthetic chromophores have been performed because they either are nonfluorescent or lack an ionizable OH group. In this paper we report the synthesis and photochemical study of two highly fluorescent GFP chromophore analogues: p-HOBDI-BF2 and p-HOPyDI:Zn. Among known fluorescent compounds, p-HOBDI-BF(2) is the closest analogue of the native GFP chromophore. These irrreversibly (p-HOBDI-BF(2)) and reversibly (p-HOPyDI:Zn) locked compounds are the first examples of fully planar GFP chromophores, in which photoisomerization-induced deactivation is suppressed and protolytic photodissociation is observed. The photophysical behavior of p-HOBDI-BF2 and p-HOPyDI:Zn (excited state pK(a)'s, solvatochromism, kinetics, and thermodynamics of proton transfer) reveals their high photoacidity, which makes them good models of intermolecular ESPT in fluorescent proteins. Moreover, p-HOPyDI:Zn is a first example of "super" photoacidity in metal-organic complexes.
- Published
- 2012
- Full Text
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