13 results on '"Archipowa, Nataliya"'
Search Results
2. Characterization of Fluorescent Dyes Frequently Used for Bioimaging: Photophysics and Photocatalytical Reactions with Proteins.
- Author
-
Archipowa, Nataliya, Wittmann, Lukas, Köckenberger, Johannes, Ertl, Fabian J., Gleixner, Jakob, Keller, Max, Heinrich, Markus R., and Kutta, Roger Jan
- Published
- 2023
- Full Text
- View/download PDF
3. Tuning Deazaflavins Towards Highly Potent Reducing Photocatalysts Guided by Mechanistic Understanding – Enhancement of the Key Step by the Internal Heavy Atom Effect.
- Author
-
Pavlovska, Tetiana, Král Lesný, David, Svobodová, Eva, Hoskovcová, Irena, Archipowa, Nataliya, Kutta, Roger Jan, and Cibulka, Radek
- Subjects
PHOTOCATALYSTS ,CHARGE exchange ,ATOMS ,ALKYL group ,CHEMICAL reduction ,PHOTOINDUCED electron transfer ,ELECTRON donors - Abstract
Deazaflavins are well suited for reductive chemistry acting via a consecutive photo‐induced electron transfer, in which their triplet state and semiquinone – the latter is formed from the former after electron transfer from a sacrificial electron donor – are key intermediates. Guided by mechanistic investigations aiming to increase intersystem crossing by the internal heavy atom effect and optimising the concentration conditions to avoid unproductive excited singlet reactions, we synthesised 5‐aryldeazaflavins with Br or Cl substituents on different structural positions via a three‐component reaction. Bromination of the deazaisoalloxazine core leads to almost 100 % triplet yield but causes photo‐instability and enhances unproductive side reactions. Bromine on the 5‐phenyl group in ortho position does not affect the photostability, increases the triplet yield, and allows its efficient usage in the photocatalytic dehalogenation of bromo‐ and chloroarenes with electron‐donating methoxy and alkyl groups even under aerobic conditions. Reductive powers comparable to lithium are achieved. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
4. Photocatalytic Oxidative [2+2] Cycloelimination Reactions with Flavinium Salts: Mechanistic Study and Influence of the Catalyst Structure.
- Author
-
Hartman, Tomáš, Reisnerová, Martina, Chudoba, Josef, Svobodová, Eva, Archipowa, Nataliya, Kutta, Roger Jan, and Cibulka, Radek
- Subjects
CYCLOELIMINATION reactions ,CATALYST structure ,ACTIVATION energy ,CHARGE exchange ,ORGANOCATALYSIS ,SALTS - Abstract
Flavinium salts are frequently used in organocatalysis but their application in photoredox catalysis has not been systematically investigated to date. We synthesized a series of 5‐ethyl‐1,3‐dimethylalloxazinium salts with different substituents in the positions 7 and 8 and investigated their application in light‐dependent oxidative cycloelimination of cyclobutanes. Detailed mechanistic investigations with a coumarin dimer as a model substrate reveal that the reaction preferentially occurs via the triplet‐born radical pair after electron transfer from the substrate to the triplet state of an alloxazinium salt. The very photostable 7,8‐dimethoxy derivative is a superior catalyst with a sufficiently high oxidation power (E*=2.26 V) allowing the conversion of various cyclobutanes (with Eox up to 2.05 V) in high yields. Even compounds such as all‐trans dimethyl 3,4‐bis(4‐methoxyphenyl)cyclobutane‐1,2‐dicarboxylate can be converted, whose opening requires a high activation energy due to a missing pre‐activation caused by bulky adjacent substituents in cis‐position. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
5. The sacrificial inactivation of the blue-light photosensor cryptochrome from Drosophila melanogaster.
- Author
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KuttaThese authors contributed equally., Roger Jan, Archipowa, Nataliya, and Scrutton, Nigel Shaun
- Abstract
Drosophila melanogaster cryptochrome functions as the primary blue-light receptor that mediates circadian photo entrainment. Absorption of a photon leads to reduction of the protein-bound FAD via consecutive electron transfer along a conserved tryptophan tetrad resembling the signalling state required for conformational changes and induction of subsequent signalling cascades. However, how the initial photochemistry and subsequent dark processes leading to downstream signalling are linked to each other at the molecular level is still poorly understood. Here, we investigated in detail the initial photochemical events in DmCRY by time-resolved and stationary absorption spectroscopy combined with quantum chemical and molecular dynamics calculations. We resolved the early events along the conserved tryptophan tetrad and the final deprotonation of the terminal tryptophanyl radical cation. These initial events lead to conformational changes, such as the known C-terminal tail release, Trp decomposition, and finally FAD release providing evidence that DmCRY does not undergo a photocycle. We propose that light is a negative regulator of DmCRY stability even under in vitro conditions where the proteasomal machinery is missing, that is in line with its biological function, i.e. entrainment of the circadian clock. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
6. Stepwise Hydride Transfer in a Biological System: Insights into the Reaction Mechanism of the Light‐Dependent Protochlorophyllide Oxidoreductase.
- Author
-
Archipowa, Nataliya, Kutta, Roger J., Heyes, Derren J., and Scrutton, Nigel S.
- Subjects
- *
HYDRIDE transfer reactions , *BIOLOGICAL systems , *PROTOCHLOROPHYLLIDE reductase , *EMISSION spectroscopy , *STEREOISOMERS - Abstract
Abstract: Hydride transfer plays a crucial role in a wide range of biological systems. However, its mode of action (concerted or stepwise) is still under debate. Light‐dependent NADPH: protochlorophyllide oxidoreductase (POR) catalyzes the stereospecific trans addition of a hydride anion and a proton across the C17−C18 double bond of protochlorophyllide. Time‐resolved absorption and emission spectroscopy were used to investigate the hydride transfer mechanism in POR. Apart from excited states of protochlorophyllide, three discrete intermediates were resolved, consistent with a stepwise mechanism that involves an initial electron transfer from NADPH. A subsequent proton‐coupled electron transfer followed by a proton transfer yield distinct different intermediates for wild type and the C226S variant, that is, initial hydride attaches to either C17 or C18, but ends in the same chlorophyllide stereoisomer. This work provides the first evidence of a stepwise hydride transfer in a biological system. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
7. Plant Protochlorophyllide Oxidoreductases A and B.
- Author
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Garrone, Alessio, Archipowa, Nataliya, Zipfel, Peter F., Hermann, Gudrun, and Dietzek, Benjamin
- Subjects
- *
OXIDOREDUCTASES , *PROTOCHLOROPHYLLIDE , *CHLOROPHYLL , *BIOSYNTHESIS , *ISOENZYMES - Abstract
The enzyme protochlorophyllide oxidoreductase (POR, EC 1.3.1.33) has a key role in plant development. It catalyzes one of the later steps in chlorophyll synthesis, the light-induced reduction of protochlorophyllide (PChlide) into chlorophyllide (Chlide) in the presence of NADPH. Two isozymes of plant POR, POR A and POR B from barley, which differ in their function during plant life, are compared with respect to their substrate binding affinity, catalytic efficiency, and catalytic mechanism. POR B as compared with POR A shows an 5-fold higher binding affinity for PChlide and an about 6-fold higher catalytic efficiency measured as kcat/Km. Based on the reaction intermediates, which can be trapped at low temperatures the same reaction mechanism operates in both POR A and POR B. In contrast to results reported for POR enzymes from cyanobacteria, the initial light-driven step, which occurs at temperatures below 180 K already involves the full chemistry of the photoreduction and yields the reaction product, Chlide, in an enzyme-bound form. The subsequent dark reactions, which include cofactor (NADP+) release and cofactor (NADPH) rebinding, show different temperature dependences for POR A and POR B and suggest a higher conformational flexibility of POR B in the surrounding active center. Both the higher substrate binding affinity and well adapted enzyme dynamics are held responsible for the increased catalytic activity of POR B as compared with POR A. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
8. Cover Feature: Photocatalytic Oxidative [2+2] Cycloelimination Reactions with Flavinium Salts: Mechanistic Study and Influence of the Catalyst Structure (3/2021).
- Author
-
Hartman, Tomáš, Reisnerová, Martina, Chudoba, Josef, Svobodová, Eva, Archipowa, Nataliya, Kutta, Roger Jan, and Cibulka, Radek
- Subjects
CYCLOELIMINATION reactions ,CATALYST structure ,OXIDATION-reduction reaction ,PHOTOCATALYSIS ,TIME-resolved spectroscopy ,SALT - Abstract
Keywords: cyclobutanes; cycloelimination reactions; electron transfer; photocatalysis; time-resolved spectroscopy EN cyclobutanes cycloelimination reactions electron transfer photocatalysis time-resolved spectroscopy 348 348 1 03/29/21 20210301 NES 210301 B The Cover Feature shows b the photocatalytic oxidative cycloelimination of a coumarin dimer by a flavinium salt inspired by the light-induced photolyase DNA repair reaction in nature. Cyclobutanes, cycloelimination reactions, electron transfer, photocatalysis, time-resolved spectroscopy. [Extracted from the article]
- Published
- 2021
- Full Text
- View/download PDF
9. Vertebrate Cryptochromes are Vestigial Flavoproteins.
- Author
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Kutta, Roger J., Archipowa, Nataliya, Johannissen, Linus O., Jones, Alex R., and Scrutton, Nigel S.
- Abstract
All cryptochromes are currently classified as flavoproteins. In animals their best-described role is as components of the circadian clock. This circadian function is variable, and can be either light-dependent or -independent; the molecular origin of this difference is unknown. Type I animal cryptochromes are photoreceptors that entrain an organism's clock to its environment, whereas Type II (including mammals) regulate circadian timing in a light-independent manner. Here, we reveal that, in contrast to Type I, Type II animal cryptochromes lack the structural features to securely bind the photoactive flavin cofactor. We provide a molecular basis for the distinct circadian roles of different animal cryptochromes, which also has significant implications for the putative role of Type II cryptochromes in animal photomagnetoreception. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
10. Dually Labeled Neurotensin NTS 1 R Ligands for Probing Radiochemical and Fluorescence-Based Binding Assays.
- Author
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Ertl FJ, Kopanchuk S, Dijon NC, Veikšina S, Tahk MJ, Laasfeld T, Schettler F, Gattor AO, Hübner H, Archipowa N, Köckenberger J, Heinrich MR, Gmeiner P, Kutta RJ, Holliday ND, Rinken A, and Keller M
- Subjects
- Ligands, Humans, Animals, Fluorescence Polarization, Cricetulus, CHO Cells, Protein Binding, Tritium chemistry, Radioligand Assay, Flow Cytometry, Receptors, Neurotensin metabolism, Fluorescent Dyes chemistry, Fluorescent Dyes chemical synthesis
- Abstract
The determination of ligand-receptor binding affinities plays a key role in the development process of pharmaceuticals. While the classical radiochemical binding assay uses radioligands, fluorescence-based binding assays require fluorescent probes. Usually, radio- and fluorescence-labeled ligands are dissimilar in terms of structure and bioactivity, and can be used in either radiochemical or fluorescence-based assays. Aiming for a close comparison of both assay types, we synthesized tritiated fluorescent neurotensin receptor ligands ([
3 H] 13 , [3 H] 18 ) and their nontritiated analogues ( 13 , 18 ). The labeled probes were studied in radiochemical and fluorescence-based (high-content imaging, flow cytometry, fluorescence anisotropy) binding assays. Equilibrium saturation binding yielded well-comparable ligand-receptor affinities, indicating that all these setups can be used for the screening of new drugs. In contrast, discrepancies were found in the kinetic behavior of the probes, which can be attributed to technical differences of the methods and require further studies with respect to the elucidation of the underlying mechanisms.- Published
- 2024
- Full Text
- View/download PDF
11. Illuminating Neuropeptide Y Y 4 Receptor Binding: Fluorescent Cyclic Peptides with Subnanomolar Binding Affinity as Novel Molecular Tools.
- Author
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Gleixner J, Kopanchuk S, Grätz L, Tahk MJ, Laasfeld T, Veikšina S, Höring C, Gattor AO, Humphrys LJ, Müller C, Archipowa N, Köckenberger J, Heinrich MR, Kutta RJ, Rinken A, and Keller M
- Abstract
The neuropeptide Y (NPY) Y
4 receptor (Y4 R), a member of the family of NPY receptors, is physiologically activated by the linear 36-amino acid peptide pancreatic polypeptide (PP). The Y4 R is involved in the regulation of various biological processes, most importantly pancreatic secretion, gastrointestinal motility, and regulation of food intake. So far, Y4 R binding affinities have been mostly studied in radiochemical binding assays. Except for a few fluorescently labeled PP derivatives, fluorescence-tagged Y4 R ligands with high affinity have not been reported. Here, we introduce differently fluorescence-labeled (Sulfo-Cy5, Cy3B, Py-1, Py-5) Y4 R ligands derived from recently reported cyclic hexapeptides showing picomolar Y4 R binding affinity. With p Ki values of 9.22-9.71 (radioligand competition binding assay), all fluorescent ligands ( 16 - 19 ) showed excellent Y4 R affinity. Y4 R saturation binding, binding kinetics, and competition binding with reference ligands were studied using different fluorescence-based methods: flow cytometry (Sulfo-Cy5, Cy3B, and Py-1 label), fluorescence anisotropy (Cy3B label), and NanoBRET (Cy3B label) binding assays. These experiments confirmed the high binding affinity to Y4 R (equilibrium p Kd : 9.02-9.9) and proved the applicability of the probes for fluorescence-based Y4 R competition binding studies and imaging techniques such as single-receptor molecule tracking., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)- Published
- 2024
- Full Text
- View/download PDF
12. Tuning Deazaflavins Towards Highly Potent Reducing Photocatalysts Guided by Mechanistic Understanding - Enhancement of the Key Step by the Internal Heavy Atom Effect.
- Author
-
Pavlovska T, Král Lesný D, Svobodová E, Hoskovcová I, Archipowa N, Kutta RJ, and Cibulka R
- Subjects
- Electron Transport, Electrons
- Abstract
Deazaflavins are well suited for reductive chemistry acting via a consecutive photo-induced electron transfer, in which their triplet state and semiquinone - the latter is formed from the former after electron transfer from a sacrificial electron donor - are key intermediates. Guided by mechanistic investigations aiming to increase intersystem crossing by the internal heavy atom effect and optimising the concentration conditions to avoid unproductive excited singlet reactions, we synthesised 5-aryldeazaflavins with Br or Cl substituents on different structural positions via a three-component reaction. Bromination of the deazaisoalloxazine core leads to almost 100 % triplet yield but causes photo-instability and enhances unproductive side reactions. Bromine on the 5-phenyl group in ortho position does not affect the photostability, increases the triplet yield, and allows its efficient usage in the photocatalytic dehalogenation of bromo- and chloroarenes with electron-donating methoxy and alkyl groups even under aerobic conditions. Reductive powers comparable to lithium are achieved., (© 2022 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)
- Published
- 2022
- Full Text
- View/download PDF
13. The sacrificial inactivation of the blue-light photosensor cryptochrome from Drosophila melanogaster.
- Author
-
Kutta RJ, Archipowa N, and Scrutton NS
- Subjects
- Animals, Electrons, Flavin-Adenine Dinucleotide chemistry, Light, Models, Chemical, Molecular Dynamics Simulation, Oxidation-Reduction, Protein Conformation, Protons, Quantum Theory, Tryptophan chemistry, Cryptochromes chemistry, Cryptochromes radiation effects, Drosophila melanogaster chemistry
- Abstract
Drosophila melanogaster cryptochrome functions as the primary blue-light receptor that mediates circadian photo entrainment. Absorption of a photon leads to reduction of the protein-bound FAD via consecutive electron transfer along a conserved tryptophan tetrad resembling the signalling state required for conformational changes and induction of subsequent signalling cascades. However, how the initial photochemistry and subsequent dark processes leading to downstream signalling are linked to each other at the molecular level is still poorly understood. Here, we investigated in detail the initial photochemical events in DmCRY by time-resolved and stationary absorption spectroscopy combined with quantum chemical and molecular dynamics calculations. We resolved the early events along the conserved tryptophan tetrad and the final deprotonation of the terminal tryptophanyl radical cation. These initial events lead to conformational changes, such as the known C-terminal tail release, Trp decomposition, and finally FAD release providing evidence that DmCRY does not undergo a photocycle. We propose that light is a negative regulator of DmCRY stability even under in vitro conditions where the proteasomal machinery is missing, that is in line with its biological function, i.e. entrainment of the circadian clock.
- Published
- 2018
- Full Text
- View/download PDF
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