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Вид документа : Однотомное издание
Шифр издания : А.с. 973614!-349931
Автор(ы) : Высоцкий Е.С., Заворуев В.В., Межевикин В.В.
Заглавие : Питательная среда для культивирования светящихся бактерий .-
Выходные данные : Б.м.,Б.г.
Коллективы : Ин-т биофизики СО АН СССР
Цена : Б.ц.
ГРНТИ : 34.27.51
Предметные рубрики: КУЛЬТИВИРОВАНИЕ КЛЕТОК
СВЕТЯЩИЕСЯ БАКТЕРИИ
ПИТАТЕЛЬНАЯ СРЕДА
ЛЮЦИФЕРАЗА
БИОСИНТЕЗ
ПАТЕНТЫ
BIOTECHNOLOGY
LUCIFERASE PRODUCTION
PATENT
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Esimbekova E. N., Kalyabina V. P., Kopylova K. V., Torgashina I. G., Kratasyuk V. A.
Заглавие : Design of bioluminescent biosensors for assessing contamination of complex matrices
Место публикации : Talanta: Elsevier B.V., 2021. - Vol. 233. - Ст.122509. - ISSN 00399140 (ISSN), DOI 10.1016/j.talanta.2021.122509
Примечания : Cited By :1
Аннотация: The presence of potentially toxic xenobiotics in complex matrices has become rather the rule than the exception. Therefore, there is a need for highly sensitive inexpensive techniques for analyzing environmental and food matrices for toxicants. Enzymes are selectively sensitive to various toxic compounds, and, thus, they can be used as the basis for detection of contaminants in complex matrices. There are, however, a number of difficulties associated with the analysis of complex matrices using enzyme assays, including the necessity to take into account properties and effects of the natural components of the test media for accurate interpretation of results. The present study describes the six-stage procedure for designing new enzyme sensors intended for assessing the quality of complex matrices. This procedure should be followed both to achieve the highest possible sensitivity of the biosensor to potentially toxic substances and to minimize the effect of the uncontaminated components of complex mixtures on the activity of the biosensor. The proposed strategy has been tested in designing a bioluminescent biosensor for integrated rapid assessment of the safety of fruits and vegetables. The biosensor is based on the coupled enzyme system NAD(P)H:FMN-oxidoreductase and luciferase as the biorecognition element. The study describes methods and techniques for attaining the desired result in each stage. The proposed six-stage procedure for designing bioluminescent enzyme biosensors can be used to design the enzymatic biosensors based on other enzymes. © 2021 Elsevier B.V.
Scopus
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kratasyuk V. A., Kolosova E. M., Sutormin O. S., Lonshakova-Mukina V. I., Baygin M. M., Rimatskaya N. V., Sukovataya I. E., Shpedt A. A.
Заглавие : Software for matching standard activity enzyme biosensors for soil pollution analysis
Место публикации : Sensors: MDPI AG, 2021. - Vol. 21, Is. 3. - Ст.1017. - С. 1-10. - ISSN 14248220 (ISSN), DOI 10.3390/s21031017
Аннотация: This work is dedicated to developing enzyme biosensor software to solve problems regarding soil pollution analysis. An algorithm and specialised software have been developed which stores, analyses and visualises data using JavaScript programming language. The developed software is based on matching data of 51 non-commercial standard soil samples and their inhibitory effects on three enzyme systems of varying complexity. This approach is able to identify the influence of chemical properties soil samples, without toxic agents, on enzyme biosensors. Such software may find wide use in environmental monitoring. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
Scopus
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Lisitsa A. E., Sukovatyi L. A., Bartsev S. I., Deeva A. A., Kratasyuk V. A., Nemtseva E. V.
Заглавие : Mechanisms of viscous media effects on elementary steps of bacterial bioluminescent reaction
Место публикации : Int. J. Mol. Sci.: MDPI AG, 2021. - Vol. 22, Is. 16. - Ст.8827. - ISSN 16616596 (ISSN), DOI 10.3390/ijms22168827
Аннотация: Enzymes activity in a cell is determined by many factors, among which viscosity of the microenvironment plays a significant role. Various cosolvents can imitate intracellular conditions in vitro, allowing to reduce a combination of different regulatory effects. The aim of the study was to analyze the media viscosity effects on the rate constants of the separate stages of the bacterial biolumi-nescent reaction. Non-steady-state reaction kinetics in glycerol and sucrose solutions was measured by stopped-flow technique and analyzed with a mathematical model developed in accordance with the sequence of reaction stages. Molecular dynamics methods were applied to reveal the effects of cosolvents on luciferase structure. We observed both in glycerol and in sucrose media that the stages of luciferase binding with flavin and aldehyde, in contrast to oxygen, are diffusion-limited. More-over, unlike glycerol, sucrose solutions enhanced the rate of an electronically excited intermediate formation. The MD simulations showed that, in comparison with sucrose, glycerol molecules could penetrate the active-site gorge, but sucrose solutions caused a conformational change of functionally important ?Glu175 of luciferase. Therefore, both cosolvents induce diffusion limitation of substrates binding. However, in sucrose media, increasing enzyme catalytic constant neutralizes viscosity effects. The activating effect of sucrose can be attributed to its exclusion from the catalytic gorge of luciferase and promotion of the formation of the active site structure favorable for the catalysis. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
Scopus
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kolosova E. M., Sutormin O. S., Stepanova L. V., Shpedt A. A., Rimatskaya N. V., Sukovataya I. E., Kratasyuk V. A.
Заглавие : Bioluminescent enzyme inhibition-based assay for the prediction of toxicity of pollutants in urban soils
Место публикации : Environ. Technol. Innov.: Elsevier B.V., 2021. - Vol. 24. - Ст.101842. - ISSN 23521864 (ISSN), DOI 10.1016/j.eti.2021.101842
Аннотация: There is a need for rapid simple and informative environmental assessment methods. The present investigation is aimed at assessing the possibility of using the combined enzyme system of luminescent bacteria: NAD(P)H:FMN-oxidoreductase + luciferase (Red + Luc) for predicting the potential toxicity of industrial urbostratozems sampled in the city of Krasnoyarsk. Three groups of urbostratozems polluted with fluorine, arsenic and lead, were tested by the methods of chemical analysis and enzymatic bioassay. Only the assessment of the arsenic-contaminated soil samples showed the dependence between the reduced activity of the enzyme system and the arsenic concentration variations. The results reveal that the sensitivity of the Red + Luc enzyme system to the soil pollutants depends on the properties of the studied soil samples. Moreover, the solubility of lead in the soil samples affects the accuracy of the enzymatic bioassays for soil toxicity testing. The results of the enzymatic bioassay of the fluoride-contaminated soil samples are ambiguous. The obtained data show the relevance of the sample preparation during integral bioassays. In addition, soil properties should be taken into account as well. The current study emphasizes the importance of conducting chemical and biological testing as a combined set to obtain comprehensive information about the anthropogenic load. © 2021 Elsevier B.V.
Scopus
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Esimbekova, Elena N., Kalyabina, Valeriya P., Kopylova, Kseniya, V, Torgashina, Irina G., Kratasyuk, Valentina A.
Заглавие : Design of bioluminescent biosensors for assessing contamination of complex matrices
Колич.характеристики :9 с
Коллективы : Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR); Government of Krasnoyarsk Territory; Krasnoyarsk Regional Fund of Science [20-44-242001]; Ministry of Science and Higher Education of Russian Federation [FSRZ-2020-0006]
Место публикации : Talanta: ELSEVIER, 2021. - Vol. 233. - Ст.122509. - ISSN 0039-9140, DOI 10.1016/j.talanta.2021.122509. - ISSN 1873-3573(eISSN)
Примечания : Cited References:87. - The reported study was funded by Russian Foundation for Basic Research, Government of Krasnoyarsk Territory, Krasnoyarsk Regional Fund of Science, to the research project No. 20-44-242001 and Ministry of Science and Higher Education of Russian Federation No. FSRZ-2020-0006.
Предметные рубрики: SAMPLE PREPARATION
PESTICIDES
FOOD
BIOMOLECULES
SENSITIVITY
Аннотация: The presence of potentially toxic xenobiotics in complex matrices has become rather the rule than the exception. Therefore, there is a need for highly sensitive inexpensive techniques for analyzing environmental and food matrices for toxicants. Enzymes are selectively sensitive to various toxic compounds, and, thus, they can be used as the basis for detection of contaminants in complex matrices. There are, however, a number of difficulties associated with the analysis of complex matrices using enzyme assays, including the necessity to take into account properties and effects of the natural components of the test media for accurate interpretation of results. The present study describes the six-stage procedure for designing new enzyme sensors intended for assessing the quality of complex matrices. This procedure should be followed both to achieve the highest possible sensitivity of the biosensor to potentially toxic substances and to minimize the effect of the uncontaminated components of complex mixtures on the activity of the biosensor. The proposed strategy has been tested in designing a bioluminescent biosensor for integrated rapid assessment of the safety of fruits and vegetables. The biosensor is based on the coupled enzyme system NAD(P)H:FMN-oxidoreductase and luciferase as the biorecognition element. The study describes methods and techniques for attaining the desired result in each stage. The proposed six-stage procedure for designing bioluminescent enzyme biosensors can be used to design the enzymatic biosensors based on other enzymes.
WOS
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Beregovaya K. A., Myshkina N. M., Chepurnykh, T., V, Kotlobay A. A., Purtov, K., V, Petushkov V. N., Rodionova N. S., Yampolsky, I., V
Заглавие : Rational Design and Mutagenesis of Fungal Luciferase from Neonothopanus nambi
Колич.характеристики :4 с
Коллективы : Russian Science FoundationRussian Science Foundation (RSF) [16-14-00052P]; President grant for leading scientific schoolsLeading Scientific Schools Program [NSh-2605.2020.4]
Место публикации : Dokl. Biochem. Biophys.: MAIK NAUKA/INTERPERIODICA/SPRINGER, 2021. - Vol. 496, Is. 1. - С. 14-17. - ISSN 1607-6729, DOI 10.1134/S1607672921010026. - ISSN 1608-3091(eISSN)
Примечания : Cited References:12. - This work was supported by the grant from the Russian Science Foundation no. 16-14-00052P, alanine screening was performed by the President grant for leading scientific schools NSh-2605.2020.4.
Аннотация: The recently described bioluminescent system from fungi has great potential for developing highly efficient tools for biomedical research. Luciferase enzyme is one of the most crucial components of this system. The luciferase from Neonothopanus nambi fungus belongs to the novel still undescribed protein family. The structure data for this protein is almost absent. A detailed study of the N. nambi luciferase properties is necessary for the improvement of analytical methods based on the fungal bioluminescent system. Here we present the positions of key amino acid residues and their effect on enzyme function described using bioinformatic and experimental approaches. These results are useful for further fungal luciferase structure determination.
WOS
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Gorokhovatsky, A. Yu, Chepurnykh, T., V, Shcheglov A. S., Mokrushina, Yu A., Baranova M. N., Goncharuk S. A., Purtov, K., V, Petushkov V. N., Rodionova N. S., Yampolsky, I., V
Заглавие : The Recombinant Luciferase of the Fungus Neonothopanus nambi: Obtaining and Properties
Колич.характеристики :4 с
Коллективы : Russian Science FoundationRussian Science Foundation (RSF) [16-14-00052-P]; President's grant for state support of the leading scientific schools of the Russian Federation [NSh-2605.2020.4]
Место публикации : Dokl. Biochem. Biophys.: MAIK NAUKA/INTERPERIODICA/SPRINGER, 2021. - Vol. 496, Is. 1. - С. 52-55. - ISSN 1607-6729, DOI 10.1134/S1607672921010051. - ISSN 1608-3091(eISSN)
Примечания : Cited References:10. - The work was supported by the Russian Science Foundation (project no. 16-14-00052-P). The creation of the luciferase-producing yeast strain nnLuz was supported by the President's grant for state support of the leading scientific schools of the Russian Federation (NSh-2605.2020.4).
Аннотация: A key component of the recently described bioluminescent system of higher fungi is luciferase, a new class of proteins. The properties of fungal luciferase and their relationship with its structure are interesting both for improving autoluminescent systems already created on its basis and for creating new ones. Therefore, it is extremely important to understand the spatial structure of this protein. We have performed heterologous expression and purification of Neonothopanus nambi luciferase, obtained a protein suitable for subsequent crystallization, and also determined some biochemical properties of the recombinant luciferase.
WOS
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Gorokhovatsky A. Y., Chepurnykh T. V., Shcheglov A. S., Mokrushina Y. A., Baranova M. N., Goncharuk S. A., Purtov K. V., Petushkov V. N., Rodionova N. S., Yampolsky I. V.
Заглавие : The Recombinant Luciferase of the Fungus Neonothopanus nambi: Obtaining and Properties
Место публикации : Doklad. Biochem. Biophys.: Pleiades journals, 2021. - Vol. 496, Is. 1. - С. 52-55. - ISSN 16076729 (ISSN), DOI 10.1134/S1607672921010051
Аннотация: Abstract: A key component of the recently described bioluminescent system of higher fungi is luciferase, a new class of proteins. The properties of fungal luciferase and their relationship with its structure are interesting both for improving autoluminescent systems already created on its basis and for creating new ones. Therefore, it is extremely important to understand the spatial structure of this protein. We have performed heterologous expression and purification of Neonothopanus nambi luciferase, obtained a protein suitable for subsequent crystallization, and also determined some biochemical properties of the recombinant luciferase. © 2021, The Author(s),.
Scopus
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10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kratasyuk, Valentina A., Kolosova, Elizaveta M., Sutormin, Oleg S., Lonshakova-Mukina, Viktoriya, I, Baygin, Matvey M., Rimatskaya, Nadezhda, V, Sukovataya, Irina E., Shpedt, Alexander A.
Заглавие : Software for Matching Standard Activity Enzyme Biosensors for Soil Pollution Analysis
Колич.характеристики :10 с
Коллективы : RFBRRussian Foundation for Basic Research (RFBR); Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science [20-44-243001]; Ministry of Science and Higher Education of the Russian Federation [FSRZ-2020-0006]
Место публикации : Sensors: MDPI, 2021. - Vol. 21, Is. 3. - Ст.1017. - ISSN 1424-8220(eISSN), DOI 10.3390/s21031017
Примечания : Cited References:20. - This research was funded by RFBR, Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science, Grant number 20-44-243001 and the Ministry of Science and Higher Education of the Russian Federation, Grant number FSRZ-2020-0006.
Аннотация: This work is dedicated to developing enzyme biosensor software to solve problems regarding soil pollution analysis. An algorithm and specialised software have been developed which stores, analyses and visualises data using JavaScript programming language. The developed software is based on matching data of 51 non-commercial standard soil samples and their inhibitory effects on three enzyme systems of varying complexity. This approach is able to identify the influence of chemical properties soil samples, without toxic agents, on enzyme biosensors. Such software may find wide use in environmental monitoring.
WOS
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11.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Beregovaya K. A., Myshkina N. M., Chepurnykh T. V., Kotlobay A. A., Purtov K. V., Petushkov V. N., Rodionova N. S., Yampolsky I. V.
Заглавие : Rational Design and Mutagenesis of Fungal Luciferase from Neonothopanus nambi
Место публикации : Doklad. Biochem. Biophys.: Pleiades journals, 2021. - Vol. 496, Is. 1. - С. 14-17. - ISSN 16076729 (ISSN), DOI 10.1134/S1607672921010026
Аннотация: Abstract: The recently described bioluminescent system from fungi has great potential for developing highly efficient tools for biomedical research. Luciferase enzyme is one of the most crucial components of this system. The luciferase from Neonothopanus nambi fungus belongs to the novel still undescribed protein family. The structure data for this protein is almost absent. A detailed study of the N. nambi luciferase properties is necessary for the improvement of analytical methods based on the fungal bioluminescent system. Here we present the positions of key amino acid residues and their effect on enzyme function described using bioinformatic and experimental approaches. These results are useful for further fungal luciferase structure determination. © 2021, Pleiades Publishing, Ltd.
Scopus
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12.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Lisitsa, Albert E., Sukovatyi, Lev A., Bartsev, Sergey, I, Deeva, Anna A., Kratasyuk, Valentina A., Nemtseva, Elena, V
Заглавие : Mechanisms of Viscous Media Effects on Elementary Steps of Bacterial Bioluminescent Reaction
Колич.характеристики :19 с
Коллективы : Ministry of Science and Higher Education of the Russian Federation [FSRZ-2020-0006]; RFBR, Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science [20-44-243002]; RFBRRussian Foundation for Basic Research (RFBR) [20-34-90118]
Место публикации : Int. J. Mol. Sci.: MDPI, 2021. - Vol. 22, Is. 16. - Ст.8827. - ISSN 1422-0067(eISSN), DOI 10.3390/ijms22168827
Примечания : Cited References:59. - The research was funded by the Ministry of Science and Higher Education of the Russian Federation (projects No. FSRZ-2020-0006); by RFBR, Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science (project No. 20-44-243002); by RFBR according to the research project No. 20-34-90118.
Предметные рубрики: FLAVIN INTERMEDIATE
REDUCED FLAVIN
RATE CONSTANTS
LUCIFERASE
Аннотация: Enzymes activity in a cell is determined by many factors, among which viscosity of the microenvironment plays a significant role. Various cosolvents can imitate intracellular conditions in vitro, allowing to reduce a combination of different regulatory effects. The aim of the study was to analyze the media viscosity effects on the rate constants of the separate stages of the bacterial bioluminescent reaction. Non-steady-state reaction kinetics in glycerol and sucrose solutions was measured by stopped-flow technique and analyzed with a mathematical model developed in accordance with the sequence of reaction stages. Molecular dynamics methods were applied to reveal the effects of cosolvents on luciferase structure. We observed both in glycerol and in sucrose media that the stages of luciferase binding with flavin and aldehyde, in contrast to oxygen, are diffusion-limited. Moreover, unlike glycerol, sucrose solutions enhanced the rate of an electronically excited intermediate formation. The MD simulations showed that, in comparison with sucrose, glycerol molecules could penetrate the active-site gorge, but sucrose solutions caused a conformational change of functionally important alpha Glu175 of luciferase. Therefore, both cosolvents induce diffusion limitation of substrates binding. However, in sucrose media, increasing enzyme catalytic constant neutralizes viscosity effects. The activating effect of sucrose can be attributed to its exclusion from the catalytic gorge of luciferase and promotion of the formation of the active site structure favorable for the catalysis.
WOS
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13.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kolosova, Elizaveta M., Sutormin, Oleg S., Stepanova L. V., Shpedt, Aleksandr A., Rimatskaya N. V., Sukovataya, Irina E., Kratasyuk, Valentina A.
Заглавие : Bioluminescent enzyme inhibition-based assay for the prediction of toxicity of pollutants in urban soils
Колич.характеристики :9 с
Коллективы : Russian Foundation for Basic Research, the Government of the Krasnoyarsk Region, Russia; Krasnoyarsk Regional Foundation for Supporting Scientific and Technological Activities, Russia [18-47-240005]; Ministry of Science and Higher Education of the Russian Federation [FSRZ-2020-0006]
Место публикации : Environ. Technol. Innov.: ELSEVIER, 2021. - Vol. 24. - Ст.101842. - ISSN 2352-1864, DOI 10.1016/j.eti.2021.101842
Примечания : Cited References:46. - This work was supported by the Russian Foundation for Basic Research, the Government of the Krasnoyarsk Region, Russia, and Krasnoyarsk Regional Foundation for Supporting Scientific and Technological Activities, Russia [grant number 18-47-240005] in the field of statistical analysis and interpretation of the data; and the work related to the sample collection was supported by the Ministry of Science and Higher Education of the Russian Federation [grant number FSRZ-2020-0006].
Предметные рубрики: FLUORIDE
BIOASSAYS
POLLUTION
METALS
WATER
Аннотация: There is a need for rapid simple and informative environmental assessment methods. The present investigation is aimed at assessing the possibility of using the combined enzyme system of luminescent bacteria: NAD(P)H:FMN-oxidoreductase + luciferase (Red + Luc) for predicting the potential toxicity of industrial urbostratozems sampled in the city of Krasnoyarsk. Three groups of urbostratozems polluted with fluorine, arsenic and lead, were tested by the methods of chemical analysis and enzymatic bioassay. Only the assessment of the arsenic-contaminated soil samples showed the dependence between the reduced activity of the enzyme system and the arsenic concentration variations. The results reveal that the sensitivity of the Red + Luc enzyme system to the soil pollutants depends on the properties of the studied soil samples. Moreover, the solubility of lead in the soil samples affects the accuracy of the enzymatic bioassays for soil toxicity testing. The results of the enzymatic bioassay of the fluoride-contaminated soil samples are ambiguous. The obtained data show the relevance of the sample preparation during integral bioassays. In addition, soil properties should be taken into account as well. The current study emphasizes the importance of conducting chemical and biological testing as a combined set to obtain comprehensive information about the anthropogenic load. (C) 2021 Elsevier B.V. All rights reserved.
WOS
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14.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Purtov, K., V, Petushkov V. N., Rodionova N. S., Chepurnykh, T., V, Kozhemyako V. B., Zagitova, R., I, Shcheglov A. S., Ziganshin R. H., Tsarkova A. S.
Заглавие : SIMILARITIES AND DIFFERENCES BETWEEN THE CHAETOPTERUS VARIOPEDATUS POLYCHAETE LUCIFERASES DEPENDING ON THE TYPE OF HABITAT
Колич.характеристики :6 с
Место публикации : Bull. Russ. State Med. Univ.: PIROGOV RUSSIAN NATL RESEARCH MEDICAL UNIV, 2021. - Is. 5. - С. 41-46. - ISSN 2500-1094, DOI 10.24075/vrgmu.2021.049. - ISSN 2542-1204(eISSN)
Примечания : Cited References:20
Предметные рубрики: BIOLUMINESCENCE
ANNELIDA
SYSTEM
Аннотация: The marine polychaete Chaetopterus variopedatus (Renier) (family Chaetopteridae) is a cosmopolitan species complex, consisting of distinct populations/subspecies. The worms release glowing (460 nm) clouds of mucus when disturbed, and their parapodia often glow brightly. Currently, it is still unclear how exactly the bioluminescence system of these polychaetes functions. It has been previously assumed that the C. variopedatus luciferase may be used for detection of ferroptosis, the recently explored pathway of programmed cell death, resulting from accumulation of the ferrous ions. This study was aimed to extract and characterize the C. variopedatus luciferases, as well as to compare luciferases obtained from C. variopedatus of different populations. When extracting the enzyme responsible for bioluminescence from the frozen samples of Brazilian C. variopedatus using the improved method, two active luciferases, L1 and L2, were obtained. We assumed that one of the listed above luciferases was responsible for luminescence of the mucus and the other luciferase was responsible for luminescence in parapodia, and used the method for the distinct samples of mucus and parapodia of the living Far Eastern C. variopedatus. However, mucus of the latter turned out to be non-glowing. It is shown that luciferase L2 is responsible for luminescence in the parapodia of the C. variopedatus polychaete, since this luciferase has been found in the total biomass of Brazilian polychaetes and parapodia of Far Eastern polychaetes. Luminescence of the Brazilian C. variopedatus mucus is attributed to the functioning of luciferase L1, which is lacking in the mucus of the Far Eastern subspecies. The range of luciferase isoforms in polychaetes C. variopedatus depends on the place of origin.
WOS
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15.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Larionova, Marina D., Wu, Lijie, Eremeeva, Elena, V, Natashin, Pavel, V, Gulnov, Dmitry, V, Nemtseva, Elena, V, Liu, Dongsheng, Liu, Zhi-Jie, Vysotski, Eugene S.
Заглавие : Crystal structure of semisynthetic obelin-v
Колич.характеристики :16 с
Коллективы : National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [32011530076]; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [20-04-00085, 20-44-240006, 20-54-53011]
Место публикации : Protein Sci.: WILEY, 2021. - Article in press. - ISSN 0961-8368, DOI 10.1002/pro.4244. - ISSN 1469-896X(eISSN)
Примечания : Cited References:69. - National Natural Science Foundation of China, Grant/Award Number: 32011530076; Russian Foundation for Basic Research, Grant/Award Numbers: 20-04-00085, 20-44-240006, 20-54-53011
Предметные рубрики: CA2+-REGULATED PHOTOPROTEIN OBELIN
PHOTOLUMINESCENCE QUANTUM YIELD
Аннотация: Coelenterazine-v (CTZ-v), a synthetic derivative with an additional benzyl ring, yields a bright bioluminescence of Renilla luciferase and its "yellow" mutant with a significant shift in the emission spectrum toward longer wavelengths, which makes it the substrate of choice for deep tissue imaging. Although Ca2+-regulated photoproteins activated with CTZ-v also display red-shifted light emission, in contrast to Renilla luciferase their bioluminescence activities are very low, which makes photoproteins activated by CTZ-v unusable for calcium imaging. Here, we report the crystal structure of Ca2+-regulated photoprotein obelin with 2-hydroperoxycoelenterazine-v (obelin-v) at 1.80 angstrom resolution. The structures of obelin-v and obelin bound with native CTZ revealed almost no difference; only the minor rearrangement in hydrogen-bond pattern and slightly increased distances between key active site residues and some atoms of 2-hydroperoxycoelenterazine-v were found. The fluorescence quantum yield (phi(FL)) of obelin bound with coelenteramide-v (0.24) turned out to be even higher than that of obelin with native coelenteramide (0.19). Since both obelins are in effect the enzyme-substrate complexes containing the 2-hydroperoxy adduct of CTZ-v or CTZ, we reasonably assume the chemical reaction mechanisms and the yields of the reaction products (phi(R)) to be similar for both obelins. Based on these findings we suggest that low bioluminescence activity of obelin-v is caused by the low efficiency of generating an electronic excited state (phi(S)). In turn, the low phi(S) value as compared to that of native CTZ might be the result of small changes in the substrate microenvironment in the obelin-v active site.
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16.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Nemtseva, Elena, V, Gulnov, Dmitry, V, Gerasimova, Marina A., Sukovatyi, Lev A., Burakova, Ludmila P., Karuzina, Natalya E., Melnik, Bogdan S., Kratasyuk, Valentina A.
Заглавие : Bacterial Luciferases from Vibrio harveyi and Photobacterium leiognathi Demonstrate Different Conformational Stability as Detected by Time-Resolved Fluorescence Spectroscopy
Колич.характеристики :17 с
Коллективы : Ministry of Science and Higher Education of the Russian Federation [FSRZ-2020-0006]; RFBRRussian Foundation for Basic Research (RFBR) [20-34-90118]; Krasnoyarsk Regional Fund of Science [20-44-243002, 20-44-240006]; RFBRRussian Foundation for Basic Research (RFBR)
Место публикации : Int. J. Mol. Sci.: MDPI, 2021. - Vol. 22, Is. 19. - Ст.10449. - ISSN 1422-0067(eISSN), DOI 10.3390/ijms221910449
Примечания : Cited References:45. - The research was partially funded by the Ministry of Science and Higher Education of the Russian Federation (projects No. FSRZ-2020-0006); by the RFBR and Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science (projects No. 20-44-243002 and 20-44-240006); and by the RFBR (project No. 20-34-90118).
Предметные рубрики: TRYPTOPHAN FLUORESCENCE
CRYSTAL-STRUCTURE
SUBUNIT
BIOLUMINESCENCE
Аннотация: Detecting the folding/unfolding pathways of biological macromolecules is one of the urgent problems of molecular biophysics. The unfolding of bacterial luciferase from Vibrio harveyi is well-studied, unlike that of Photobacterium leiognathi, despite the fact that both of them are actively used as a reporter system. The aim of this study was to compare the conformational transitions of these luciferases from two different protein subfamilies during equilibrium unfolding with urea. Intrinsic steady-state and time-resolved fluorescence spectra and circular dichroism spectra were used to determine the stages of the protein unfolding. Molecular dynamics methods were applied to find the differences in the surroundings of tryptophans in both luciferases. We found that the unfolding pathway is the same for the studied luciferases. However, the results obtained indicate more stable tertiary and secondary structures of P. leiognathi luciferase as compared to enzyme from V. harveyi during the last stage of denaturation, including the unfolding of individual subunits. The distinctions in fluorescence of the two proteins are associated with differences in the structure of the C-terminal domain of alpha-subunits, which causes different quenching of tryptophan emissions. The time-resolved fluorescence technique proved to be a more effective method for studying protein unfolding than steady-state methods./p
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17.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Nemtseva E. V., Gulnov D. V., Gerasimova M. A., Sukovatyi L. A., Burakova L. P., Karuzina N. E., Melnik B. S., Kratasyuk V. A.
Заглавие : Bacterial luciferases from vibrio harveyi and photobacterium leiognathi demonstrate different conformational stability as detected by time-resolved fluorescence spectroscopy
Место публикации : Int. J. Mol. Sci.: MDPI, 2021. - Vol. 22, Is. 19. - Ст.10449. - ISSN 16616596 (ISSN), DOI 10.3390/ijms221910449
Аннотация: Detecting the folding/unfolding pathways of biological macromolecules is one of the urgent problems of molecular biophysics. The unfolding of bacterial luciferase from Vibrio harveyi is well-studied, unlike that of Photobacterium leiognathi, despite the fact that both of them are actively used as a reporter system. The aim of this study was to compare the conformational transitions of these luciferases from two different protein subfamilies during equilibrium unfolding with urea. Intrinsic steady-state and time-resolved fluorescence spectra and circular dichroism spectra were used to determine the stages of the protein unfolding. Molecular dynamics methods were applied to find the differences in the surroundings of tryptophans in both luciferases. We found that the unfolding pathway is the same for the studied luciferases. However, the results obtained indicate more stable tertiary and secondary structures of P. leiognathi luciferase as compared to enzyme from V. harveyi during the last stage of denaturation, including the unfolding of individual subunits. The distinctions in fluorescence of the two proteins are associated with differences in the structure of the C-terminal domain of ?-subunits, which causes different quenching of tryptophan emissions. The time-resolved fluorescence technique proved to be a more effective method for studying protein unfolding than steady-state methods. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.
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18.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Dubovtseva I. Y., Aksenenko M. B., Nikolaeva E. D., Averchuk A. S., Moshev A. V., Savchenko A. A., Markova S. V., Ruksha T. G.
Заглавие : FOXC1-Mediated Effects of miR-204-5p on Melanoma Cell Proliferation
Место публикации : Mol Biol (Mosk): NLM (Medline), 2021. - Vol. 55, Is. 4. - С. 667-675. - ISSN 00268984 (ISSN), DOI 10.31857/S0026898421030058
Аннотация: MicroRNAs epigenetically regulate physiological and pathological processes. Previously, we found that miR-204-5p is expressed at low levels in melanoma cells, and an increase in its level leads to a change in proliferation, migration, and invasion of these cancer cells. Now, using bioinformatics analysis, it has been shown that the target of miR-204-5p is FOXC1 transcription factor, which is implicated in carcinogenesis. Using the luciferase reporter assay, it was found that miR-204-5p suppresses expression of the FOXC1 gene by binding to its 3' non-coding region. Transfection of small interfering RNA (siRNA) targeting FOXC1 into melanoma cells caused a decrease in miR-204-5p levels, which is consistent with the generally accepted concept of feedback regulation of miRNA expression by target genes. According to the results of the MTT test and fluorescence microscopy, the proliferation level of melanoma cells under the influence of siRNA to FOXC1 decreased 72 h after transfection. Changes in the ratio of cells by cell cycle phase were analyzed using flow cytometry. Regulatory relationships between FOXC1 and miR-204-5p, and an inhibitory effect of FOXC1 knockdown on melanoma cell proliferation were revealed. Based on the results, it can be assumed that miR-204-5p regulates proliferation of melanoma cells by affecting FOXC1 expression.
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19.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Dubovtseva, I. Yu, Aksenenko M. B., Nikolaeva E. D., Averchuk A. S., Moshev, A., V, Savchenko A. A., Markova, S., V, Ruksha T. G.
Заглавие : FOXC1-Mediated Effects of miR-204-5p on Melanoma Cell Proliferation
Колич.характеристики :8 с
Место публикации : Mol. Biol.: PLEIADES PUBLISHING INC, 2021. - Vol. 55, Is. 4. - С. 610-617. - ISSN 0026-8933, DOI 10.1134/S0026893321020199. - ISSN 1608-3245(eISSN)
Примечания : Cited References:24
Предметные рубрики: FOXC1
Аннотация: MicroRNAs epigenetically regulate physiological and pathological processes. Previously, we found that miR-204-5p is expressed at low levels in melanoma cells, and an increase in its level leads to a change in proliferation, migration, and invasion of these cancer cells. Now, using bioinformatics analysis, it has been shown that the target of miR-204-5p is FOXC1 transcription factor, which is implicated in carcinogenesis. Using the luciferase reporter assay, it was found that miR-204-5p suppresses expression of the FOXC1 gene by binding to its 3' non-coding region. Transfection of small interfering RNA (siRNA) targeting FOXC1 into melanoma cells caused a decrease in miR-204-5p levels, which is consistent with the generally accepted concept of feedback regulation of miRNA expression by target genes. According to the results of the MTT test and fluorescence microscopy, the proliferation level of melanoma cells under the influence of siRNA to FOXC1 decreased 72 h after transfection. Changes in the ratio of cells by cell cycle phase were analyzed using flow cytometry. Regulatory relationships between FOXC1 and miR-204-5p, and an inhibitory effect of FOXC1 knockdown on melanoma cell proliferation were revealed. Based on the results, it can be assumed that miR-204-5p regulates proliferation of melanoma cells by affecting FOXC1 expression.
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20.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Lisitsa A. E., Sukovatyi L. A., Kratasyuk V. A., Nemtseva E. V.
Заглавие : Viscous Media Slow Down the Decay of the Key Intermediate in Bacterial Bioluminescent Reaction
Место публикации : Doklad. Biochem. Biophys.: Pleiades Publishing, 2020. - Vol. 492, Is. 1. - С. 162-165. - ISSN 16076729 (ISSN), DOI 10.1134/S1607672920020106
Аннотация: Abstract: The effects of medium viscosity on the decay rate of the 4a-hydroperoxyflavin intermediate of the bioluminescent reaction was investigated. It was found that at low concentrations of glycerol or sucrose (viscosity 1.1–1.3 cP) the decay rate rises, whereas a further increase in viscosity to 6.2 cP leads to a decrease in the decay rate following a power function with an exponent of 0.82–0.84. Using molecular dynamics methods, it was shown that the presence of glycerol and sucrose molecules causes a change in the mobility of the amino acid residues in the active center of luciferase, particularly those responsible for binding of flavin. The results obtained are indicative of two opposite effects of viscous media with glycerol and sucrose: (1) destabilization of 4a-hydroperoxyflavin due to a change in the structural and dynamic properties of the protein and (2) stabilization of this intermediate by the decrease in the diffusion rate of its decay products. © 2020, Pleiades Publishing, Ltd.
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