Труды сотрудников института физики

/ L. Y. Antipina [et al.] // J. Struct. Chem. - 2011. - Vol. 52, Is. 5. - P. 870-875. - Cited References: 19. - The work was supported by RFBR (07-04-00930-a), the "Molecular and Cell Biology" Program of the Presidium of the Russian Academy of Sciences, and the Program of the Siberian Division of the Russian Academy of Sciences (project No. 2) within the implementation of the Federal Targeted Program "Scientific and Scientific Pedagogical Personnel of Innovative Russia, 2010" (P333 and P213). . - ISSN 0022-4766РУБ Chemistry, Inorganic & Nuclear + Chemistry, Physical

Аннотация: The Ca2+-regulated photoprotein obelin determines the luminescence of the marine hydroid Obelia longissima. Bioluminescence is initiated by calcium and appears as a result of the oxidative decarboxylation related to the coelenterazine substrate. The luciferase of the luminescent marine coral Renilla muelleri (RM) also uses coelenterazine as a substrate. However, three proteins are involved in the in vivo bioluminescence of these animals: luciferase, green fluorescent protein, and Ca2+-regulated coelenterazine-binding protein (CBP). In fact, CBP that contains one strongly bound coelenterazine molecule is the RM luciferase substrate in the in vivo bioluminescent reaction. Coelenterazine becomes available for oxygen and the reaction with luciferase only after binding CBP with calcium ions. Unlike Ca2+-regulated photoproteins, the coelenterazine molecule is not activated by oxygen in the CBP molecule. In this work, by means of quantum chemical methods the behavior of substrates in these proteins is analyzed. It is shown that coelenterazine can form different tautomers: CLZ(2H) and CLZ(7H). The formation of 2-hydroperoxy-coelenterazine is studied. According to the obtained data, these proteins use different forms of the substrates for the reaction. In obelin, the substrate is in the CLZ(2H) form that affords hydrogen peroxide. In RM, coelenterazine is in the CLZ(7H) form, and therefore, CBP is not activated by oxygen.

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Держатели документа:
Russian Acad Sci, LV Kirensky Phys Inst, Siberian Div, Krasnoyarsk, Russia
Russian Acad Sci, Inst Biophys, Siberian Div, Krasnoyarsk, Russia
MF Reshetnev Siberian State Aerosp Univ, Krasnoyarsk, Russia

Доп.точки доступа:
Antipina, L. Yu.; Tomilin, F. N.; Томилин, Феликс Николаевич; Vysotski, E. S.; Высоцкий, Евгений Степанович; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич

/ R. R. Alieva [et al.] // J. Photochem. Photobiol. B Biol. - 2016. - Vol. 162. - P. 318-323, DOI 10.1016/j.jphotobiol.2016.07.004. - Cited References: 49. - This work was supported by the state budget allocated to the fundamental research at the Russian Academy of Sciences (project No 01201351504); the Russian Foundation for Basic Research, Grant No 15-43-04377-sibir; and Russian president's grant NSh-7559.2016.2. . - ISSN 1011-1344РУБ Biochemistry & Molecular Biology + Biophysics

Аннотация: Coelenteramide-containing fluorescent proteins are products of bioluminescent reactions of marine coelenterates. They are called ‘discharged photoproteins’. Their light-induced fluorescence spectra are variable, depending considerably on external conditions. Current work studies a dependence of light-induced fluorescence spectra of discharged photoproteins obelin, aequorin, and clytin on excitation energy. It was demonstrated that photoexcitation to the upper electron-excited states (260–300 nm) of the discharged photoproteins initiates a fluorescence peak in the near UV region, in addition to the blue-green emission. To characterize the UV fluorescence, the light-induced fluorescence spectra of coelenteramide (CLM), fluorophore of the discharged photoproteins, were studied in methanol solution. Similar to photoproteins, the CLM spectra depended on photoexcitation energy; the additional peak (330 nm) in the near UV region was observed in CLM fluorescence at higher excitation energy (260–300 nm). Quantum chemical calculations by time depending method with B3LYP/cc-pVDZ showed that the conjugated pyrazine-phenolic fragment and benzene moiety of CLM molecule are responsible for the additional UV fluorescence peak. Quantum yields of CLM fluorescence in methanol were 0.028 ± 0.005 at 270–340 nm photoexcitation. A conclusion was made that the UV emission of CLM might contribute to the UV fluorescence of the discharged photoproteins. The study develops knowledge on internal energy transfer in biological structures – complexes of proteins with low-weight aromatic molecules. © 2016 Elsevier B.V.

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Держатели документа:
Institute of Biophysics SB RAS, Akademgorodok 50/50, Krasnoyarsk, Russian Federation
Institute of Physics SB RAS, Akademgorodok 50/38, Krasnoyarsk, Russian Federation
Siberian Federal University, Svobodny Prospect 79, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Alieva, R. R.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kuzubov, A. A.; Кузубов, Александр Александрович; Ovchinnikov, S. G.; Овчинников, Сергей Геннадьевич; Kudryasheva, N. S.

/ A. . Gorban, T. . Popova, A. . Zinovyev // Physica A. - 2005. - Vol. 353. - P. 365-387, DOI 10.1016/j.physa.2005.01.043. - Cited References: 46 . - ISSN 0378-4371РУБ Physics, Multidisciplinary

Аннотация: Three results are presented. First, we prove the existence of a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties. The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic "pure" types of this model, observed in nature: "parallel triangles", "perpendicular triangles", degenerated case and the flower-like type. Second, we answered the question: how big are the position-specific information and the contribution connected with correlations between nucleotide. The accuracy of the mean-field (context-free) approximation is estimated for bacterial genomes. We show that codon us-age of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea). Description of these two codon-usage trajectories is the third result. All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site: http://www.ihes.fr/similar to zinovyev/7clusters. (c) 2005 Elsevier B.V. All rights reserved.

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Держатели документа:
Univ Leicester, Dept Math, Leicester LE1 7RH, Leics, England
RAS, SB, Inst Computat Modelling, Krasnoyarsk, Russia
Bures Sur Yvette & Bioinformat Serv Inst Curie, Inst Hautes Etudes Sci, Paris, France
ИВМ СО РАН
Department of Mathematics, University of Leicester, Leicester, University Road, Leicester LE1 7RH, United Kingdom
Institute of Computational Modelling, SB RAS, Krasnoyarsk, Russian Federation
Institut des Hautes Etudes Scientifiques, Bures-sur-Yvette and Bioinformatics Service of Institut Curie, Paris, France

Доп.точки доступа:
Popova, T.; Zinovyev, A.

/ E. I. Shishatskaya [et al.] // Food Chem. Toxicol. - 2016. - Vol. 96. - P. 302-308, DOI 10.1016/j.fct.2016.08.025. - Cited References: 46 . - ISSN 0278-6915РУБ Food Science & Technology + Toxicology

Аннотация: We studied the feasibility of using a short-term culture of monocytes, isolated from peripheral donor blood, to assess the biological activity of different types of bionanomaterials (BNM): biodegradable polimeric particles, fiber and film substrates of micro- and nano-dimensions, fullerenes (F) and nanodiamonds (ND), which are either currently in use and/or potentially applicable in medicine. Additionally, the effect of creating a protein corona on ND and F particles was investigated. The cellular reduction of (4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) is a well-established tool for assessing the viability/metabolic activity of cells. The scanning electron microscopy assay can detect fine changes in cell morphology. In the present study BNM have been shown to affect; in a size, chemical composition and morphological characteristics-dependent manner, the ability of monocytes to reduce MTT as well as their morphology. Moreover, the specific effects of ND and F on MTT reduction and cell morphology were exhibited in a dose-dependent manner and sensitive to the formation of surface protein corona. Our results suggest that short-term culture of monocytes is a sensitive model system for assessing the biological effects of BMPs in vitro. © 2016 Elsevier Ltd

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Siberian Federal University, Svobodnuy Av. 79, Krasnoyarsk, Russian Federation
Laboratory of Anatomy, Histology, Embryology, School of Medicine, University of Crete, Heraklion, Greece
Institute of Physics, Russian Academy of Science, Siberian Division, Akademgorodok, 50, Build. 38, Krasnoyarsk, Russian Federation
Laboratory of Toxicology, Medical School, University of Crete, Heraklion, Greece

Доп.точки доступа:
Shishatskaya, E. I.; Шишацкая, Екатерина Игоревна; Nikitovic, D.; Shabanov, A. V.; Шабанов, Александр Васильевич; Tzanakakis, G. N.; Tsatsakis, A. M.; Menzianova, N. G.

/ G. S. Zamay [et al.] // VI Euro-Asian Symposium "Trends in MAGnetism" (EASTMAG-2016) : abstracts / ed.: O. A. Maksimova, R. D. Ivantsov. - Krasnoyarsk : KIP RAS SB, 2016. - Ст. P12.5. - P. 562. - This work was supported by Ministry of Education and Science of Russian Federation Federal Target Program # 14.604.21.0105 (RFMEFI60414X0105) . - ISBN 978-5-904603-06-9


Доп.точки доступа:
Zamay, G. S.; Замай, Г. С.; Zamay, T.; Замай, Татьяна; Kolovsky, V.; Коловский, Василий; Shabanov, A. V.; Шабанов, Александр Васильевич; Kolovskaya, O. S.; Коловская, О. С.; Krat, A. V.; Крат, А. В.; Modestov, A.; Модестов, Андрей; Sokolov, A. E.; Соколов, Алексей Эдуардович; Chetvergov, N. A.; Чесноков, Н. А.; Gargaun, A.; Berezovski, M.; Zamay, S. S.; Замай, С. С.; Zamay, A. S.; Замай, Анна Сергеевна; Volochaev, M. N.; Волочаев, Михаил Николаевич; Svetlichnyi, V.; Светличный, Валерий; Lapin, I. N.; Лапин, И. Н.; Shabalina, A.; Шабалина, Анастасия; Euro-Asian Symposium "Trends in MAGnetism"(6 ; 2016 ; Aug. ; 15-19 ; Krasnoyarsk); "Trends in MAGnetism", Euro-Asian Symposium(6 ; 2016 ; Aug. ; 15-19 ; Krasnoyarsk); Институт физики им. Л.В. Киренского Сибирского отделения РАН

Нет сведений об экземплярах

/ G. S. Zamay [et al.] // Sci. Rep. - 2016. - Vol. 6. - Ст. 34350, DOI 10.1038/srep34350. - Cited References:24. - Authors thank Dr. Mahmoud Labib and Galina Kudryasheva. This work was supported by Ministry of Education and Science of Russian Federation Federal Target Program #14.604.21.0105 for Anna S. Zamay. Electron microscopy was carried out at the Multiple-Access Center of Krasnoyarsk Research Center Siberian branch of Russian Academy of Science. . - ISSN 2045-2322РУБ Multidisciplinary Sciences

Аннотация: The development of an aptamer-based electrochemical sensor for lung cancer detection is presented in this work. A highly specific DNA-aptamer, LC-18, selected to postoperative lung cancer tissues was immobilized onto a gold microelectrode and electrochemical measurements were performed in a solution containing the redox marker ferrocyanide/ferricyanide. The aptamer protein targets were harvested from blood plasma of lung cancer patients by using streptavidin paramagnetic beads and square wave voltammetry of the samples was performed at various concentrations. In order to enhance the sensitivity of the aptasensor, silica-coated iron oxide magnetic beads grafted with hydrophobic C8 and C4 alkyl groups were used in a sandwich detection approach. Addition of hydrophobic beads increased the detection limit by 100 times. The detection limit of the LC-18 aptasensor was enhanced by the beads to 0.023 ng/mL. The formation of the aptamer -protein -bead sandwich on the electrode surface was visualized by electron microcopy. As a result, the electrochemical aptasensor was able to detect cancer-related targets in crude blood plasma of lung cancer patients.

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Держатели документа:
Krasnoyarsk State Med Univ, Lab Biomol & Med Technol, 1 P Zheleznyaka, Krasnoyarsk 660022, Russia.
Russian Acad Sci, Siberian Branch, Inst Chem & Chem Technol, 50-24 Akademgorodok, Krasnoyarsk 660036, Russia.
Design Dept Iskra, 1 Televizornaya, Krasnoyarsk 660028, Russia.
Russian Acad Sci, Siberian Branch, Krasnoyarsk Res Ctr, 50 Akademgorodok, Krasnoyarsk 660036, Russia.
Krasnoyarsk Reg Clin Canc Ctr, 1 Smolenskaya, Krasnoyarsk 660022, Russia.
Univ Ottawa, Dept Chem, 10 Marie Curie,DIorio Hall,Room 201, Ottawa, ON K1N 6N5, Canada.
Russian Acad Sci, Siberian Branch, Inst Phys, 50-38 Akademgorodok, Krasnoyarsk 660036, Russia.

Доп.точки доступа:
Zamay, G. S.; Zamay, T. N.; Kolovskii, V. A.; Shabanov, A. V.; Шабанов, Александр Васильевич; Glazyrin, Y. E.; Veprintsev, D. V.; Krat, A. V.; Zamay, S. S.; Kolovskaya, O. S.; Gargaun, A.; Sokolov, A. E.; Соколов, Алексей Эдуардович; Modestov, A. A.; Artyukhov, I. P.; Chesnokov, N. V.; Petrova, M. M.; Berezovski, M. V.; Zamay, A. S.; Ministry of Education and Science of Russian Federation Federal Target Program [14.604.21.0105]

/ N. S. Kudryasheva, E. S. Kovel // Int. J. Mol. Sci. - 2019. - Vol. 20, Is. 18. - Ст. 4451, DOI 10.3390/ijms20184451. - Cited References: 106. - This work was supported by PRAN-32, Program: “Nanostructures: physics, chemistry, biology, technological basis”; RFBR N 18-29-19003; RFBR-Krasnoyarsk Regional Foundation N 18-44-242002, 18-44-240004. . - ISSN 1422-0067
Аннотация: The current paper reviews the applications of luminescence bioassays for monitoring the results of low-intensity exposures which produce a stimulative effect. The impacts of radioactivity of different types (alpha, beta, and gamma) and bioactive compounds (humic substances and fullerenols) are under consideration. Bioassays based on luminous marine bacteria, their enzymes, and fluorescent coelenteramide-containing proteins were used to compare the results of the low-intensity exposures at the cellular, biochemical, and physicochemical levels, respectively. High rates of luminescence response can provide (1) a proper number of experimental results under comparable conditions and, therefore, proper statistical processing, with this being highly important for "noisy" low-intensity exposures; and (2) non-genetic, i.e., biochemical and physicochemical mechanisms of cellular response for short-term exposures. The results of cellular exposures were discussed in terms of the hormesis concept, which implies low-dose stimulation and high-dose inhibition of physiological functions. Dependencies of the luminescence response on the exposure time or intensity (radionuclide concentration/gamma radiation dose rate, concentration of the bioactive compounds) were analyzed and compared for bioassays of different organization levels.

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Держатели документа:
Institute of Biophysics, Federal Research Center "Krasnoyarsk Science Center, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Institute of Physics, Federal Research Center "Krasnoyarsk Science Center, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Kovel, E. S.; Ковель, Екатерина Сергеевна

/ L. Lupu, P. Wiegand, N. Huttmann [et al.] // ChemMedChem. - 2020. - Vol. 15, Is. 4. - P. 363-369, DOI 10.1002/cmdc.201900489. - Cited References: 40. - We gratefully acknowledge the advice and assistance of Prof. Friedemann Volklein and Oliver Muller, MSc in the preparation of chips for the SPR affinity determinations. We thank Dr. Stefan Maeser, Biogen GmbH, Munchen, for valuable advice and critical reading of the manuscript. This work has been partially funded (Chip-MS epitope analysis) by the LOEWE-3 Funding Agency, Hessen-Agentur, Wiesbaden, Germany; Grant 696/19-16 . - ISSN 1860-7179. - ISSN 1860-7187РУБ Chemistry, Medicinal + Pharmacology & Pharmacy

Аннотация: C‐Met protein is a glycosylated receptor tyrosine kinase of the hepatocyte growth factor (HGF), composed of an α and a β chain. Upon ligand binding, C‐Met transmits intracellular signals by a unique multi‐substrate docking site. C‐Met can be aberrantly activated leading to tumorigenesis and other diseases, and has been recognized as a biomarker in cancer diagnosis. C‐Met aptamers have been recently considered a useful tool for detection of cancer biomarkers. Herein we report a molecular interaction study of human C‐Met expressed in kidney cells with two DNA aptamers of 60 and 64 bases (CLN0003 and CLN0004), obtained using the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure. Epitope peptides of aptamer‐C‐Met complexes were identified by proteolytic affinity‐mass spectrometry in combination with SPR biosensor analysis (PROTEX‐SPR‐MS), using high‐pressure proteolysis for efficient digestion. High affinities (KD, 80–510 nM) were determined for aptamer‐C‐Met complexes, with two‐step binding suggested by kinetic analysis. A linear epitope, C‐Met (381–393) was identified for CLN0004, while the CLN0003 aptamer revealed an assembled epitope comprised of two peptide sequences, C‐Met (524–543) and C‐Met (557–568). Structure modeling of C‐Met‐aptamers were consistent with the identified epitopes. Specificities and affinities were ascertained by SPR analysis of the synthetic epitope peptides. The high affinities of aptamers to C‐Met, and the specific epitopes revealed render them of high interest for cellular diagnostic studies.

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Держатели документа:
Steinbeis Ctr Biopolymer Anal & Biomed Mass Spect, Marktstr 29, D-65428 Russelsheim, Germany.
Univ Ottawa, Dept Chem & Biomol Sci, Ottawa, ON K1N 6N5, Canada.
Rhein Main Univ, Dept Engn Sci, D-65428 Russelsheim, Germany.
Russian Acad Sci, Siberian Branch, Kirensky Inst Phys, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Krasnoyarsk 66041, Russia.
Russian Acad Sci, Fed Res Ctr, Lab Digital Controlled Drugs & Theranost, Siberian Branch,Krasnoyarsk Sci Ctr, Krasnoyarsk 660036, Russia.
Pressure Biosci Inc, 14 Norfolk Ave, South Easton, MA 02375 USA.

Доп.точки доступа:
Lupu, Loredana; Wiegand, Pascal; Huttmann, N.; Rawer, Stephan; Kleinekofort, Wolfgang; Shugureva, Irina; Kichkailo, Anna S.; Tomilin, F. N.; Томилин, Феликс Николаевич; Lazarev, Alexander; Berezovski, Maxim V.; Przybylski, Michael; LOEWE-3 Funding Agency, Hessen-Agentur, Wiesbaden, Germany [696/19-16]

/ T. E. Smolyarova, A. V. Lukyanenko, L. V. Shanidze [et al.] // The Fifth Asian School-Conference on Physics and Technology of Nanostructured Materials : Proceedings. - VLadivostok : Dalnauka Publishing, 2020. - Ст. VII.31.03p. - P. 195. - The work is carried out with the assistance of Krasnoyarsk Regional Center of Research Equipment of Federal Research Center «Krasnoyarsk Science Center SB RAS» and Russian Foundation for Basic Research, Government of Krasnoyarsk Territory, Krasnoyarsk Regional Fund of Science to the research project № 18-42-243013. . - ISBN 978-5-8044-1698-1

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Держатели документа:
Institute of Biophysics KSC SB RAS, 50/50 Academgorodok St., Krasnoyarsk, 660036, Russia
Krasnoyarsk Science Center of SB RAS, 50 Academgorodok St., Krasnoyarsk, 660036, Russia
Siberian Federal University, 76 Svobodny Av., Krasnoyarsk, 660041, Russia

Доп.точки доступа:
Smolyarova, T. E.; Lukyanenko, A. V.; Лукьяненко, Анна Витальевна; Shanidze, L. V.; Шанидзе, Лев Викторович; Krasitskaya, V. V.; Tarasov, A. S.; Тарасов, Антон Сергеевич; Volkov, N. V.; Волков, Никита Валентинович; Asian School-Conference on Physics and Technology of Nanostructured Materials(5 ; 2020 ; 30 Jul - 3 Aug ; Vladivostok); Азиатская школа-конференция по физике и технологии наноструктурированных материалов(5 ; 2013 ; 30 июля - 3 авг. ; Владивосток)

/ T. E. Smolyarova, L. V. Shanidze, A. V. Lukyanenko [et al.] // Talanta. - 2022. - Vol. 239. - Ст. 123092, DOI 10.1016/j.talanta.2021.123092. - Cited References: 44. - The reported study was funded by RFBR according to the research project № 20-32-90134. The authors thank RFBR, Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science (projects nos. 20-42-243007 and 20-42-240013) and the Government of the Russian Federation, Mega Grant for the Creation of Competitive World-Class Laboratories (Agreement no. 075-15-2019-1886) for financial support. Electron microscopy investigations were conducted with the help of equipment of the Krasnoyarsk Territorial Shared Resource Center, Krasnoyarsk Scientific Center, Russian Academy of Sciences . - ISSN 0039-9140. - ISSN 1873-3573
   Перевод заглавия: Биосенсор для белков на основе полевого нанопроволочного транзистора с барьером Шоттки
Аннотация: A top-down nanofabrication approach involving molecular beam epitaxy and electron beam lithography was used to obtain silicon nanowire-based back gate field-effect transistors with Schottky contacts on silicon-on-insulator (SOI) wafers. The resulting device is applied in biomolecular detection based on the changes in the drain-source current (IDS). In this context, we have explained the physical mechanisms of charge carrier transport in the nanowire using energy band diagrams and numerical 2D simulations in TCAD. The results of the experiment and numerical modeling matched well and may be used to develop novel types of nanowire-based biosensors.

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russia
Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russia
Institute of Biophysics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russia
Siberian Federal University, Krasnoyarsk, 660041, Russia
Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russia

Доп.точки доступа:
Smolyarova, T. E.; Смолярова, Татьяна Евгеньевна; Shanidze, Lev V.; Шанидзе, Лев Викторович; Lukyanenko, A. V.; Лукьяненко, Анна Витальевна; Baron, F. A.; Барон, Филипп Алексеевич; Krasitskaya, Vasilisa V.; Kichkailo, Anna S.; Tarasov, A. S.; Тарасов, Антон Сергеевич; Volkov, N. V.; Волков, Никита Валентинович

/ N. Cazacu, C. G. Chilom, S. Iftimie [et al.] // Nanomaterials. - 2022. - Vol. 12, Is. 2. - Ст. 249, DOI 10.3390/nano12020249. - Cited References: 59. - This research was funded by JINR Themes 02-1-1107-2011/2021, 04-5-1131-2017/2021 and 04-4-1133-2018/2023 and with the financial support of the RO-JINR Projects Nos. 366/11.05.2021 (items 7, 86, 97) and 365/11.05.2021 (items 8, 87 and 98). This work also benefited from the use of the SasView application, originally developed under NSF Award DMR-0520547. SasView also contains the code developed with funding from the EU Horizon 2020 program under the SINE2020 project Grant No 654000. The APC was funded by JINR Theme 02-1-1107-2011/2021, Project No. 366/11.05.2021, item 7. This study used the infrastructure of the Applied Genetics Resource Facility of MIPT (Suport Grant 075-15-2021-684) . - ISSN 2079-4991РУБ Chemistry, Multidisciplinary + Nanoscience & Nanotechnology + Materials Science, Multidisciplinary + Physics, Applied

Аннотация: The synthesis of nanoparticles inside microorganisms is an economical alternative to chemical and physical methods of nanoparticle synthesis. In this study, ferrihydrite nanoparticles synthesized by Klebsiella oxytoca bacterium in special conditions were characterized by scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDS), small-angle X-ray (SAXS), UV-Vis spectroscopy, fluorescence, fluorescence resonance energy transfer (FRET), and molecular docking. The morphology and the structure of the particles were characterized by means of SEM and SAXS. The elemental content was determined by means of the EDS method. The absorption properties of the ferrihydrite nanoparticles were investigated by UV-Vis spectroscopy. The binding mechanism of the biogenic ferrihydrite nanoparticles to Bovine Serum Albumin (BSA) protein, studied by fluorescence, showed a static and weak process, combined with FRET. Protein denaturation by temperature and urea in the presence of the ferrihydrite nanoparticles demonstrated their influence on the unfolding process. The AutoDock Vina and UCSF Chimera programs were used to predict the optimal binding site of the ferrihydrite to BSA and to find the location of the hydrophobic cavities in the sub-domain IIA of the BSA structure.

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Univ Bucharest, Fac Phys, Dept Elect Solid State & Biophys, RO-077125 Magurele, Romania.
Horia Hulubei Natl Inst Phys & Nucl Engn, Dept Nucl Phys, RO-077125 Magurele, Romania.
Joint Inst Nucl Res, Dubna 141980, Russia.
Moscow Inst Phys & Technol, Dolgoprudnyi 141701, Russia.
Russian Acad Sci, Siberian Branch, Fed Res Ctr KSC, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Sch Engn Phys & Radio Elect, Phys Dept, Krasnoyarsk 660041, Russia.
Russian Acad Sci, Siberian Branch, Kirensky Inst Phys, Krasnoyarsk 660036, Russia.

Доп.точки доступа:
Cazacu, Nicoleta; Chilom, Claudia G.; Iftimie, Sorina; Balasoiu, Maria; Ladygina, Valentina P.; Stolyar, S. V.; Столяр, Сергей Викторович; Orelovich, Oleg L.; Kovalev, Yuriy S.; Rogachev, Andrey V.

/ V. V. Krasitskaya, A. N. Kudryavtsev, R. N. Yaroslavtsev [et al.] // Int. J. Mol. Sci. - 2022. - Vol. 23, Is. 10. - Ст. 5410, DOI 10.3390/ijms23105410. - Cited References: 37. - This study was supported by the Russian Science Foundation and the Krasnoyarsk Territorial Foundation for Support of Scientific and R&D Acitvities, project No. 22-14-20020 . - ISSN 1661-6596
Аннотация: Starch-coated magnetic iron oxide nanoparticles have been synthesized by a simple, fast, and cost-effective co-precipitation method with cornstarch as a stabilizing agent. The structural and magnetic characteristics of the synthesized material have been studied by transmission electron microscopy, Mossbauer spectroscopy, and vibrating sample magnetometry. The nature of bonds between ferrihydrite nanoparticles and a starch shell has been examined by Fourier transform infrared spectroscopy. The data on the magnetic response of the prepared composite particles have been obtained by magnetic measurements. The determined magnetic characteristics make the synthesized material a good candidate for use in magnetic separation. Starch-coated magnetic iron oxide nanoparticles have been tested as an affinity sorbent for one-step purification of several recombinant proteins (cardiac troponin I, survivin, and melanoma inhibitory activity protein) bearing the maltose-binding protein as an auxiliary fragment. It has been shown that, due to the highly specific binding of this fragment to the starch shell, the target fusion protein is selectively immobilized on magnetic nanoparticles and eluted with the maltose solution. The excellent efficiency of column-free purification, high binding capacity of the sorbent (100–500 µg of a recombinant protein per milligram of starch-coated magnetic iron oxide nanoparticles), and reusability of the obtained material have been demonstrated.

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Держатели документа:
Institute of Biophysics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, 660036, Russian Federation
Kirensky Institute of Physics SB RAS, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, 660036, Russian Federation
Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, 660036, Russian Federation
School of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, 660041, Russian Federation

Доп.точки доступа:
Krasitskaya, V. V.; Kudryavtsev, A. N.; Yaroslavtsev, R. N.; Ярославцев, Роман Николаевич; Gerasimova, Yu. V.; Герасимова, Юлия Валентиновна; Velikanov, D. A.; Великанов, Дмитрий Анатольевич; Bayukov, O. A.; Баюков, Олег Артемьевич; Stolyar, S. V.; Столяр, Сергей Викторович; Frank, L. A.

/ A. N. Kudryavtsev, V. V. Krasitskaya, M. K. Efremov [et al.] // Int. J. Mol. Sci. - 2023. - Vol. 24, Is. 3. - Ст. 2144, DOI 10.3390/ijms24032144. - Cited References: 24. - This research was supported by the state budget allocated to the fundamental research at the Russian Academy of Sciences, project No. 0287-2022-0002 and the Interagency Supercomputer Center of the Russian Academy of Sciences, MVS-100K and MVS-10P . - ISSN 1661-6596. - ISSN 1422-0067
Аннотация: Ca2+-triggered coelenterazine-binding protein (CBP) is a natural form of the luciferase substrate involved in the Renilla bioluminescence reaction. It is a stable complex of coelenterazine and apoprotein that, unlike coelenterazine, is soluble and stable in an aquatic environment and yields a significantly higher bioluminescent signal. This makes CBP a convenient substrate for luciferase-based in vitro assay. In search of a similar substrate form for the luciferase NanoLuc, a furimazine-apoCBP complex was prepared and verified against furimazine, coelenterazine, and CBP. Furimazine-apoCBP is relatively stable in solution and in a frozen or lyophilized state, but as distinct from CBP, its bioluminescence reaction with NanoLuc is independent of Ca2+. NanoLuc turned out to utilize all the four substrates under consideration. The pairs of CBP-NanoLuc and coelenterazine-NanoLuc generate bioluminescence with close efficiency. As for furimazine-apoCBP-NanoLuc pair, the efficiency with which it generates bioluminescence is almost twice lower than that of the furimazine-NanoLuc. The integral signal of the CBP-NanoLuc pair is only 22% lower than that of furimazine-NanoLuc. Thus, along with furimazine as the most effective NanoLuc substrate, CBP can also be recommended as a substrate for in vitro analytical application in view of its water solubility, stability, and Ca2+-triggering “character”.

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Institute of Biophysics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia
School of Fundamental Biology and Biotechnology, School of Non-Ferrous Metals and Material Science, Siberian Federal University, pr. Svobodny 79, 660041 Krasnoyarsk, Russia
Kirensky Institute of Physics, Federal Research Center “Krasnoyarsk Science Center SB”, 660036 Krasnoyarsk, Russia

Доп.точки доступа:
Kudryavtsev, Alexander N.; Krasitskaya, Vasilisa V.; Efremov, Maxim K.; Zangeeva, Sayana V.; Rogova, A. V.; Рогова, Анастасия Владимировна; Tomilin, F. N.; Томилин, Феликс Николаевич; Frank, Ludmila A.

/ S. Poolsup, E. Zaripov, N. Huttmann [et al.] // Mol. Ther. Nucleic Acids. - 2023. - Vol. 31. - P. 731-743, DOI 10.1016/j.omtn.2023.02.010. - Cited References: 74. - M.V.B. thanks the Canadian Institutes of Health Research grant OV1-170353 for providing financial support. Molecular modeling and docking were supported by a grant from the Russian Science Foundation (project number 21-73-20240) for A.S.K. S.P. is thankful to Dr. Bob Dass, Dylan Tanner, and Dr. Degang Liu, Sartorius for generously providing excellent technical training and consumable support for binding assay on BLI, and Aldo Jordan for assisting with creating the figures. The authors also thank John L. Holmes’s mass spectrometry facility for providing access to perform nLC-MS/MS. Lastly, the authors thank the JCSS Joint Super Computer Center of the Russian Academy of Sciences for providing supercomputers for computer simulations . - ISSN 2162-2531
Аннотация: The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6–3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.

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Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia
Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Poolsup, S.; Zaripov, E.; Huttmann, N.; Minic, Z.; Artyushenko, P. V.; Shchugoreva, I. A.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.; Berezovski, M. V.

/ S. A. Vyunisheva, S. A. Myslivets, N. N. Davletshin [et al.] // Spectrochim. Acta A. - 2023. - Vol. 300. - Ст. 122885, DOI 10.1016/j.saa.2023.122885. - Cited References: 23 . - ISSN 1386-1425. - ISSN 1873-3557
   Перевод заглавия: Внутрирезонаторное усиление флуоресценции GFP, индуцированное фемтосекундными лазерными импульсами
Аннотация: The phenomenon of fluorescence is widely used in molecular biology for studying the interaction of light with biological objects. In this article, we present an experimental investigation of the enhancement of laser-induced fluorescence of Clytia gregaria green fluorescent protein. The laser-induced fluorescence method applied in our work combines the advantages of femtosecond laser pulses and a photonic crystal cavity, with the time dependence of the fluorescence signal studied. It is shown that a green fluorescent protein solution placed in a microcavity and excited by femtosecond laser pulses leads to an increase in fluorescence on the microcavity modes, which can be estimated by two orders of magnitude. The dependences of fluorescence signal saturation on the average integrated optical pump power are demonstrated and analyzed. The results obtained are of interest for the development of potential applications of biophotonics and extension of convenient methods of laser-induced fluorescence.

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Держатели документа:
Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 38, Krasnoyarsk, 660036, Russia
Sukachev Institute of Forest, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 28, Krasnoyarsk, 660036, Russia
Institute of Engineering Physics and Radio Electronics, Siberian Federal University, Academician Kirensky Str. 26, Krasnoyarsk, 660074, Russia
Institute of Biophysics, Federal Research Center KSC SB RAS, Akademgorodok 50, Bldg. 50, Krasnoyarsk, 660036, Russia
Department of Chemical Technology of Wood and Biotechnology, Reshetnev Siberian State University of Science and Technology, Mira Ave. 82, Krasnoyarsk, 660049, Russia

Доп.точки доступа:
Vyunisheva, S. A.; Вьюнышева Софья Александровна; Myslivets, S. A.; Мысливец, Сергей Александрович; Davletshin, Nikolay N.; Давлетшин, Николай Николаевич; Eremeeva, Elena V.; Vysotski, Eugene S.; Pavlov, Igor N.; Vyunishev, A. M.; Вьюнышев, Андрей Михайлович

/ E. E. Bashmakova, A. N. Kudryavtsev, A. E. Tupikin [et al.] // Anal. Methods. - 2024, DOI 10.1039/D4AY00706A. - Cited References: 23 . - Article in press. - ISSN 1759-9660. - ISSN 1759-9679
Аннотация: Melanoma inhibitory activity protein (MIA) does obviously offer the potential to reveal clinical manifestations of melanoma. Despite a pressing need for effective diagnosis of this highly fatal disease, there are no clinically approved MIA detection ELISA kits available. A recommended MIA threshold has not yet been defined, mostly by reason of variability in immunoglobulins' affinity and stability, the difference in sample preparation and assay conditions. Here we present a pair of high-affinity DNA aptamers developed as an alternative recognition and binding element for MIA detection. Their stability and reproducible synthesis are expected to ensure this analysis under standard conditions. The devised aptamer-based solid-phase microassay of model standard and control human sera involves luciferase NLuc as a highly sensitive reporter. Bioluminescence dependence on MIA concentration ranges in a linear manner from 2.5 to 250 ng mL−1, providing a MIA detection limit of 1.67 ± 0.57 ng mL−1.

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Держатели документа:
Institute of Biophysics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
Kirensky Institute of Physics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk, Russia
Siberian Federal University, Krasnoyarsk, Russia

Доп.точки доступа:
Bashmakova, E. E.; Kudryavtsev, A. N.; Tupikin, A. E.; Kabilov, M. R.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Frank, L. A.