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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Antipina L. Yu., Tomilin F. N., Vysotski E. S., Ovchinnikov S. G.
Заглавие : A quantum chemical study of the formation of 2-hydroperoxy-coelenterazine in the Сa2+-regulated photoprotein obelin
Место публикации : J. Struct. Chem.: Springer, 2011. - Vol. 52, Is. 5. - P.870-875. - ISSN 0022-4766
Примечания : 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).
Предметные рубрики: CALCIUM-DISCHARGED OBELIN
SEMIEMPIRICAL METHODS
1.7 ANGSTROM
OPTIMIZATION
PARAMETERS
MECHANISM
FLUORESCENCE
ELEMENTS
PROTEIN
EMITTER
Ключевые слова (''Своб.индексиров.''): coelenterazine--2-hydroperoxy-coelenterazine--obelia longissima--renilla muelleri
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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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Alieva R. R., Tomilin F. N., Kuzubov A. A., Ovchinnikov S. G., Kudryasheva N. S.
Заглавие : Ultraviolet fluorescence of coelenteramide and coelenteramide-containing fluorescent proteins. Experimental and theoretical study
Место публикации : J. Photochem. Photobiol. B Biol.: Elsevier, 2016. - Vol. 162. - P.318-323. - ISSN 10111344 (ISSN), DOI 10.1016/j.jphotobiol.2016.07.004
Примечания : 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.
Предметные рубрики: DENSITY-FUNCTIONAL THEORY
ELECTRON-EXCITED-STATES
PHOTOPROTEIN OBELIN
DISCHARGED-OBELIN
LIGHT-EMITTERS
BIOLUMINESCENCE
AEQUORIN
LUMINESCENCE
MECHANISM
CHEMILUMINESCENCE
Ключевые слова (''Своб.индексиров.''): coelenteramide--fluorescent protein--discharged photoproteins--obelin--aequorin--fluorescence--excitation energy--fluorescence--b3lyp
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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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Gorban A., Popova T., Zinovyev A.
Заглавие : Codon usage trajectories and 7-cluster structure of 143 complete bacterial genornic sequences
Разночтения заглавия :авие SCOPUS: Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences
Место публикации : Physica A: ELSEVIER SCIENCE BV, 2005. - Vol. 353. - P365-387. - ISSN 0378-4371, DOI 10.1016/j.physa.2005.01.043
Примечания : Cited References: 46
Предметные рубрики: DNA-BASE COMPOSITION
ASYMMETRIC SUBSTITUTION PATTERNS
PROTEIN-CODING REGIONS
MICROBIAL GENOMES
GENE IDENTIFICATION
MARKOV-MODELS
G+C CONTENT
BIAS
PREDICTION
SELECTION
Ключевые слова (''Своб.индексиров.''): genome--cluster--codon usage--correlations--entropy--mean field--cluster--codon usage--correlations--entropy--genome--mean field--approximation theory--correlation methods--database systems--entropy--functions--genes--mathematical models--clusters--codon usage--genomes--mean field--bacteria
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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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Shishatskaya E. I., Nikitovic D., Shabanov A. V., Tzanakakis G. N., Tsatsakis A. M., Menzianova N. G.
Заглавие : Short-term culture of monocytes as an in vitro evaluation system for bionanomaterials designated for medical use
Место публикации : Food Chem. Toxicol.: Elsevier, 2016. - Vol. 96. - P.302-308. - ISSN 02786915 (ISSN), DOI 10.1016/j.fct.2016.08.025
Примечания : Cited References: 46
Предметные рубрики: MAGNETIC NANOPARTICLES
CELLULAR REDUCTION
PROTEIN CORONA
CELLS
MECHANOTRANSDUCTION
NANOMATERIALS
LOCALIZATION
BIOMATERIALS
CYTOSKELETON
ACTIVATION
Ключевые слова (''Своб.индексиров.''): biocompatible biopolymers--polyhydroxyalkanoates--nanomaterials--nanodiamonds--fullerenes--bio-nanomaterials--monocytes
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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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Zamay G. S., Zamay T., Kolovsky V., Shabanov A. V., Kolovskaya O. S., Krat A. V., Modestov A., Sokolov A. E., Chetvergov N. A., Gargaun A., Berezovski M., Zamay S. S., Zamay A. S., Volochaev M. N., Svetlichnyi V., Lapin I. N., Shabalina A.
Заглавие : Magnetic beads increase the detection limit of aptamer-based electrochemical sensor
Коллективы : Euro-Asian Symposium "Trends in MAGnetism", "Trends in MAGnetism", Euro-Asian Symposium, Институт физики им. Л.В. Киренского Сибирского отделения РАН
Место публикации : 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. - ISBN 978-5-904603-06-9 (Шифр -478014040)
Примечания : This work was supported by Ministry of Education and Science of Russian Federation Federal Target Program # 14.604.21.0105 (RFMEFI60414X0105)
Ключевые слова (''Своб.индексиров.''): magnetic beads--protein--aptamer--electrochemical sensor
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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Zamay G. S., Zamay T. N., Kolovskii V. A., Shabanov A. V., Glazyrin Y. E., Veprintsev D. V., Krat A. V., Zamay S. S., Kolovskaya O. S., Gargaun A., Sokolov A. E., Modestov A. A., Artyukhov I. P., Chesnokov N. V., Petrova M. M., Berezovski M. V., Zamay A. S.
Заглавие : Electrochemical aptasensor for lung cancer-related protein detection in crude blood plasma samples
Коллективы : Ministry of Education and Science of Russian Federation Federal Target Program [14.604.21.0105]
Место публикации : Sci. Rep. - 2016. - Vol. 6. - Ст.34350. - ISSN 2045-2322, DOI 10.1038/srep34350
Примечания : 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.
Предметные рубрики: SQUARE-WAVE VOLTAMMETRY
GENE-EXPRESSION
SERUM
BIOSENSORS
DIAGNOSIS
ADENOCARCINOMA
BIOMARKERS
SENSOR
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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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kudryasheva N. S., Kovel E. S.
Заглавие : Monitoring of Low-Intensity Exposures via Luminescent Bioassays of Different Complexity: Cells, Enzyme Reactions, and Fluorescent Proteins
Место публикации : Int. J. Mol. Sci. - 2019. - Vol. 20, Is. 18. - Ст.4451. - ISSN 14220067 (ISSN), DOI 10.3390/ijms20184451
Примечания : 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.
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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Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Lupu, Loredana, Wiegand, Pascal, Huttmann N., Rawer, Stephan, Kleinekofort, Wolfgang, Shugureva, Irina, Kichkailo, Anna S., Tomilin F. N., Lazarev, Alexander, Berezovski, Maxim V., Przybylski, Michael
Заглавие : Molecular epitope determination of aptamer complexes of the multidomain protein C-met by proteolytic affinity-mass spectrometry
Коллективы : LOEWE-3 Funding Agency, Hessen-Agentur, Wiesbaden, Germany [696/19-16]
Место публикации : ChemMedChem. - 2020. - Vol. 15, Is. 4. - P.363-369. - ISSN 1860-7179, DOI 10.1002/cmdc.201900489. - ISSN 1860-7187(eISSN)
Примечания : 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
Предметные рубрики: DNA APTAMERS
ANTIBODIES
RECOGNITION
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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Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Smolyarova T. E., Lukyanenko A. V., Shanidze L. V., Krasitskaya V. V., Tarasov A. S., Volkov N. V.
Заглавие : Protein biosensor based on nanowire field effect transistor
Коллективы : Asian School-Conference on Physics and Technology of Nanostructured Materials, Азиатская школа-конференция по физике и технологии наноструктурированных материалов
Место публикации : The Fifth Asian School-Conference on Physics and Technology of Nanostructured Materials: Proceedings. - VLadivostok: Dalnauka Publishing, 2020. - Ст.VII.31.03p. - P.195. - ISBN 978-5-8044-1698-1
Примечания : 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.
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10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Smolyarova T. E., Shanidze, Lev V., Lukyanenko A. V., Baron F. A., Krasitskaya, Vasilisa V., Kichkailo, Anna S., Tarasov A. S., Volkov N. V.
Заглавие : Protein biosensor based on Schottky barrier nanowire field effect transistor
Место публикации : Talanta. - 2022. - Vol. 239. - Ст.123092. - ISSN 0039-9140 (ISSN), DOI 10.1016/j.talanta.2021.123092. - ISSN 1873-3573 (eISSN)
Примечания : 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
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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11.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Cazacu, Nicoleta, Chilom, Claudia G., Iftimie, Sorina, Balasoiu, Maria, Ladygina, Valentina P., Stolyar S. V., Orelovich, Oleg L., Kovalev, Yuriy S., Rogachev, Andrey V.
Заглавие : Biogenic ferrihydrite nanoparticles produced by Klebsiella oxytoca: Characterization, physicochemical properties and bovine serum albumin interactions
Место публикации : Nanomaterials. - 2022. - Vol. 12, Is. 2. - Ст.249. - ISSN 2079-4991(eISSN), DOI 10.3390/nano12020249
Примечания : 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)
Предметные рубрики: MAGNETIC-PROPERTIES
REDUCTION
MOSSBAUER
FERRITIN
DOCKING
BINDING
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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12.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Krasitskaya V. V., Kudryavtsev A. N., Yaroslavtsev R. N., Gerasimova Yu. V., Velikanov D. A., Bayukov O. A., Stolyar S. V., Frank L. A.
Заглавие : Starch-coated magnetic iron oxide nanoparticles for affinity purification of recombinant proteins
Место публикации : Int. J. Mol. Sci. - 2022. - Vol. 23, Is. 10. - Ст.5410. - ISSN 16616596 (ISSN), DOI 10.3390/ijms23105410
Примечания : 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
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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13.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kudryavtsev, Alexander N., Krasitskaya, Vasilisa V., Efremov, Maxim K., Zangeeva, Sayana V., Rogova A. V., Tomilin F. N., Frank, Ludmila A.
Заглавие : Ca2+-triggered coelenterazine-binding protein Renilla: Expected and unexpected features
Место публикации : Int. J. Mol. Sci. - 2023. - Vol. 24, Is. 3. - Ст.2144. - ISSN 16616596 (ISSN), DOI 10.3390/ijms24032144. - ISSN 14220067 (eISSN)
Примечания : 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
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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14.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Poolsup S., Zaripov E., Huttmann N., Minic Z., Artyushenko P. V., Shchugoreva I. A., Tomilin F. N., Kichkailo A. S., Berezovski M. V.
Заглавие : Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics
Место публикации : Mol. Ther. Nucleic Acids. - 2023. - Vol. 31. - P.731-743. - ISSN 21622531 (eISSN), DOI 10.1016/j.omtn.2023.02.010
Примечания : 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
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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15.

Вид документа : Статья из журнала
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Автор(ы) : Vyunisheva S. A., Myslivets S. A., Davletshin, Nikolay N., Eremeeva, Elena V., Vysotski, Eugene S., Pavlov, Igor N., Vyunishev A. M.
Заглавие : Intracavity enhancement of GFP fluorescence induced by femtosecond laser pulses
Колич.характеристики :5 с
Место публикации : Spectrochim. Acta A. - 2023. - Vol. 300. - Ст.122885. - ISSN 13861425 (ISSN), DOI 10.1016/j.saa.2023.122885. - ISSN 18733557 (eISSN)
Примечания : Cited References: 23
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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16.

Вид документа : Статья из журнала
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Автор(ы) : Bashmakova E. E., Kudryavtsev A. N., Tupikin A. E., Kabilov M. R., Sokolov A. Е., Frank L. A.
Заглавие : Bioluminescent aptamer-based microassay for detection of melanoma inhibitory activity protein (MIA)
Место публикации : Anal. Methods. - 2024. - Article in press. - ISSN 17599660 (ISSN), DOI 10.1039/D4AY00706A. - ISSN 17599679 (eISSN)
Примечания : Cited References: 23
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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