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Moiseeva AN, Makoveeva KA, Furkina EB, Artyushova EV, German MN, Khomenko IA, Konevega AL, Kormazeva ES, Novikov VI, Aksenov NV, Gustova NS, Aliev RA. Co-production of 155Tb and 152Tb irradiating 155Gd / 151Eu tandem target with a medium energy α-particle beam. Nucl Med Biol 2023; 126-127:108389. [PMID: 37783103 DOI: 10.1016/j.nucmedbio.2023.108389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/27/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023]
Abstract
INTRODUCTION Four terbium isotopes 149,152,155,161Tb emitting various types of radiation can be used for both diagnostics and therapy. 152Tb emits positrons and is ideal for PET. 155Tb is considered a promising Auger emitter and a diagnostic pair for other terbium therapeutic isotopes. Several methods for the production of 155Tb using charged particle accelerators have been proposed, but they all have significant limitations. The restricted availability of this isotope hinders its medical applications. We have proposed a new method for production of 155Tb, irradiating enriched 155Gd by alpha particles. The possibility of simultaneous production of two isotopes of terbium, 152,155Tb, was also studied for more efficient cyclotron beam use. METHODS Irradiation of 155Gd enriched targets and 155Gd / 151Eu tandem target with alpha-particles with an energy of 54 MeV was carried out at the U-150 cyclotron at the NRC "Kurchatov Institute". The cross sections of nuclear reactions on enr-155Gd were measured by the stack foil technique, detecting the gamma-radiation of the activation products. The separation of rare earth elements was performed by extraction chromatography with the LN Resin. 155Tb was produced via 155Dy decay. RESULTS The cross sections for the 155,156Tb and 155,157Dy production were measured by the irradiation of a gadolinium target enriched with the 155Gd isotope with alpha-particles in an energy range of 54 → 33 MeV. The yield of 155Dy on a thick target at 54 MeV was 130 MBq/μAh, which makes it possible to obtain 1 GBq of 155Tb in 11 hour-irradiation with 20 μA beam current. The possibility of simultaneous production of 152,155Tb by irradiation of 155Gd and 151Eu tandem target with medium-energy alpha-particles is implemented. Optimal irradiation energy ranges of alpha -particles as 54 → 42 MeV for 155Tb and 42 → 34 MeV for 152Tb were suggested. Product activity and radionuclidic purity were calculated.
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Affiliation(s)
- A N Moiseeva
- National Research Center "Kurchatov Institute", Russia.
| | - K A Makoveeva
- National Research Center "Kurchatov Institute", Russia
| | - E B Furkina
- National Research Center "Kurchatov Institute", Russia
| | | | - M N German
- National Research Center "Kurchatov Institute", Russia
| | - I A Khomenko
- National Research Center "Kurchatov Institute", Russia
| | - A L Konevega
- National Research Center "Kurchatov Institute", Russia
| | - E S Kormazeva
- National Research Center "Kurchatov Institute", Russia
| | - V I Novikov
- National Research Center "Kurchatov Institute", Russia
| | - N V Aksenov
- Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Russia
| | - N S Gustova
- Flerov Laboratory of Nuclear Reactions, Joint Institute for Nuclear Research, Russia
| | - R A Aliev
- National Research Center "Kurchatov Institute", Russia
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Egorov VV, Shvetsov AV, Pichkur EB, Shaldzhyan AA, Zabrodskaya YA, Vinogradova DS, Nekrasov PA, Gorshkov AN, Garmay YP, Kovaleva AA, Stepanova LA, Tsybalova LM, Shtam TA, Myasnikov AG, Konevega AL. Inside and outside of virus-like particles HBc and HBc/4M2e: A comprehensive study of the structure. Biophys Chem 2023; 293:106943. [PMID: 36495688 DOI: 10.1016/j.bpc.2022.106943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 12/11/2022]
Abstract
Hepatitis B virus core antigen (HBc) with the insertion of four external domains of the influenza A M2 protein (HBc/4M2e) form virus-like particles whose structure was studied using a combination of molecular modeling and cryo-electron microscopy (cryo-EM). It was also shown that self-assembling of the particles occurs inside bacterial cells, but despite the big inner volume of the core shell particle, purified HBc/4M2e contain an insignificant amount of bacterial proteins. It was shown that a fragment of the M2e corresponding to 4M2e insertion is prone to formation of amyloid-like fibrils. However, as the part of the immunodominant loop, M2e insertion does not show a tendency to intermolecular interaction. A full-atomic HBc-4M2e model with the resolution of about 3 Å (3.13 Å for particles of Т = 4 symmetry, 3.7 Å for particles of Т = 3 symmetry) was obtained by molecular modeling methods based on cryo-EM data.
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Affiliation(s)
- V V Egorov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation; Institute of Experimental Medicine, Academika Pavlova, 12, 197376 St. Petersburg, Russian Federation.
| | - A V Shvetsov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation; Peter the Great St.Petersburg Polytechnic University, Politehnicheskaya 29, St. Petersburg, Russian Federation
| | - E B Pichkur
- National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation
| | - A A Shaldzhyan
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - Ya A Zabrodskaya
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation; Peter the Great St.Petersburg Polytechnic University, Politehnicheskaya 29, St. Petersburg, Russian Federation
| | - D S Vinogradova
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation
| | - P A Nekrasov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - A N Gorshkov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - Yu P Garmay
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation
| | - A A Kovaleva
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - L A Stepanova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - L M Tsybalova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, 197376, Prof. Popov St. 15/17, St. Petersburg, Russian Federation
| | - T A Shtam
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation
| | - A G Myasnikov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation
| | - A L Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre «Kurchatov Institute», Orlova roscha 1, Gatchina 188300, Russian Federation; National Research Center "Kurchatov Institute", Akademika Kurchatova pl. 1, 123182 Moscow, Russian Federation; Peter the Great St.Petersburg Polytechnic University, Politehnicheskaya 29, St. Petersburg, Russian Federation
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Lebedev DV, Egorov VV, Shvetsov AV, Zabrodskaya YA, Isaev-Ivanov VV, Konevega AL. Erratum to:Neutron Scattering Techniques and Complementary Methods for Structural and Functional Studies of Biological Macromolecules and Large Macromolecular Complexes. CRYSTALLOGR REP+ 2022. [DOI: 10.1134/s1063774521340034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Paleskava A, Kaiumov MY, Kirillov SV, Konevega AL. Peculiarities in Activation of Hydrolytic Activity of Elongation Factors. Biochemistry (Mosc) 2021; 85:1422-1433. [PMID: 33280582 DOI: 10.1134/s0006297920110103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Translational GTPases (trGTPases) belong to the family of G proteins and play key roles at all stages of protein biosynthesis on the ribosome. Unidirectional and cyclic functioning of G proteins is ensured by their ability to switch between the active and inactive states due to GTP hydrolysis accelerated by the auxiliary GTPase-activating proteins. Although trGTPases interact with the ribosomes in different conformational states, they bind to the same conserved region, which, unlike in classical GTPase-activating proteins, is represented by ribosomal RNA. The resulting catalytic sites have almost identical structure in all elongation factors suggesting a common mechanism of GTP hydrolysis. However, fine details of the activated state formation and significantly different rates of GTP hydrolysis indicate the existence of distinctive features upon GTP hydrolysis catalyzed by the different factors. Here, we present a contemporary view on the mechanism of GTPase activation and GTP hydrolysis by the elongation factors EF-Tu, EF-G, and SelB based on the analysis of structural, biochemical, and bioinformatics data.
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Affiliation(s)
- A Paleskava
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute", Gatchina, Leningrad Region, 188300, Russia
| | - M Yu Kaiumov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute", Gatchina, Leningrad Region, 188300, Russia
| | - S V Kirillov
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute", Gatchina, Leningrad Region, 188300, Russia
| | - A L Konevega
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of NRC "Kurchatov Institute", Gatchina, Leningrad Region, 188300, Russia.
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Lebedev DV, Egorov VV, Shvetsov AV, Zabrodskaya YA, Isaev-Ivanov VV, Konevega AL. Neutron Scattering Techniques and Complementary Methods for Structural and Functional Studies of Biological Macromolecules and Large Macromolecular Complexes. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521020103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract
The review describes the application of small-angle scattering (SAS) of neutrons and complementary methods to study the structures of biomacromolecules. Here we cover SAS techniques, such as the contrast variation, the neutron spin-echo, and the solution of direct and inverse problems of three-dimensional reconstruction of the structures of macromolecules from SAS spectra by means of molecular modeling. A special section is devoted to specific objects of research, such as supramolecular complexes, influenza virus nucleoprotein, and chromatin.
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Shvetsov AV, Lebedev DV, Zabrodskaya YA, Shaldzhyan AA, Egorova MA, Vinogradova DS, Konevega AL, Gorshkov AN, Ramsay ES, Radulescu A, Sergeeva MV, Plotnikova MA, Komissarov AB, Taraskin AS, Lebedev KI, Garmay YP, Kuznetsov VV, Isaev-Ivanov VV, Vasin AV, Tsybalova LM, Egorov VV. Cold and distant: structural features of the nucleoprotein complex of a cold-adapted influenza A virus strain. J Biomol Struct Dyn 2020; 39:4375-4384. [PMID: 32490728 DOI: 10.1080/07391102.2020.1776636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Two influenza A nucleoprotein variants (wild-type: G102R; and mutant: G102R and E292G) were studied with regard to macro-molecular interactions in oligomeric form (24-mers). The E292G mutation has been previously shown to provide cold adaptation. Molecular dynamics simulations of these complexes and trajectory analysis showed that the most significant difference between the obtained models was distance between nucleoprotein complex strands. The isolated complexes of two ribonucleoprotein variants were characterized by transmission electron microscopy and differential scanning fluorimetry (DSF). Presence of the E292G substitution was shown by DSF to affect nucleoprotein complex melting temperature. In the filament interface peptide model, it was shown that the peptide corresponding in primary structure to the wild-type NP (SGYDFEREGYS) is prone to temperature-dependent self-association, unlike the peptide corresponding to E292G substitution (SGYDFGREGYS). It was also shown that the SGYDFEREGYS peptide is capable of interacting with a monomeric nucleoprotein (wild type); this interaction's equilibrium dissociation constant is five orders of magnitude lower than for the SGYDFGREGYS peptide. Using small-angle neutron scattering (SANS), the supramolecular structures of isolated complexes of these proteins were studied at temperatures of 15, 32, and 37 °C. SANS data show that the structures of the studied complexes at elevated temperature differ from the rod-like particle model and react differently to temperature changes. The data suggest that the mechanism behind cold adaptation with E292G is associated with a weakening of the interaction between strands of the ribonucleoprotein complex and, as a result, the appearance of inter-chain interface flexibility necessary for complex function at low temperature.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- A V Shvetsov
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia
| | - D V Lebedev
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia
| | - Y A Zabrodskaya
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A A Shaldzhyan
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - M A Egorova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - D S Vinogradova
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,NanoTemper Technologies Rus, St. Petersburg, Russia
| | - A L Konevega
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia
| | - A N Gorshkov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - E S Ramsay
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A Radulescu
- Jülich Centre, Neutron Science at Heinz Maier-Leibnitz Zentrum, Garching, Munich, Germany
| | - M V Sergeeva
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - M A Plotnikova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A B Komissarov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - A S Taraskin
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - K I Lebedev
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia.,Pavlov First Saint Petersburg State Medical University, St. Petersburg, Russia
| | - Yu P Garmay
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
| | - V V Kuznetsov
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - V V Isaev-Ivanov
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia
| | - A V Vasin
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia.,St. Petersburg State Chemical-Pharmaceutical Academy, St. Petersburg, Russia
| | - L M Tsybalova
- Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia
| | - V V Egorov
- Petersburg Nuclear Physics Institute named by B. P, Konstantinov of National Research Center "Kurchatov Institute", Gatchina, Russia.,National Research Centre Kurchatov Institute, Moscow, Russia.,Smorodintsev Research Institute of Influenza, Russian Ministry of Health, St. Petersburg, Russia.,Federal State Budgetary Scientific Institution "Institute of Experimental Medicine", St. Petersburg, Russia
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Shtam TA, Samsonov RA, Volnitskiy AV, Kamyshinsky RA, Verlov NA, Kniazeva MS, Korobkina EA, Orehov AS, Vasiliev AL, Konevega AL, Malek AV. [Isolation of extracellular micro-vesicles from cell culture medium: comparative evaluation of methods]. Biomed Khim 2019; 64:23-30. [PMID: 29460831 DOI: 10.18097/pbmc20186401023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Extracellular vesicles (EV) are secreted by cells of multicellular organisms. EV mediate specific mode of intercellular communication by "horizontal" exchange of substances and information. This phenomenon seems to have an essential biological significance and became a subject of intensive research. Biogenesis, structural and functional features of the EV is being commonly studies in in vitro condition. Several methods of EV isolation from cell culture medium are established, however selection of method might influence on obtained results. The choice of the optimal method depends usually from the amount of medium and the aims of the research while is still challenging issue. We performed a comparative analysis of four different methods of EV isolation from cell culture medium: differential ultracentrifugation, ultracentrifugation with a 30% sucrose/D2O "cushion", precipitation with plant proteins and immune-affinity capturing. EV isolated by different approaches were compared in terms of following parameters: size, concentration, morphology of EV, contamination by non-vesicular particles, content of exosomal tetraspanins on the EV surface, content of total proteins, RNA, and several glioma-associated miRNAs. Applied methods included nano-patricle tracking analysis (NTA), dynamic light scattering (DLS), cryo-electron microscopy, flow cytometry and RT-qPCR. On the base of obtained results, we developed practical recommendations that may help researchers to make a best choice of EV isolation method.
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Affiliation(s)
- T A Shtam
- Petersburg Nuclear Physics Institute of National Research Centre "Kurchatov Institute", Saint-Petersburg, Gatchina, Russia; Oncosystem" Ltd., Skolkovo, Russia; N.N.Petrov National Medical Research center of Oncology, Saint-Petersburg, Russia; Peter the Great Saint-Petersburg Polytechnic University, St. Petersburg, Russia
| | - R A Samsonov
- Oncosystem" Ltd., Skolkovo, Russia; N.N.Petrov National Medical Research center of Oncology, Saint-Petersburg, Russia
| | - A V Volnitskiy
- Petersburg Nuclear Physics Institute of National Research Centre "Kurchatov Institute", Saint-Petersburg, Gatchina, Russia
| | - R A Kamyshinsky
- National Research Center "Kurchatov Institute", Moscow, Russia
| | - N A Verlov
- Petersburg Nuclear Physics Institute of National Research Centre "Kurchatov Institute", Saint-Petersburg, Gatchina, Russia
| | - M S Kniazeva
- Peter the Great Saint-Petersburg Polytechnic University, St. Petersburg, Russia
| | - E A Korobkina
- Peter the Great Saint-Petersburg Polytechnic University, St. Petersburg, Russia
| | - A S Orehov
- National Research Center "Kurchatov Institute", Moscow, Russia
| | - A L Vasiliev
- National Research Center "Kurchatov Institute", Moscow, Russia
| | - A L Konevega
- Petersburg Nuclear Physics Institute of National Research Centre "Kurchatov Institute", Saint-Petersburg, Gatchina, Russia; Peter the Great Saint-Petersburg Polytechnic University, St. Petersburg, Russia
| | - A V Malek
- Oncosystem" Ltd., Skolkovo, Russia; N.N.Petrov National Medical Research center of Oncology, Saint-Petersburg, Russia
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Shtam TA, Samsonov RB, Volnitskiy AV, Kamyshinsky RA, Verlov NA, Kniazeva MS, Korobkina EA, Orehov AS, Vasiliev AL, Konevega AL, Malek AV. Isolation of Extracellular Microvesicles from Cell Culture Medium: Comparative Evaluation of Methods. Biochem Moscow Suppl Ser B 2018. [DOI: 10.1134/s1990750818020117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Tereshchenkov AG, Shishkina AV, Karpenko VV, Chertkov VA, Konevega AL, Kasatsky PS, Bogdanov AA, Sumbatyan NV. New Fluorescent Macrolide Derivatives for Studying Interactions of Antibiotics and Their Analogs with the Ribosomal Exit Tunnel. Biochemistry (Mosc) 2017; 81:1163-1172. [PMID: 27908240 DOI: 10.1134/s0006297916100138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Novel fluorescent derivatives of macrolide antibiotics related to tylosin bearing rhodamine, fluorescein, Alexa Fluor 488, BODIPY FL, and nitrobenzoxadiazole (NBD) residues were synthesized. The formation of complexes of these compounds with 70S E. coli ribosomes was studied by measuring the fluorescence polarization depending on the ribosome amount at constant concentration of the fluorescent substance. With the synthesized fluorescent tylosin derivatives, the dissociation constants for ribosome complexes with several known antibiotics and macrolide analogs previously obtained were determined. It was found that the fluorescent tylosin derivatives containing BODIPY FL and NBD groups could be used to screen the binding of novel antibiotics to bacterial ribosomes in the macrolide-binding site.
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Affiliation(s)
- A G Tereshchenkov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.
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Konevega AL, Soboleva NG, Makhno VI, Peshekhonov AV, Katunin VI. [The effect of modification of tRNA nucleotide-37 on the tRNA interaction with the P- and A-site of the 70S ribosome Escherichia coli]. Mol Biol (Mosk) 2006; 40:669-83. [PMID: 16913226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A modified nucleotide on the 3'-side of the anticodon loop of tRNA is one of the most important structure element regulating codon-anticodone interaction on the ribosome owing to the stacking interaction with the stack of codon-anticodon bases. The presence and identity (pyrimidine, purine or modified purine) of this nucleotide has an essential influence on the energy of the stacking interaction on A- and P-sites of the ribosome. There is a significant influence of the 37-modification by itself on the P-site, whereas there is no such one on the A-site of the ribosome. Comparison of binding enthalpies of tRNA interactions on the P- or A-site of the ribosome with the binding enthalpies of the complex of two tRNAs with the complementary anticodones suggests that the ribosome by itself significantly endows in the thermodynamics of codon-anticodon complex formation. It happens by additional ribosomal interactions with the molecule of tRNA or indirectly by the stabilization of codon-anticodon conformation. In addition to the stacking, tRNA binding in the A and P sites is futher stabilized by the interactions involving some magnesium ions. The number of them involved in those interactions strongly depends on the nucleotide identity in the 37-position of tRNA anticodon loop.
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Konevega AL, Soboleva NG, Makhno VI, Peshekhonov AV, Katunin VI. Effect of modification of tRNA nucleotide 37 on the tRNA interaction with the A and P sites of the Escherichia coli 70S ribosome. Mol Biol 2006. [DOI: 10.1134/s0026893306040121] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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13
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Soboleva NG, Makhno VI, Konevega AL, Semenkov IP, Katunin VI. [The effect of modification of nucleotide-37 on the interaction of aminoacyl-tRNA with the A-site of the 70S ribosome]. Mol Biol (Mosk) 2003; 37:121-7. [PMID: 12624954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
To estimate the effect of modified nucleotide-37, the interaction of two yeast aminoacyl-tRNAs (Phe-tRNAK+YPhe and Phe-tRNAK-YPhe) with the A site of complex [70S.poly(U).deacylated tRNA(Phe) in the P site] was assayed at 0-20 degrees C. As comparisons with native Phe-tRNAK+YPhe showed, removal of the Y base decreased the association constant of Phe-tRNAK-YPhe and the complex by an order of magnitude at any temperature, and increased the enthalpy of their interaction by 23 kJ/mol. When the Y base was present in the anticodon loop of deacylated tRNA(Phe) bound to the P site of the 70S ribosome, twice higher affinity for the A site was observed for Phe-tRNAK-YPhe but not for Phe-tRNAK+YPhe. Thus, the modified nucleotide 3' of the Phe-tRNA(Phe) anticodon stabilized the codon-anticodon interaction both in the A and in the P sites of the 70S ribosome.
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Affiliation(s)
- N G Soboleva
- Konstantinov Institute of Nuclear Physics, Russian Academy of Sciences, Gatchina, Leningrad Oblast, 188300 Russia
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