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Zagustina NA, Misharina TA, Veprizky AA, Zhukov VG, Ruzhitsky AO, Terenina MB, Krikunova NI, Kulikova AK, Popov VO. Elimination of volatile compounds of leaf tobacco from air emissions using biofiltration. APPL BIOCHEM MICRO+ 2012. [DOI: 10.1134/s000368381204014x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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52
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Zagustina NA, Misharina TA, Vepritskiĭ AA, Zhukov VG, Ruzhitskiĭ AO, Terenina MB, Krikunova NI, Kulikova AK, Popov VO. [Elimination of volatile compounds of leaf tobacco from air emissions using biofiltration]. PRIKLADNAIA BIOKHIMIIA I MIKROBIOLOGIIA 2012; 48:425-36. [PMID: 23035576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The composition of the volatile organic compounds (VOCs) of various leaf tobacco brands and their blends has been studied. The differences in the content of nicotine, solanone, tetramethyl hexadecenol, megastigmatrienones, and other compounds, determining the specific tobacco smell, have been revealed. A microbial consortium, which is able to deodorize simulated tobacco emissions and decompose nicotine, has been formed by long-term adaptation to the VOCs of tobacco leaves in a laboratory reactor, functioning as a trickle-bed biofilter. Such a biofilter eliminates 90% of the basic toxic compound (nicotine) and odor-active compounds; the filtration efficiency does not change for tobacco brands with different VOC concentrations or in the presence of foreign substances. The main strains, isolated from the formed consortium and participating in the nicotine decomposition process, belong to the genera Pseudomonas, Bacillus, and Rhodococcus. An examination of the biofilter trickling fluid has shown full decomposition of nicotine and odor-active VOCs. The compounds, revealed in the trickling fluid, did not have any odor and were nontoxic. The obtained results make it possible to conduct scaling of the biofiltration process to eliminate odor from air emissions in the tobacco industry.
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Slutskaya ES, Bezsudnova EY, Mardanov AV, Gumerov VM, Rakitina TV, Popov VO, Lipkin VM. Characterization of a novel M42 aminopeptidase from crenarchaeon Desulfurococcus kamchatkensis. DOKL BIOCHEM BIOPHYS 2012; 442:30-2. [DOI: 10.1134/s1607672912010097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Indexed: 11/23/2022]
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54
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Bonartsev AP, Yakovlev SG, Filatova EV, Soboleva GM, Makhina TK, Bonartseva GA, Shaitan KV, Popov VO, Kirpichnikov MP. Sustained release of the antitumor drug paclitaxel from poly(3-hydroxybutyrate)-based microspheres. BIOCHEMISTRY (MOSCOW) SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2012. [DOI: 10.1134/s1990750812010027] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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55
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Hendrickson OD, Safenkova IV, Zherdev AV, Dzantiev BB, Popov VO. Methods of detection and identification of manufactured nanoparticles. Biophysics (Nagoya-shi) 2012. [DOI: 10.1134/s0006350911060066] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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56
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Lysenko EA, Turtikova OV, Morozkina EV, Khotchenkov VP, Popov VO, Shenkman BS. [Effects of recombinant mechano-dependent growth factor against the background of chronic alcoholisation in rats]. ROSSIISKII FIZIOLOGICHESKII ZHURNAL IMENI I.M. SECHENOVA 2012; 98:283-292. [PMID: 22650072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In alcoholised rats, proliferation of satellite cells consistently decreased as well as the number of myonuclei, while phosphorylation of p90RSK became reduced. The mechano-growth factor abministration increased the proliferate activity of the myogenic precursors and restored the myonuclei pool. Phosphorylation of p90RSK increased too.
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57
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Petrova TE, Bezsudnova EY, Dorokhov BD, Slutskaya ES, Polyakov KM, Dorovatovskiy PV, Ravin NV, Skryabin KG, Kovalchuk MV, Popov VO. Expression, purification, crystallization and preliminary crystallographic analysis of a thermostable DNA ligase from the archaeon Thermococcus sibiricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:163-5. [PMID: 22297989 PMCID: PMC3274393 DOI: 10.1107/s1744309111050913] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 11/26/2011] [Indexed: 11/10/2022]
Abstract
DNA ligases join single-strand breaks in double-stranded DNA by catalyzing the formation of a phosphodiester bond between adjacent 5'-phosphate and 3'-hydroxyl termini. Their function is essential to maintain the integrity of the genome in DNA replication, recombination and repair. A recombinant ATP-dependent DNA ligase from the hyperthermophilic anaerobic archaeon Thermococcus sibiricus was expressed in Escherichia coli and purified. Crystals were grown by vapour diffusion using the hanging-drop method with 17%(w/v) PEG 4000 and 8.5%(v/v) 2-propanol as precipitants. A diffraction experiment was performed with a single crystal, which diffracted X-rays to 3.0 Å resolution. The crystal belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 58.590, b = 87.540, c = 126.300 Å.
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58
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Gorbacheva MA, Yarosh AG, Dorovatovskii PV, Rakitina TV, Boiko KM, Korzhenevskii DA, Lipkin AV, Popov VO, Shumilin IA. A novel approach to studying the structural and functional properties of proteins with unknown functions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012; 38:99-105. [DOI: 10.1134/s1068162012010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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59
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Nilov DK, Shabalin IG, Popov VO, Svedas VK. Investigation of formate transport through the substrate channel of formate dehydrogenase by steered molecular dynamics simulations. BIOCHEMISTRY (MOSCOW) 2011; 76:172-4. [PMID: 21568849 DOI: 10.1134/s0006297911020027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Steered molecular dynamics simulation has revealed the mechanism of formate transport via the substrate channel of formate dehydrogenase. It is shown that the structural organization of the channel promotes the transport of formate anion in spite of the fact that the channel is too narrow even for such a small molecule. The conformational mobility of Arg284 residue, one of the residues forming the wall of the substrate channel, provides for the binding and delivery of formate to the active site.
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60
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Gendrikson OD, Safenkova IV, Zherdev AV, Dzantiev BB, Popov VO. [Methods of detection and identification of manufactured nanoparticles]. BIOFIZIKA 2011; 56:965-994. [PMID: 22279742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The actual methods of detection and identification of manufactured nanoparticles in both simple and complex multi-component matrix for assessing biological effects and safety of nanotechnology products have been reviewed. The detection of priority species of biologically active nanoparticles, which include fullerenes, single- and multi-walled carbon nanotubes, nanoparticles of silver, gold, titanium oxide, aluminum, cerium, zinc and silicon, has been given a special attention. The requirements for sample preparation have been discussed. The results of the successful application for the detection of manufactured nanoparticles in bioassays with methods of scanning and transmission electron microscopy, confocal laser scanning microscopy, atomic force microscopy, scanning tunneling microscopy, size exclusion chromatography, field-flow fractionation, electrophoretic, light scattering, spectrophotometry, fluorescent spectroscopy, X-ray and other spectrometry, mass spectrometry, "particle counters", immunochemistry have been reviewed. The possibilities and limitations of different techniques, and their complementarity have been analyzed.
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61
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Bonartsev AP, Iaovlev SG, Filatova EV, Soboleva GM, Makhina TK, Bonartseva GA, Shaĭtan KV, Popov VO, Kirpichnikov MP. [Sustained release of the antitumor drug paclitaxel from poly(3-hydroxybutyrate)-based microspheres]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2011; 57:232-40. [PMID: 21870610 DOI: 10.18097/pbmc20115702232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Development of systems of medicines with sustained action on the basis of biodegradable polymers is a promising trend in modem pharmacology. Polyhydroxyalkanoates (POA) attract increasing attention due to their biodegradability and high biocompatibility, which make them suitable for development of novel drug dosage forms. We obtained microspheres on the basis of poly(3-hydroxybutyrate) (PHB) loaded with the antitumor drug paclitaxel. Morphology, drug release kinetics and effect on tumor cells in vitro of microspheres were studied. The data on the kinetics of drug release, biocompatibility and biological activity of the biopolymer microspheres in vitro showed that the studied system of prolonged drug release had lower toxicity and higher efficiency compared to the traditional dosage forms of paclitaxel.
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Khomenkov VG, Shevelev AB, Zhukov VG, Zagustina NA, Bezborodov AM, Popov VO. Organization of metabolic pathways and molecular-genetic mechanisms of xenobiotic degradation in microorganisms: A review. APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683808020014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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63
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Tikhonova TV, Slutskaya ES, Filimonenkov AA, Boyko KM, Kleimenov SY, Konarev PV, Polyakov KM, Svergun DI, Trofimov AA, Khomenkov VG, Zvyagilskaya RA, Popov VO. Isolation and oligomeric composition of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens. BIOCHEMISTRY (MOSCOW) 2011; 73:164-70. [DOI: 10.1134/s0006297908020077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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64
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Shishkin SS, Kovalyov LI, Kovalyova MA, Lisitskaya KV, Eremina LS, Ivanov AV, Gerasimov EV, Sadykhov EG, Ulasova NY, Sokolova OS, Toropygin IY, Popov VO. Prostate Cancer Proteomics" Database. Acta Naturae 2010. [DOI: 10.32607/20758251-2010-2-4-95-104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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65
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Filimonenkov AA, Zvyagilskaya RA, Tikhonova TV, Popov VO. Isolation and characterization of nitrate reductase from the halophilic sulfur-oxidizing bacterium Thioalkalivibrio nitratireducens. BIOCHEMISTRY (MOSCOW) 2010; 75:744-51. [PMID: 20636266 DOI: 10.1134/s000629791006009x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A novel nitrate reductase (NR) was isolated from cell extract of the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens strain ALEN 2 and characterized. This enzyme is a classical nitrate reductase containing molybdopterin cofactor in the active site and at least one iron-sulfur cluster per subunit. Mass spectrometric analysis showed high homology of NR with the catalytic subunit NarG of the membrane nitrate reductase from the moderately halophilic bacterium Halomonas halodenitrificans. In solution, NR exists as a monomer with a molecular weight of 130-140 kDa and as a homotetramer of about 600 kDa. The specific nitrate reductase activity of NR is 12 micromol/min per mg protein, the maximal values being observed within the neutral range of pH. Like other membrane nitrate reductases, NR reduces chlorate and is inhibited by azide and cyanide. It exhibits a higher thermal stability than most mesophilic enzymes.
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66
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Shabalin IG, Serov AE, Skirgello OE, Timofeev VI, Samygina VR, Popov VO, Tishkov VI, Kuranova IP. Recombinant formate dehydrogenase from Arabidopsis thaliana: Preparation, crystal growth in microgravity, and preliminary X-ray diffraction study. CRYSTALLOGR REP+ 2010. [DOI: 10.1134/s1063774510050159] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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67
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Lyashenko AV, Bezsudnova EY, Gumerov VM, Lashkov AA, Mardanov AV, Mikhailov AM, Polyakov KM, Popov VO, Ravin NV, Skryabin KG, Zabolotniy VK, Stekhanova TN, Kovalchuk MV. Expression, purification and crystallization of a thermostable short-chain alcohol dehydrogenase from the archaeon Thermococcus sibiricus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:655-7. [PMID: 20516592 PMCID: PMC2882762 DOI: 10.1107/s1744309110002654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 01/21/2010] [Indexed: 11/10/2022]
Abstract
Alcohol dehydrogenases belong to the oxidoreductase family and play an important role in a broad range of physiological processes. They catalyze the cofactor-dependent reversible oxidation of alcohols to the corresponding aldehydes or ketones. The NADP-dependent short-chain alcohol dehydrogenase TsAdh319 from the thermophilic archaeon Thermococcus sibiricus was overexpressed, purified and crystallized. Crystals were obtained using the hanging-drop vapour-diffusion method using 25%(w/v) polyethylene glycol 3350 pH 7.5 as precipitant. The crystals diffracted to 1.68 A resolution and belonged to space group I222, with unit-cell parameters a = 55.63, b = 83.25, c = 120.75 A.
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68
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Popov VO. The 75th anniversary of the Bach Institute of Biochemistry, RAS. APPL BIOCHEM MICRO+ 2010. [DOI: 10.1134/s0003683810030014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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69
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Trofimov AA, Polyakov KM, Boĭko KM, Filimonenkov AA, Dorovatovskiĭ PV, Tikhonova TV, Popov VO, Koval’chuk MV. Structure of octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens in a complex with phosphate. CRYSTALLOGR REP+ 2010. [DOI: 10.1134/s1063774510010104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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70
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Shabalin IG, Polyakov KM, Tishkov VI, Popov VO. Atomic Resolution Crystal Structure of NAD +Dependent Formate Dehydrogenase from Bacterium Moraxella sp. C-1. Acta Naturae 2009. [DOI: 10.32607/actanaturae.10784] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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71
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Shabalin IG, Polyakov KM, Tishkov VI, Popov VO. Atomic Resolution Crystal Structure of NAD +Dependent Formate Dehydrogenase from Bacterium Moraxella sp. C-1. Acta Naturae 2009. [DOI: 10.32607/20758251-2009-1-3-89-93] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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72
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Shabalin IG, Filippova EV, Polyakov KM, Sadykhov EG, Safonova TN, Tikhonova TV, Tishkov VI, Popov VO. Structures of the apo and holo forms of formate dehydrogenase from the bacteriumMoraxellasp. C-1: towards understanding the mechanism of the closure of the interdomain cleft. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:1315-25. [DOI: 10.1107/s0907444909040773] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 10/06/2009] [Indexed: 11/10/2022]
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73
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Shabalin IG, Polyakov KM, Tishkov VI, Popov VO. Atomic Resolution Crystal Structure of NAD(+)-Dependent Formate Dehydrogenase from Bacterium Moraxella sp. C-1. Acta Naturae 2009; 1:89-93. [PMID: 22649619 PMCID: PMC3347530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The crystal structure of the ternary complex of NAD+-dependent formate dehydrogenase from the methylotrophic bacterium Moraxella sp. C-1 with the cofactor (NAD+) and the inhibitor (azide ion) was established at 1.1 A resolution. The complex mimics the structure of the transition state of the enzymatic reaction. The structure was refined with anisotropic displacitalicents parameters for non-hydrogen atoms to a R factor of 13.4%. Most of the nitrogen, oxygen, and carbon atoms were distinguished based on the analysis of the titalicperature factors and electron density peaks, with the result that side-chain rotamers of histidine residues and most of asparagine and glutamine residues were unambiguously determined. A comparative analysis of the structure of the ternary complex determined at the atomic resolution and the structure of this complex at 1.95 A resolution was performed. In the atomic resolution structure, the covalent bonds in the nicotinamide group are somewhat changed in agreitalicent with the results of quantum mechanical calculations, providing evidence that the cofactor acquires a bipolar form in the transition state of the enzymatic reaction.
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74
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Furalyov VA, Kravchenko IV, Popov VO. Small interfering RNA targeting the human myostatin gene. Mol Biol 2009. [DOI: 10.1134/s0026893309040098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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75
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Furalev VA, Kravchenko IV, Popov VO. [Small interfering RNAs targeting human myostatin]. Mol Biol (Mosk) 2009; 43:636-641. [PMID: 19807026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Ten human myostatin small interfering RNAs which sequence was found by two different software products were synthesized and tested for activity. It was found that three of them have pronounced biological activity and decrease myostatin mRNA level to 22-27% of control value. These small interfering RNAs stimulate human myoblast proliferation and decrease their differentiation reliably. The obtained small interfering RNAs can be used for development of new approaches for the treatment of sarcopenia and different myodystrophies.
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