Tamara V Tikhonova

Tamara V Tikhonova
Russian Academy of Sciences | RAS · A.N. Bach Institute of Biochemistry

Ph.D.

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72
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Publications

Publications (72)
Article
Full-text available
Flavocytochrome c sulfide dehydrogenase (FCC) is one of the central enzymes of the respiratory chain in sulfur-oxidizing bacteria. FCC catalyzes oxidation of sulfide and polysulfide ions to elemental sulfur accompanied by electron transfer to cytochrome c. The catalytically active form of the enzyme is a non-covalently linked heterodimer composed o...
Article
Full-text available
Biogenic transformation of Fe minerals, associated with extracellular electron transfer (EET), allows microorganisms to exploit high-potential refractory electron acceptors for energy generation. EET-capable thermophiles are dominated by hyperthermophilic archaea and Gram-positive bacteria. Information on their EET pathways is sparse. Here, we desc...
Article
Detailed impedance and voltammetric studies of hexameric octaheme nitrite reductase immobilized on carbon-based nanomaterials, specifically nanotubes and nanoparticles, were performed. Well-pronounced bioelectrocatalytic reduction of nitrite on enzyme-modified electrodes was obtained. Analysis of the impedance data indicated the absence of long-liv...
Article
Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from t...
Article
Full-text available
The genomes of Thiohalobacter thiocyanaticus and Guyparkeria (formerly known as Halothiobacillus) sp. SCN-R1, two gammaproteobacterial halophilic sulfur-oxidizing bacteria (SOB) capable of thiocyanate oxidation via the “cyanate pathway”, have been analyzed with a particular focus on their thiocyanate-oxidizing potential and sulfur oxidation pathway...
Article
Full-text available
The structure of the anti-C60 fullerene antibody Fab fragment (FabC60) was solved by X-ray crystallography. The computer-aided docking of C60 into the antigen-binding pocket of FabC60 showed that binding of C60 to FabC60 is governed by the enthalpy and entropy; namely, by - stacking interactions with aromatic residues of the antigen-binding site an...
Article
Full-text available
The structure of the anti-C60 fullerene antibody Fab fragment (FabC 60 ) was solved by X-ray crystallography. The computer-aided docking of C 60 into the antigen-binding pocket of FabC 60 showed that binding of C 60 to FabC 60 is governed by the enthalpy and entropy; namely, by π-π stacking interactions with aromatic residues of the antigen-binding...
Article
Flavocytochrome c sulfide dehydrogenase from Thioalkalivibrio paradoxus ( Tp FCC) is a heterodimeric protein consisting of flavin- and monohaem c -binding subunits. Tp FCC was co-purified and co-crystallized with the dimeric copper-binding protein Tp CopC. The structure of the Tp FCC–( Tp CopC) 2 complex was determined by X-ray diffraction at 2.6 Å...
Article
Full-text available
The structure of cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens was determined by cryo-electron microscopy (cryo-EM) at a 2.56 Å resolution. Possible structural heterogeneity of the enzyme was assessed. The backbone and side-chain orientations in the cryo-EM-based model are, in general, similar to those in the hi...
Article
Full-text available
Fungal high redox potential laccases are proposed as cathodic biocatalysts in implantable enzymatic fuel cells to generate high cell voltages. Their application is limited mainly through their acidic pH optimum and chloride inhibition. This work investigates evolutionary and engineering strategies to increase the pH optimum of a chloride-tolerant,...
Article
Full-text available
Bacteria Tv. nitratireducens and Tv. paradoxus from soda lakes grow optimally in sodium carbonate/NaCl brines at pH range from 9.5 to 10 and salinity from 0.5 to 1.5 M Na⁺. Octaheme nitrite reductases (ONRs) from haloalkaliphilic bacteria of genus Thioalkalivibrio are stable and active in a wide range of pH (up to 11) and salinity (up to 1 M NaCl)....
Data
Comparison of hydrophobic cores of ONRs. (DOC)
Data
Comparison of the amino acid compositions of ONRs. (DOC)
Data
Subfamily-specific amino acid residues and structural comparison of ONRs. (DOC)
Data
Phylogenetic analysis of ONRs. (DOCX)
Data
Amino acid substitutions between GsNiR and TvNiR. (DOC)
Data
Comparative analysis of ONRs (amino acid residues are indicated in single letter code). *—p < 0.05 for comparison with nnONR. (DOCX)
Article
Closely related penta- and octaheme nitrite reductases catalyze the reduction of nitrite, nitric oxide, and hydroxylamine to ammonium and of sulfite to sulfide. NrfA pentaheme nitrite reductase plays the key role in anaerobic nitrate respiration and the protection of bacterial cells from stresses caused by nitrogen oxides and hydrogen peroxide. Oct...
Article
Full-text available
Study of the adaptation mechanisms of proteins from extremophiles paves the way for the development of new biocatalysts that are resistant to extreme conditions. Here, we studied the structural adaptation of active center channels of octaheme nitrite reductase from the haloalkophilic bacterium Thioalkalivibrio nitratireducens (TvNiR) to high pH. Co...
Article
Bacteria utilizing insoluble mineral forms of metal oxides as electron acceptors in respiratory processes are widespread in the nature. The electron transfer from a pool of reduced quinones in the cytoplasmic membrane across the periplasm to the bacterial outer membrane and then to an extracellular acceptor is a key step in bacterial dissimilatory...
Article
Full-text available
Laccases belong to the class of multicopper oxidases catalyzing the oxidation of phenols accompanied by the reduction of molecular oxygen to water without the formation of hydrogen peroxide. The activity of laccases depends on the number of Cu atoms per enzyme molecule. The structure of type 2 copper-depleted laccase from Botrytis aclada has been s...
Article
Octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens catalyzes the reduction of nitrite to ammonium and of sulfite to sulfide. The reducing properties of X-ray radiation and the high quality of the enzyme crystals allow study of the catalytic reaction of cytochrome c nitrite reductase directly in a crystal of...
Article
Full-text available
Laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. These enzymes contain four Cu atoms per molecule organized into three sites: T1, T2 and T3. In all laccases, the T1 copper ion is coordinated by two histidi...
Article
The multiheme cytochromes from Thioalkalivibrio nitratireducens (TvNiR) and Escherichia coli (EcNrfA) reduce nitrite to ammonium. Both enzymes contain His/His-ligated hemes to deliver electrons to their active sites, where a Lys-ligated heme has a distal pocket containing a catalytic triad of His, Tyr, and Arg residues. Protein-film electrochemistr...
Article
Full-text available
Octaheme oxidoreductases are widespread among various bacterial taxa involved in the biogeochemical nitrogen cycle. The evolution of octaheme oxidoreductases of the nitrogen cycle from the evolutionarily more ancient pentaheme nitrite reductases was accompanied by changes in function from reduction of nitrogen oxides to their oxidation under changi...
Article
Unlabelled: Octaheme nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio paradoxus was isolated and characterized. A comparative structural and functional analysis of two homologous octaheme nitrite reductases from closely related Thioalkalivibrio species was performed. It was shown that both enzymes have similar catalytic prope...
Article
Octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR), like the previously characterized pentahaem nitrite reductases (NrfAs), catalyzes the six-electron reductions of nitrite to ammonia and of sulfite to sulfide. The active site of both TvNiR and NrfAs is formed by the lysine-coordinated haem and His, Tyr and Arg re...
Article
The structures of complexes of octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens (TvNiR) with the substrate sulfite (1.4 Å resolution; R(cryst) = 0.126) and the inhibitor cyanide (1.55 Å resolution; R(cryst) = 0.148) have been established. The complex with sulfite was prepared by the reduction of the protei...
Chapter
Octaheme cytochrome c nitrite reductase (TvNiR) from bacterium Thioalkalivibrio nitratireducens catalyzes the six-electron reduction of nitrite and two-electron reduction of hydroxylamine to ammonium without release of any intermediates. TvNiR also catalyzes the six-electron reduction of sulfite to sulfide. High-resolution structures of the TvNiR a...
Article
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...
Article
Octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR) catalyzes the reduction of nitrite and hydroxylamine to ammonia. The structures of the free enzyme and of the enzyme in complexes with the substrate (nitrite ion) and the inhibitor (azide ion) have been solved previously. In this study we report the structures of...
Article
Full-text available
NAD(+)-dependent formate dehydrogenase (FDH) catalyzes the oxidation of formate ion to carbon dioxide coupled with the reduction of NAD(+) to NADH. The crystal structures of the apo and holo forms of FDH from the methylotrophic bacterium Moraxella sp. C-1 (MorFDH) are reported at 1.96 and 1.95 A resolution, respectively. MorFDH is similar to the pr...
Article
Full-text available
DNA ligases catalyze the sealing of 5'-phosphate and 3'-hydroxyl termini at single-strand breaks in double-stranded DNA and their function is essential to maintain the integrity of the genome in DNA metabolism. An ATP-dependent DNA ligase from the archaeon Thermococcus sp. 1519 was overexpressed, purified and crystallized. Crystals were obtained us...
Article
Bacterial pentaheme cytochrome c nitrite reductases (NrfAs) are key enzymes involved in the terminal step of dissimilatory nitrite reduction of the nitrogen cycle. Their structure and functions are well studied. Recently, a novel octaheme cytochrome c nitrite reductase (TvNiR) has been isolated from the haloalkaliphilic bacterium Thioalkalivibrio n...
Article
A new procedure for isolation of cytochrome c nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio nitratireducens increasing significantly the yield of the purified enzyme is presented. The enzyme is isolated from the soluble fraction of the cell extract as a hexamer, as shown by gel filtration chromatography and small angle X-ra...
Article
Thiohalophilus thiocyanoxidans is a first halophilic sulfur-oxidizing chemolithoautotrophic bacterium capable of growth with thiocyanate as an electron donor at salinity up to 4 M NaCl. The cells, grown with thiocyanate, but not with thiosulfate, contained an enzyme complex hydrolyzing thiocyanate to sulfide and ammonia under anaerobic conditions w...
Article
Full-text available
Strongly bounded associates of B800–850 (LH2) and B800–830 (LH3) complexes from photosynthetic purple bacterium Thiorhodospira sibirica were investigated. It was shown that associates contain 8–10 complexes (LH2:LH3 ≈ 1:1). Absorption spectra of the monomer LH2 and the monomer LH3 complexes were calculated. Excitation of B800 absorption band of ass...
Article
The three-dimensional structures of the wild-type red (zRFP574) and green (zGFP506) fluorescent proteins (FP) from the button polyp Zoanthus have been determined at 1.51 and 2.2 A resolution, respectively. In addition, the crystal structures of a zGFP506 variant (zGFP506_N66D) with replacement of the first chromophore-forming residue (Asn66 to Asp)...
Article
Full-text available
The three-dimensional structure of yellow fluorescent proteins zYFP538 (zFP538) from the button polyp Zoanthus sp. was determined at a resolution of 1.8 angstrom by X-ray analysis. The monomer of zYFP538 adopts a structure characteristic of the green fluorescent protein (GFP) family, a beta-barrel formed from 11 antiparallel beta segments and one i...
Article
The hydroxylase component of membrane-bound (particulate) methane monooxygenase (pMMO) from Methylococcus capsulatus strain M was isolated and purified to homogeneity. The pMMO molecule comprises three subunits of molecular masses 47, 26, and 23 kD and contains three copper atoms and one iron atom. In solution the protein exists as a stable oligome...
Article
Full-text available
Formate dehydrogenase (FDH) from the methylotrophic bacterium Pseudomonas sp. 101 catalyzes oxidation of formate to NI2 with the coupled reduction of nicotinamide adenine dinucleotide (NAD+). The three-dimensional structures of the apo form (the free enzyme) and the holo form (the ternary FDH-NAD+-azide complex) of FDH have been established earlier...
Article
The three-dimensional structure of the red fluorescent protein (RFP) zRFP574 from the button polyp Zoanthus sp. (two dimers per asymmetric unit, 231 x 4 amino acids) has been determined at 2.4 A resolution in space group C222(1). The crystal structure, refined to a crystallographic R factor of 0.203 (R(free) = 0.249), adopts the beta-barrel fold co...
Article
A highly active cytochrome c nitrite reductase from the haloalkaliphilic sulfur-oxidizing non-ammonifying bacterium Tv. nitratireducens strain ALEN 2 (TvNiR) was isolated and purified to apparent electrophoretic homogeneity. The enzyme catalyzes reductive conversion of nitrite and hydroxylamine to ammonia without release of any intermediates, as we...
Article
Full-text available
A novel cytochrome c nitrite reductase (TvNiR) was isolated from the haloalkalophilic bacterium Thioalkalivibrio nitratireducens. The enzyme catalyses nitrite and hydroxylamine reduction, with ammonia as the only product of both reactions. It consists of 525 amino-acid residues and contains eight haems c. TvNiR crystals were grown by the hanging-dr...
Article
Full-text available
Formate dehydrogenase (FDG) from methylotrophic bacteria Pseudomonas sp. 101 catalyzes the reaction of oxidation of the formate ion to carbon dioxide, which is accompanied by the reduction of nicotinamid adenine dinucleotide (NAD+). The structures of the apo and holo (enzyme-NAD-azide triple complex) forms of the enzyme were determined earlier. In...
Article
Inclusion of an oligomeric enzyme, NAD+-dependent hydrogenase from the hydrogen-oxidizing bacterium Ralstonia eutropha, into a system of reverse micelles of different sizes resulted in its dissociation into catalytically active heterodimers and subunits, which were characterized in reactions with various substrates. It was found that: 1) the native...
Article
Amino acid residues His and Cys of the NAD-dependent hydrogenase from the hydrogen-oxidizing bacterium Ralstonia eutropha H16 were chemically modified with specific reagents. The modification of His residues of the nonactivated hydrogenase resulted in decrease in both hydrogenase and diaphorase activities of the enzyme. Activation of NADH hydrogena...
Article
Sequence alignment shows that residue Arg 284 (according to the numbering of the residues in formate dehydrogenase, FDH, from the methylotrophic bacterium Pseudomonas sp. 101) is conserved in NAD-dependent FDHs and D-specific 2-hydroxyacid dehydrogenases. Mutation of Arg 284 to glutamine and alanine results in a change of the catalytic, thermodynam...
Article
The effects of pH on the maximal rates of the hydrogenase and diaphorase reactions with various acceptors catalyzed by NAD-dependent hydrogenase from Alcaligenes eutrophus H16 were studied. The data indicate that at all pH values investigated, the electron transfer to the acceptor is the rate-limiting stage; hence, the reaction rate is essentially...
Article
The kinetics of NAD-dependent formate dehydrogenase from methylotrophic yeast Hansenula polymorpha was studied. The dependence of the initial reaction rate on the substrate concentration and the inhibition of the enzyme with the reaction products and substrate analogues were investigated. The mechanism of the enzyme action includes the formation of...
Article
Full-text available
The classical Bowman-Birk inhibitor from soya retards strongly the hydrolysis of elastin catalyzed by leukocyte elastase, cathepsin G and a mixture of both. The inhibitory effect is practically unaffected by both the adsorption of the enzymes on elastin and prolongation of the enzymatic reaction.
Article
Full-text available
Cathepsin G stimulates the hydrolysis of elastin from bovine neck ligament catalyzed by human leukocyte elastase. Stimulation factor depends on the ratio of the enzyme concentrations and ionic strength and equals 1.0-2.0. The classical Bowman-Birk inhibitor from soya retards strongly the hydrolysis of elastin catalyzed by leukocyte elastase, cathep...
Article
Full-text available
A kinetic study of the interaction of the classical Bowman-Birk type soybean inhibitor (BBI 2-IV) with human granulocyte alpha-chymotrypsin and cathepsin G has been carried out. The K(a) values for the inhibitor-proteinase systems--alpha-chymotrypsin and cathepsin G (2.0 x 10(5) and 6.4 x 10(6) M-1 s-1, respectively) have been established.
Article
Full-text available
A kinetic study of the interaction of the classical Bowman-Birk type soybean inhibitor (BBI 2-IV) with human granulocyte alpha-chymotrypsin and cathepsin G has been carried out. The K(a) values for the inhibitor-proteinase systems--alpha-chymotrypsin and cathepsin G (2.0 x 10(5) and 6.4 x 10(6) M-1 s-1, respectively) have been established.
Article
A one-step procedure for human leukocyte elastase purification using an affinity adsorbent based on protein soybean Bowman-Birk proteinase inhibitor has been developed. The leukocyte elastase was purified 70-fold with a 70-100% yield. The enzyme preparations did not contain cathepsin G and displayed a high specific activity. The soybean Bowman-Birk...
Article
A classical soybean inhibitor (Bowman-Birk inhibitor, BBI 2-IV) and two high molecular weight glycine-enriched inhibitors of the same type (3-II and 4-II) have been isolated, purified to homogeneity and characterized. All of the BBI isoforms have been found to effectively inhibit cathepsin G and human granulocyte elastase. The constants for leucocy...
Article
A classical soybean inhibitor (Bowman-Birk inhibitor, BBI 2-IV) and two high molecular weight glycine-enriched inhibitors of the same type (3-II and 4-II) have been isolated, purified to homogeneity and characterized. All of the BBI isoforms have been found to effectively inhibit cathepsin G and human granulocyte elastase. The constants for leucocy...
Article
Full-text available
The significant differences in the racemization rates of amino acids and the corresponding amides make it possible to carry out selective racemization of amides in the presence of optically active amino acids.
Article
The influence of pH, temperature, EDTA and metal ions on the rate of hydrolysis of methyl esters of d- and l-tryptophan by pronase from Streptomyces griseus has been studied. pH, Ca2+ and Co2+ ions have different effects on the hydrolysis of d- and l-substrates, which permits the enantioselectivity of the reaction to be regulated. Maximum enantiose...
Article
An investigation of the hydrolysis of various substrates (l-Trp-OMe, l-Phe-OMe, l-Leu-OMe and l-Val-OMe) by pronase has shown that the highest activity is displayed with l-Leu-OMe substrate. Addition of Ca2+ ions significantly enhances the rate of hydrolysis of l-Leu-OMe without affecting the hydrolysis of d-Leu-OMe. Thus, the enantioselectivity of...

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