Biochemistry (Moscow) (BIOCHEMISTRY-MOSCOW+)

Publications in this journal

• Article: Bartonellae: Stealthy pathogens or novel drug factories (Letter to the Editorial Board of Biokhimiya/Biochemistry (Moscow))

  G. Matera, A. Quirino, A. G. Lamberti, A. Focà, M. C. Liberto
  Biochemistry (Moscow) 05/2012; 76(9):1073-1074.
• Article: Investigation of formate transport through the substrate channel of formate dehydrogenase by steered molecular dynamics simulations

  D. K. Nilov, I. G. Shabalin, V. O. Popov, V. K. Švedas
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  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. Key wordsformate dehydrogenase–substrate channel–steered molecular dynamics
  Biochemistry (Moscow) 05/2012; 76(2):172-174.
• Article: Reply to the letter of G. Matera, A. Quirino, A. G. Lamberti, A. Focà, and M. C. Liberto

  D. S. Kabanov, I. R. Prokhorenko
  Biochemistry (Moscow) 05/2012; 76(9):1075-1077.
• Article: Erratum: “Binding of ATP and Its Derivatives to Selenophosphate Synthetase from Escherichia coli”

  Y. V. Preabrazhenskaya, I. Y. Kim, T. C. Stadtman
  Biochemistry (Moscow) 04/2012; 75(10):1302-1302.
• Article: Effect of cholinergic drugs on the activity of basic carboxypeptidases in rat nervous tissue

  V. B. Solov’ev, M. T. Gengin, O. V. Solov’eva, O. V. Pavlova, E. S. Lobzina
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  ABSTRACT: Effects of a single administration of cholinergic drugs (arecoline, atropine, nicotine, mecamylamine) on the activity of carboxypeptidase H and of phenylmethylsulfonyl fluoride-inhibited carboxypeptidase, which are involved in metabolism of neuropeptides, were studied in brain parts and the adrenal glands of rats. The enzyme activities were determined fluorimetrically using specific inhibitors and substrates. In the majority of cases the enzyme activities decreased, and this decrease was retained for at least 72 h. Changes in the activities of the studied enzymes depended on the type of cholinergic action, the nervous system part, and the time after the injection. The changes in activities of the studied carboxypeptidases are supposed to be a possible mechanism responsible for changes in the levels of neuropeptides under the influence of high doses of the drugs. Key wordsnervous system–carboxypeptidases–cholinergic drugs
  Biochemistry (Moscow) 04/2012; 76(10):1172-1177.
• Article: An overview on nucleases (DNase, RNase, and phosphodiesterase) in snake venoms

  B. L. Dhananjaya, C. J. M. D’souza
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  ABSTRACT: In this review, we have compiled the data on pharmacological activities associated with endogenous purine release related enzymes—nucleases (DNases, RNases, and phosphodiesterases). The results of studies on toxic effects of these enzymes, emphasizing the future directions in this field, are summarized. One of the major problems facing toxicologists is the identification and characterization of specific venom nucleases since they share similar substrate specificities and biochemical properties. In this review, we have attempted to clarify some of the discrepancies about these enzymes. Further, we have tried to correlate the existence of nuclease enzymes in relation to endogenous release of purines, a multitoxin, during snake envenomation, and we also discuss the possible actions of purines. We hope that this review will stimulate renewed interest among toxicologists to biologically characterize these enzymes and elucidate their role in envenomation. Key wordspurines-DNase-RNase-phosphodiesterase-snake envenomation-adenosine
  Biochemistry (Moscow) 04/2012; 75(1):1-6.
• Article: Anionic polymers of the cell wall of Bacillus subtilis subsp. subtilis VKM B-501T

  A. S. Shashkov, N. V. Potekhina, S. N. Senchenkova, E. B. Kudryashova
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  ABSTRACT: Teichoic acid and disaccharide-1-phosphate polymer were identified in the cell walls of Bacillus subtilis subsp. subtilis VKM B-501T. The teichoic acid represents 1,3-poly(glycerol phosphate) 80% substituted by α-D-glucopyranose residues at O-2 of glycerol. The linear repeating unit of disaccharide-1-phosphate polymer contains the residues of β-D-glucopyranose, N-acetyl-α-D-galactosamine, and phosphate and has the following structure: -6)-β-D-Glcp-(1→3)-α-D-GalpNAc-(1-P-. The structures of two anionic polymers were determined by chemical and NMR-spectroscopic methods. The 1H- and 13C-NMR spectral data on disaccharide-1-phosphate polymer are presented for the first time.
  Biochemistry (Moscow) 04/2012; 74(5):543-548.
• Article: Novel inhibitors of glyceraldehyde-3-phosphate dehydrogenase: Covalent modification of NAD-binding site by aromatic thiols

  K. A. Chernorizov, J. L. Elkina, P. I. Semenyuk, V. K. Švedas, V. I. Muronetz
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  ABSTRACT: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH, EC 1.2.1.12) is a glycolytic enzyme catalyzing the formation of 1,3-diphosphoglycerate from glyceraldehyde-3-phosphate and inorganic phosphate. In cooperation with E3 ubiquitin-kinase Siah1, GAPDH directly participates in the apoptotic death of neurons in Parkinson’s disease. Potential GAPDH inhibitors were screened in silico, and three compounds with high affinity to the NAD-binding site and theoretically capable of forming a disulfide bond with amino acid residue Cys149 were found among cysteine and glutathione derivatives. The inhibitory effect of these compounds was tested on GAPDH from rabbit muscles using isothermal calorimetry and kinetic methods. As a result of experimental screening, we selected two compounds that inhibit GAPDH by forming disulfide bonds with the Cys149 residue in the enzyme active site. Since Cys149 is the key residue not only for the catalyzed reaction, but also for interaction with Siah1, the compounds can be assumed to inhibit the formation of the proapoptotic complex GAPDH-Siah1 and therefore have potential effect against Parkinson’s disease. Key wordsglyceraldehyde-3-phosphate dehydrogenase–covalent inhibition–cysteine and glutathione derivatives–NAD-binding domain–apoptosis–Parkinson’s disease
  Biochemistry (Moscow) 04/2012; 75(12):1444-1449.
• Article: Interaction of ceruloplasmin and 5-lipoxygenase

  A. V. Sokolov, E. A. Golenkina, V. A. Kostevich, V. B. Vasilyev, G. F. Sud’ina
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  ABSTRACT: The interaction between ceruloplasmin (CP), the multicopper oxidase of human plasma, and 5-lipoxygenase (5-LO), the key enzyme of leukotriene synthesis, is shown for the first time. By Western-blotting and mass spectrometry of tryptic fragments, it is shown that 5-LO from protein extract of human leukocytes binds with immobilized CP. Dose-dependent influence of intact CP on leukotrienes synthesis is found: CP reduced leukotrienes synthesis in leukocytes in a dose above 50 μg/ml (normal CP concentration in plasma is about 300–400 μg/ml). Proteolyzed CP and apo-form of CP is unable to inhibit activity of 5-LO. CP increased activity of 5-LO at low doses (5–10 μg/ml). On the whole, the influence of CP on phagocytosis index of leukocytes coordinates with influence on activity of 5-LO: the index increased in the range of 2–10 μg/ml CP and decreased at doses of CP above 40 μg/ml. The dual role of CP in regulation of cellular response of leukocytes is discussed. Key wordsprotein-protein interaction–inflammation–leukotrienes–5-lipoxygenase–ceruloplasmin
  Biochemistry (Moscow) 04/2012; 75(12):1464-1469.
• Article: Electron transfer properties and catalytic competence of cytochrome b5 in the fusion protein Hmwb5-EGFP in reactions catalyzed by cytochrome P450 3A4

  A. V. Yantsevich, A. A. Gilep, S. A. Usanov
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  ABSTRACT: In the present paper we describe studies on molecular mechanisms of protein-protein interactions between cytochrome P450 3A4 (CYP3A4) and cytochrome b 5, the latter being incorporated into the artificial recombinant protein Hmwb 5-EGFP containing full-length cytochrome b 5 (functional module) and a mutant form of the green fluorescent protein EGFP (signal module) fused into a single polypeptide chain. It is shown that cytochrome b 5 within the fusion protein Hmwb 5-EGFP can be reduced by NADPH-cytochrome P450 reductase in the presence of NADPH, the rate of reduction being dependent on solution ionic strength, indicating that the signal module does not prevent the interaction of the flavo- and hemeproteins. Interaction of cytochrome P450 3A4 and Hmwb 5-EGFP was estimated based on spin equilibrium shift of cytochrome P450 3A4 to high-spin state in the presence of Hmwb 5-EGFP, as well as based on steady-state fluorescence anisotropy of the EGFP component of the fusion protein in the presence of CYP3A4. The engineering of chimeric protein Hmwb 5-EGFP gives an independent method to determine dissociation constant for the complex of cytochrome P450 and cytochrome b 5 that is less sensitive to environmental factors compared to spectrophotometric titration used before. Reconstitution of catalytic activity of cytochrome P450 3A4 in the reaction of testosterone 6β-hydroxylation in the presence of Hmwb 5-EGFP indicates that cytochrome b 5 in the fusion protein is able to stimulate the hydroxylation reaction. Using other fusion proteins containing either cytochrome b 5 or its hydrophilic domain to reconstitute catalytic activity of cytochrome P450 3A4 showed that the hydrophobic domain of cytochrome b 5 participates not only in hemeprotein interaction, but also in electron transfer from cytochrome b 5 to cytochrome P450.
  Biochemistry (Moscow) 04/2012; 74(8):862-873.
• Article: Affinity chromatography of GroEL chaperonin based on denatured proteins: Role of electrostatic interactions in regulation of GroEL affinity for protein substrates

  N. Yu. Marchenko, V. V. Marchenkov, A. L. Kaysheva, I. A. Kashparov, N. V. Kotova, P. A. Kaliman, G. V. Semisotnov
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  ABSTRACT: The chaperonin GroEL of the heat shock protein family from Escherichia coli cells can bind various polypeptides lacking rigid tertiary structure and thus prevent their nonspecific association and provide for acquisition of native conformation. In the present work we studied the interaction of GroEL with six denatured proteins (α-lactalbumin, ribonuclease A, egg lysozyme in the presence of dithiothreitol, pepsin, β-casein, and apocytochrome c) possessing negative or positive total charge at neutral pH values and different in hydrophobicity (affinity for a hydrophobic probe ANS). To prevent the influence of nonspecific association of non-native proteins on their interaction with GroEL and make easier the recording of the complexing, the proteins were covalently attached to BrCN-activated Sepharose. At low ionic strength (lower than 60 mM), tight binding of the negatively charged denatured proteins with GroEL (which is also negatively charged) needed relatively low concentrations (∼10 mM) of bivalent cations Mg2+ or Ca2+. At the high ionic strength (∼600 mM), a tight complex was produced also in the absence of bivalent cations. In contrast, positively charged denatured proteins tightly interacted with GroEL irrespectively of the presence of bivalent cations and ionic strength of the solution (from 20 to 600 mM). These features of GroEL interaction with positively and negatively charged denatured proteins were confirmed by polarized fluorescence (fluorescence anisotropy). The findings suggest that the affinity of GroEL for denatured proteins can be determined by the balance of hydrophobic and electrostatic interactions.
  Biochemistry (Moscow) 04/2012; 71(12):1357-1364.
• Article: IgG-binding proteins of bacteria

  E. V. Sidorin, T. F. Solov’eva
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  ABSTRACT: Proteins capable of non-immune binding of immunoglobulins G (IgG) of various mammalian species, i.e. without the involvement of the antigen-binding sites of the immunoglobulins, are widespread in bacteria. These proteins are located on the surface of bacterial cells and help them to evade the host’s immune response due to protection against the action of complement and to decrease in phagocytosis. This review summarizes data on the structure of immunoglobulin-binding proteins (IBP) and their complexes with IgG. Common and distinctive structural features of IBPs of gram-positive bacteria (staphylococci, streptococci, peptostreptococci) are discussed. Conditions for IBP expression by bacteria and their functional heterogeneity are considered. Data on IBPs of gram-negative bacteria are presented. Key wordsimmunoglobulin G–immunoglobulin-binding proteins–Fc-fragment of IgG
  Biochemistry (Moscow) 04/2012; 76(3):295-308.
• Article: Effect of Plastoquinone Derivative 10-(6′-Plastoquinonyl)decyltriphenylphosphonium (SkQ1) on Contents of Steroid Hormones and NO Level in Rats

  V. A. Chistyakov, V. A. Serezhenkov, A. A. Alexandrova, N. P. Milyutina, V. N. Prokof’ev, E. V. Mashkina, L. V. Gutnikova, S. V. Dem’yanenko
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  ABSTRACT: Introduction of the plastoquinone derivative 10-(6′-plastoquinonyl)decyltriphenylphosphonium (SkQ1) into male Wistar rats once a day for two weeks in doses of 25 and 250 nmol/kg led to elevation of 17ß-estradiol level in blood serum by 33 and 41%, respectively. At the same time, nitrate and nitrite contents in the rat blood serum increased by 49 and 34%, respectively. ESR spectroscopy with diethyldithiocarbamate-iron complex as a spin trap showed more than twofold increase in NO production in lungs, but not in blood, liver, and intestines, following the SkQ1 daily introduction at a dose of 25 nmol/kg. Key wordsSkQ1–penetrating cations–steroid hormones–estradiol–nitrate–nitrite–nitric oxide
  Biochemistry (Moscow) 04/2012; 75(11):1383-1387.
• Article: Programmed cell death in plants: Protective effect of phenolic compounds against chitosan and H2O2

  V. D. Samuilov, L. A. Vasil’ev, E. V. Dzyubinskaya, D. B. Kiselevsky, A. V. Nesov
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  ABSTRACT: Addition of chitosan or H2O2 caused destruction of nuclei of epidermal cells (EC) in the epidermis isolated from pea leaves. Phenol, a substrate of the apoplastic peroxidase-oxidase, in concentrations of 10−10–10−6 M prevented the destructive effect of chitosan. Phenolic compounds 2,4-dichlorophenol, catechol, and salicylic acid, phenolic uncouplers of oxidative phosphorylation pentachlorophenol and 2,4-dinitrophenol, and a non-phenolic uncoupler carbonyl cyanide m-chlorophenylhydrazone, but not tyrosine or guaiacol, displayed similar protective effects. A further increase in concentrations of the phenolic compounds abolished their protective effects against chitosan. Malate, a substrate of the apoplastic malate dehydrogenase, replenished the pool of apoplastic NADH that is a substrate of peroxidase-oxidase, prevented the chitosan-induced destruction of the EC nuclei, and removed the deleterious effect of the increased concentration of phenol (0.1 mM). Methylene Blue, benzoquinone, and N,N,N′,N′-tetramethyl-p-phenylenediamine (TMPD) capable of supporting the optimal catalytic action of peroxidase-oxidase cancelled the destructive effect of chitosan on the EC nuclei. The NADH-oxidizing combination of TMPD with ferricyanide promoted the chitosan-induced destruction of the nuclei. The data suggest that the apoplastic peroxidase-oxidase is involved in the antioxidant protection of EC against chitosan and H2O2. Key wordsapoplastic peroxidase-programmed cell death-chitosan-hydrogen peroxide-phenolic compounds-protective action-plants-epidermal cells
  Biochemistry (Moscow) 04/2012; 75(2):257-263.
• Article: New function of the amino group of thiamine diphosphate in thiamine catalysis

  L. E. Meshalkina, G. A. Kochetov, G. Hubner, K. Tittmann, R. Golbik
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  ABSTRACT: In this work, we investigated the rate of formation of the central intermediate of the transketolase reaction with thiamine diphosphate (ThDP) or 4′-methylamino-ThDP as cofactors and its stability using stopped-flow spectroscopy and circular dichroism (CD) spectroscopy. The intermediates of the transketolase reaction were analyzed by NMR spectroscopy. The kinetic stability of the intermediate was shown to be dependent on the state of the amino group of the coenzyme. The rates of the intermediate formation were the same in the case of the native and methylated ThDP, but the rates of the protonation or oxidation of the complex in the ferricyanide reaction were significantly higher in the complex with methylated ThDP. A new negative band was detected in the CD spectrum of the complex transketolase—4′-methylamino-ThDP corresponding to the protonated dihydroxyethyl-4′-methylamino-ThDP released from the active sites of the enzyme. These data suggest that transketolase in the complex with the NH2-methylated ThDP exhibits dihydroxyethyl-4′-methylamino-ThDP-synthase activity. Thus, the 4′-amino group of the coenzyme provides kinetic stability of the central intermediate of the transketolase reaction, dihydroxyethyl-ThDP.
  Biochemistry (Moscow) 04/2012; 74(3):293-300.
• Article: Notable and anniversary dates in biochemistry for 2008

  N. P. Voskresenskaya
  Biochemistry (Moscow) 04/2012; 73(3):363-365.
• Article: Chemiluminescent in vitro estimation of the inhibitory constants of antioxidants ascorbic and uric acids in Fenton’s reaction in urine

  E. L. Pavlova, V. M. Savov
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  ABSTRACT: The goal of this research was to measure in vitro the inhibitory constants of the antioxidants ascorbic and uric acid in urine, with lucigenin enhanced chemiluminescence (CL) in Fenton’s system. Maximum CL emission is registered in urine containing H2O2 (5·10−4 M), Fe2+ (5·10−5 M), EDTA (5·10−5 M), and chemical enhancer lucigenin (10−4 M) at pH 5.5 and 36°C. Ascorbic acid exhibits up to 4-fold stronger antioxidant effect than uric acid. The constants of antioxidant inhibition in urine were measured at concentrations 10−3 and 10−4 M: for ascorbic acid, 5.92 ± 0.04 and 24.05 ± 1.82 μmol·sec−1; for uric acid, 1.60 ± 0.02 and 21.45 ± 0.97 μmol·sec−1, respectively. Three phases of CL kinetics of urine are well observed: spontaneous CL (0–10 sec), fast flash of CL (10–50 sec), and latent period (50–300 sec). The antioxidant efficiency of ascorbic and uric acids in the final stage of catabolic processes in the body is discussed.
  Biochemistry (Moscow) 04/2012; 71(8):861-863.
• Article: Binding Sites for Transcription Factor SF-1 in Promoter Regions of Genes Encoding Mouse Steroidogenesis Enzymes 3βHSDI and P450c17

  T. V. Busygina, G. V. Vasiliev, N. V. Klimova, E. V. Ignatieva, A. V. Osadchuk
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  ABSTRACT: Using gel retardation of DNA samples and specific antibodies, binding sites for the transcription factor SF-1 were found in positions −53/−44-and −285/−270 in the promoter region of the mouse Cyp17 gene and in position −117/−108 of the promoter region of the mouse 3βHSDI gene.
  Biochemistry (Moscow) 04/2012; 70(10):1152-1156.
• Article: Lipids of nuclear fractions from neurons and glia of rat neocortex under conditions of artificial hypobiosis

  I. K. Kolomiytseva, L. N. Markevich, D. A. Ignat’ev, O. V. Bykova
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  ABSTRACT: Lipid contents were studied in tissue and nuclei isolated from neurons and glia of neocortex of rats under conditions of normothermia and in the state of artificial hypobiosis caused by hypothermia-hypoxia-hypercapnia. Compared to the neocortex tissue, both nuclear fractions were fivefold impoverished in phospholipids and cholesterol and strongly enriched with mono- and diglycerides and fatty acids. The nuclear fractions from neurons and glia contained similar amounts of phospholipids, and only the cardiolipin content in the neuronal nuclei was lower than in the glial nuclei. The state of artificial hypobiosis in rats led to an increase in the cholesterol/phospholipids ratio (mol/mol) in the nuclei from the neurons and glia; amounts of cholesterol and sphingomyelin in the nuclei from the glia were increased. The increases in the cholesterol and sphingomyelin contents and in the cholesterol/phospholipids ratio suggest an involvement of lipid-dependent signaling systems of the nuclei in the functional response of mammalian neocortex cells to artificial hypobiosis. Key wordslipids-rats-hypobiosis-nuclei-neurons-glia
  Biochemistry (Moscow) 04/2012; 75(9):1132-1138.