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Каталог книг и продолжающихся изданий библиотеки Института биофизики СО РАН (2)

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Dynamics of activity of the key enzymes of polyhydroxyalkanoate metabolism in Ralstonia eutropha B5786 / T. G. Volova [et al.] // Applied Biochemistry and Microbiology. - 2004. - Vol. 40, Is. 2. - P170-177, DOI 10.1023/B:ABIM.0000018921.04863.d5 . - ISSN 0003-6838
Кл.слова (ненормированные):
acetyl coenzyme A acyltransferase -- bacterial enzyme -- carbon -- carbon dioxide -- fructose -- hydrogen -- hydroxybutyrate dehydrogenase -- oxidoreductase -- poly(3 hydroxybutyric acid) -- polyhydroxyalkanoic acid -- synthetase -- article -- bacterial metabolism -- carbon source -- catalysis -- controlled study -- degradation -- depolymerization -- enzyme activity -- enzyme analysis -- molecular dynamics -- nonhuman -- protein function -- Ralstonia eutropha -- recording -- statistical significance -- synthesis -- Bacteria (microorganisms) -- Ralstonia -- Wautersia eutropha
Аннотация: The dynamics of accumulation of polyhydroxybutyrate (PHB) and the activities of key enzymes of PHB metabolism (?-ketothiolase, acetoacetyl-CoA reductase, PHB synthase, D-hydroxybutyrate dehydrogenase, and PHB depolymerase) in the hydrogen bacterium Ralstonia eutropha B5786 were studied under various conditions of carbon nutrition and substrate availability. The highest activities of ?-ketothiolase, acetoacetyl-CoA reductase, and PHB synthase were recorded during acceleration of PHB synthesis. The activities of enzymes catalyzing PHB depolymerization (PHB depolymerase and D-hydroxybutyrate dehydrogenase) were low, being expressed only upon stimulated endogenous PHB degradation. The change of carbon source (CO2 or fructose) did not affect the time course of the enzyme activity significantly.

Scopus
Держатели документа:
Institute of Biophysics, Siberian Division, Russian Academy of Sciences, Akademgorodok, Krasnoyarsk, 660036, Russian Federation : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Volova, T.G.; Kalacheva, G.S.; Gorbunova, O.V.; Zhila, N.O.

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Catalytic activity of nanodiamond particles in organic reactions / V. S. Bondar [et al.] // Doklady Biochemistry and Biophysics. - 2008. - Vol. 418, Is. 1. - P11-13, DOI 10.1007/s10628-008-1003-7 . - ISSN 1607-6729
Кл.слова (ненормированные):
diamond -- nanoparticle -- organic compound -- article -- catalysis -- chemistry -- ultraviolet spectrophotometry -- Catalysis -- Diamond -- Nanoparticles -- Organic Chemicals -- Spectrophotometry, Ultraviolet

Scopus
Держатели документа:
Institute of Biophysics, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Bondar, V.S.; Purtov, K.V.; Puzyr, A.P.; Baron, A.V.; Gitel'zon, I.I.

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Calcium-regulated photoproteins of marine coelenterates [Text] / E. S. Vysotski, S. V. Markova, L. A. Frank // Mol. Biol. - 2006. - Vol. 40, Is. 3. - P355-367, DOI 10.1134/S0026893306030022. - Cited References: 99 . - ISSN 0026-8933

РУБ Biochemistry & Molecular Biology
Рубрики:
BIOLUMINOMETRIC HYBRIDIZATION ASSAYS
   HYDROID OBELIA-GENICULATA
   GREEN-FLUORESCENT PROTEIN
   POLYMERASE-CHAIN-REACTION
   BIOLUMINESCENT IMMUNOASSAY
   RECOMBINANT AEQUORIN
   CRYSTAL-STRUCTURE
   BIOTINYLATED AEQUORIN
   ANGSTROM RESOLUTION
   CA2+-REGULATED PHOTOPROTEINS
Кл.слова (ненормированные):
bioluminescence -- obelin -- aequorin -- intracellular calcium -- molecular diagnosis
Аннотация: Calcium-regulated photoproteins are bioluminescent proteins that are responsible for the luminescence of marine coelenterates. A photoprotein molecule is a stable enzyme-substrate complex consisting of a single polypeptide chain and an oxygen-preactivated substrate, 2-hydroperoxcoelenterazine, which is tightly but noncovalently bound with the protein. Bioluminescence is triggered by Ca2+ and results from decarboxylation of the substrate bound with the protein. This review considers the current information about the structure of photoproteins, the mechanism of the bioluminescent reaction, the function of particular amino acid residues of the active center in catalysis and the formation of the emitter, and the use of photoproteins in bioluminescent microanalysis.

Держатели документа:
Russian Acad Sci, Siberian Div, Inst Biophys, Krasnoyarsk 660036, Russia
ИБФ СО РАН : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Vysotski, E.S.; Markova, S.V.; Frank, L.A.

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High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH [Text] / Z. . Wawrzak [et al.] // Proteins. - 1999. - Vol. 35, Is. 4. - P. 425-439, DOI 10.1002/(SICI)1097-0134(19990601)35:4425::AID-PROT63.0.CO;2-1. - Cited References: 33 . - ISSN 0887-3585

РУБ Biochemistry & Molecular Biology + Biophysics
Рубрики:
MAGNAPORTHE-GRISEA
   HEMAGGLUTININ
   GLYCOPROTEIN
   REFINEMENT
   MELANIN
   DISEASE
   SITE
Кл.слова (ненормированные):
structure-based design -- enzyme inhibitors -- X-ray crystallography -- fungicides -- melanin biosynthesis
Аннотация: Scytalone dehydratase is a molecular target of inhibitor design efforts aimed at preventing the fungal disease caused by Magnaporthe grisea. A method for cocrystallization of enzyme with inhibitors at neutral pH has produced several crystal structures of enzyme-inhibitor complexes at resolutions ranging from 1.5 to 2.2 Angstrom Four high resolution structures of different enzyme-inhibitor complexes are described. In contrast to the original X-ray structure of the enzyme, the four new structures have well-defined electron density for the loop region comprising residues 115-119 and a different conformation between residues 154 and 160. The structure of the enzyme complex with an aminoquinazoline inhibitor showed that the inhibitor is in a position to form a hydrogen bond with the amide of the Asn131 side chain and with two water molecules in a fashion similar to the salicylamide inhibitor in the original structure, thus confirming design principles. The aminoquinazoline structure also allows for a more confident assignment of donors and accepters in the hydrogen bonding network, The structures of the enzyme complexes with two dichlorocyclopropane carboxamide inhibitors showed the two chlorine atoms nearly in plane with the amide side chain of Asn131. The positions of Phe53 and Phe158 are significantly altered in the new structures in comparison to the two structures obtained from crystals grown at acidic pH, The multiple structures help define the mobility of active site amino acids critical for catalysis and inhibitor binding. Proteins 1999;35:425-439. (C) 1999 Wiley-Liss, Inc.

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Держатели документа:
Dupont Co, Stine Haskell Res Ctr, Agr Prod, Newark, DE 19714 USA
Dupont Co, Expt Stn, Life Sci, Wilmington, DE USA
Karolinska Inst, Dept Med Biochem & Biophys, Stockholm, Sweden
Russian Acad Sci, Inst Biophys, Krasnoyarsk, Russia
ИБФ СО РАН : 660036, Красноярск, Академгородок, д. 50, стр. 50

Доп.точки доступа:
Wawrzak, Z...; Sandalova, T...; Steffens, J.J.; Basarab, G.S.; Lundqvist, T...; Lindqvist, Y...; Jordan, D.B.

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Effect of viscosity on efficiency of enzyme catalysis of bacterial luciferase coupled with lactate dehydrogenase and NAD(P)H:FMN-Oxidoreductase / O. S. Sutormin [et al.] // Mol. Cat. - 2018. - Vol. 458. - P60-66, DOI 10.1016/j.mcat.2018.08.012 . - ISSN 2468-8231
Кл.слова (ненормированные):
Bioluminescence -- Coupling of enzymes -- In vivo simulated media -- Metabolic chain -- Protein stability
Аннотация: One of the current trends of the modern biology figures out cellular enzyme behaviour. Numerous researches look more closely at the chemical composition of creating in vivo simulated media conditions. The aim of this work was to find out a thermodynamic cooperativity of enzymes in a triple-enzyme chain (lactate dehydrogenase + NAD(P)H: FMN-oxidoreductase + bacterial luciferase) under in vivo simulated condition. The thermodynamic cooperativity effects were found out based on the influence of the viscogens (glycerol and sucrose) on the thermal stability of the triple-enzyme system. The results showed that the viscogens do not lead to an increase in the thermal stability of the triple-enzyme system. In addition, organic solvents (sucrose and glycerol) added as viscous agents to the reaction medium altered the kinetics of this triple-enzyme chain, including changing the light emission decay constant (kdec) and quantum yield of luminescence (Q). Plus, sucrose was found to be more efficient in limiting the flexibility of enzymes than glycerol. The high sensitivity of the triple-enzyme system to the viscogens may be connected with a fact that lactate dehydrogenase does not bound with couple enzyme system NAD(P)H: FMN-oxidoreductase + bacterial luciferase inside the real cell. Since this approach may be used as a method to understand the real connection between enzymes in cellular multi-enzyme metabolic chains inside the luminous bacteria cell. © 2018 Elsevier B.V.

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Держатели документа:
Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russian Federation
Institute of Biophysics, Russian Academy of Sciences, Siberian Branch, Federal Research Center ‘Krasnoyarsk Science Center SB RAS’, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Sutormin, O. S.; Sukovataya, I. E.; Pande, S.; Kratasyuk, V. A.

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Mechanisms of viscous media effects on elementary steps of bacterial bioluminescent reaction / A. E. Lisitsa, L. A. Sukovatyi, S. I. Bartsev [et al.] // Int. J. Mol. Sci. - 2021. - Vol. 22, Is. 16. - Ст. 8827, DOI 10.3390/ijms22168827 . - ISSN 1661-6596
Кл.слова (ненормированные):
Bacterial luciferase -- Diffusion limitation -- Non-steady-state reaction kinetics -- Viscosity
Аннотация: Enzymes activity in a cell is determined by many factors, among which viscosity of the microenvironment plays a significant role. Various cosolvents can imitate intracellular conditions in vitro, allowing to reduce a combination of different regulatory effects. The aim of the study was to analyze the media viscosity effects on the rate constants of the separate stages of the bacterial biolumi-nescent reaction. Non-steady-state reaction kinetics in glycerol and sucrose solutions was measured by stopped-flow technique and analyzed with a mathematical model developed in accordance with the sequence of reaction stages. Molecular dynamics methods were applied to reveal the effects of cosolvents on luciferase structure. We observed both in glycerol and in sucrose media that the stages of luciferase binding with flavin and aldehyde, in contrast to oxygen, are diffusion-limited. More-over, unlike glycerol, sucrose solutions enhanced the rate of an electronically excited intermediate formation. The MD simulations showed that, in comparison with sucrose, glycerol molecules could penetrate the active-site gorge, but sucrose solutions caused a conformational change of functionally important ?Glu175 of luciferase. Therefore, both cosolvents induce diffusion limitation of substrates binding. However, in sucrose media, increasing enzyme catalytic constant neutralizes viscosity effects. The activating effect of sucrose can be attributed to its exclusion from the catalytic gorge of luciferase and promotion of the formation of the active site structure favorable for the catalysis. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

Scopus
Держатели документа:
Biophysics Department, Siberian Federal University, Svobodny 79, Krasnoyarsk, 660041, Russian Federation
The Institute of Biophysics SB RAS, Akademgorodok 50/50, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Lisitsa, A. E.; Sukovatyi, L. A.; Bartsev, S. I.; Deeva, A. A.; Kratasyuk, V. A.; Nemtseva, E. V.

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Mechanisms of Viscous Media Effects on Elementary Steps of Bacterial Bioluminescent Reaction / A. E. Lisitsa, L. A. Sukovatyi, S. I. Bartsev [et al.] // Int. J. Mol. Sci. - 2021. - Vol. 22, Is. 16. - Ст. 8827, DOI 10.3390/ijms22168827. - Cited References:59. - The research was funded by the Ministry of Science and Higher Education of the Russian Federation (projects No. FSRZ-2020-0006); by RFBR, Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science (project No. 20-44-243002); by RFBR according to the research project No. 20-34-90118. . - ISSN 1422-0067

РУБ Biochemistry & Molecular Biology + Chemistry, Multidisciplinary
Рубрики:
FLAVIN INTERMEDIATE
   REDUCED FLAVIN
   RATE CONSTANTS
   LUCIFERASE
Кл.слова (ненормированные):
bacterial luciferase -- non-steady-state reaction kinetics -- viscosity -- diffusion limitation
Аннотация: Enzymes activity in a cell is determined by many factors, among which viscosity of the microenvironment plays a significant role. Various cosolvents can imitate intracellular conditions in vitro, allowing to reduce a combination of different regulatory effects. The aim of the study was to analyze the media viscosity effects on the rate constants of the separate stages of the bacterial bioluminescent reaction. Non-steady-state reaction kinetics in glycerol and sucrose solutions was measured by stopped-flow technique and analyzed with a mathematical model developed in accordance with the sequence of reaction stages. Molecular dynamics methods were applied to reveal the effects of cosolvents on luciferase structure. We observed both in glycerol and in sucrose media that the stages of luciferase binding with flavin and aldehyde, in contrast to oxygen, are diffusion-limited. Moreover, unlike glycerol, sucrose solutions enhanced the rate of an electronically excited intermediate formation. The MD simulations showed that, in comparison with sucrose, glycerol molecules could penetrate the active-site gorge, but sucrose solutions caused a conformational change of functionally important alpha Glu175 of luciferase. Therefore, both cosolvents induce diffusion limitation of substrates binding. However, in sucrose media, increasing enzyme catalytic constant neutralizes viscosity effects. The activating effect of sucrose can be attributed to its exclusion from the catalytic gorge of luciferase and promotion of the formation of the active site structure favorable for the catalysis.

WOS
Держатели документа:
Siberian Fed Univ, Biophys Dept, Svobodny 79, Krasnoyarsk 660041, Russia.
Inst Biophys SB RAS, Akad Gorodok 50-50, Krasnoyarsk 660036, Russia.

Доп.точки доступа:
Lisitsa, Albert E.; Sukovatyi, Lev A.; Bartsev, Sergey, I; Deeva, Anna A.; Kratasyuk, Valentina A.; Nemtseva, Elena, V; Nemtseva, Elena; Ministry of Science and Higher Education of the Russian Federation [FSRZ-2020-0006]; RFBR, Krasnoyarsk Territory and Krasnoyarsk Regional Fund of Science [20-44-243002]; RFBRRussian Foundation for Basic Research (RFBR) [20-34-90118]

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