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Self-organization of enzyme-catalyzed reactions studied by the maximum entropy production principle
Andrej Dobovišek, Marko Vitas, Tina Blaževič, Rene Markovič, Marko Marhl, Aleš Fajmut, 2023, original scientific article

Abstract: The self-organization of open reaction systems is closely related to specific mechanisms that allow the export of internally generated entropy from systems to their environment. According to the second law of thermodynamics, systems with effective entropy export to the environment are better internally organized. Therefore, they are in thermodynamic states with low entropy. In this context, we study how self-organization in enzymatic reactions depends on their kinetic reaction mechanisms. Enzymatic reactions in an open system are considered to operate in a non-equilibrium steady state, which is achieved by satisfying the principle of maximum entropy production (MEPP). The latter is a general theoretical framework for our theoretical analysis. Detailed theoretical studies and comparisons of the linear irreversible kinetic schemes of an enzyme reaction in two and three states are performed. In both cases, in the optimal and statistically most probable thermodynamic steady state, a diffusion-limited flux is predicted by MEPP. Several thermodynamic quantities and enzymatic kinetic parameters, such as the entropy production rate, the Shannon information entropy, reaction stability, sensitivity, and specificity constants, are predicted. Our results show that the optimal enzyme performance may strongly depend on the number of reaction steps when linear reaction mechanisms are considered. Simple reaction mechanisms with a smaller number of intermediate reaction steps could be better organized internally and could allow fast and stable catalysis. These could be features of the evolutionary mechanisms of highly specialized enzymes.
Keywords: enzymes, kinetic data analysis, steady state, self-organization, maximum entropy production
Published in DKUM: 08.05.2024; Views: 178; Downloads: 8
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Biochemical characterization of black and green mutant elderberry during fruit ripening
Maja Mikulič Petkovšek, Anton Ivančič, Saša Gačnik, Robert Veberič, Metka Hudina, Silvija Marinovic, Christian Molitor, Heidi Halbwirth, 2023, original scientific article

Abstract: The content of sugars, organic acids, phenolic compounds and selected enzyme activities in the anthocyanin pathway were analyzed in NIGRA (Sambucus nigra var. nigra—black fruits) and VIRIDIS (S. nigra var. viridis—green fruits) fruits over four stages of ripening. The share of glucose and fructose in green fruits was higher than in colored fruits, and the sugar content increased significantly until the third developmental stage. Ripe NIGRA berries had 47% flavonol glycosides, 34% anthocyanins, 3% hydroxycinnamic acids and 14% flavanols, whereas the major phenolic group in the VIRIDIS fruits, making up 88% of the total analyzed polyphenols, was flavonols. NIGRA fruits were rich in anthocyanins (6020 [mi]g g$^{-1}$ FW), showing strong activation of the late anthocyanin pathway (dihydroflavonol 4-reductase, anthocyanidin synthase). In both color types, phenylalanine ammonia lyase and chalcone synthase/chalcone isomerase activities were highest in the first stage and decreased during ripening. In VIRIDIS fruit, no anthocyanins and only one flavanol (procyanidin dimer) were found. This was most likely caused by a lack of induction of the late anthocyanin pathway in the last period of fruit ripening. The VIRIDIS genotype may be useful in studying the regulatory structures of anthocyanin biosynthesis and the contribution of distinct flavonoid classes to the health benefits of elderberries.
Keywords: black elderberry, Sambucus nigra, green genotype, polyphenolics, sugars, organic acids, phenylpropanoid enzymes
Published in DKUM: 28.03.2024; Views: 145; Downloads: 7
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Production of enzymes from medicinal mushrooms : master's thesis
Gonzalo Herranz Gómez, 2022, master's thesis

Abstract: The purpose of this master's thesis was to determine the ability of certain organisms of the kingdom Fungi to produce a series of enzymes in their active form by solid-state fermentation. In this study, two types of fungi were used, Pleurotus ostreatus and Ganoderma lucidum. For this purpose, different growth media, cultivation times (8 and 10 days), extraction procedures (shaking and homogenization) and extraction medium (distilled water, sodium citrate buffer and sodium phosphate buffer) were used. First, for P. ostreatus mushroom, the optimization of the extraction procedure and time for isolation of enzymes in their active form (α-amylase, glucoamylase, cellulase, laccase, and protease) was studied. It was observed that the highest total protein concentration in mycelium extract was obtained by 8 min of homogenization (0.8607 mg/mL, and distilled water). Using the shaking procedure, the highest enzyme activities were achieved for α-amylase (24 h, 8.0413 U/mL, and sodium citrate buffer) and protease (3 h, 0.0040 U/mL, and sodium citrate buffer). With the homogenization process, the highest activities were achieved for the enzymes glucoamylase (10 min, 6.7113 U/mL, and sodium citrate buffer) and laccase (8 min, 12.2500 U/mL, and sodium citate buffer). For the mushroom G. lucidum, the growth medium and the extraction procedure were optimized, using the same extraction medium (sodium citrate buffer). In this case, α-amylase, glucoamylase, cellulase, laccase, protease, catalase, peroxidase, superoxidase dismutase (SOD), and lipase were studied. It was observed that the highest total protein concentration was obtained with 4 min of homogenization (0.0338 mg/mL). Furthermore, using the homogenization process, the highest activities were achieved for α-amylase (4 min, 16.3459 U/mL) and SOD (4 min, 9.2615 U/mL). With the shaking procedure, the highest activities were achieved for cellulase (3 h, 1.6332 U/mL), lipase (3 h, 16.924 U/mL), glucoamylase (3 h, 14.6737 U/mL), peroxidase (3 h, 0.0156 U/mL), protease (3 h, 0.0080 U/mL) and laccase (24 h, 20.7083 U/mL).
Keywords: medicinal mushrooms, Pleurotus ostreatus, Ganoderma lucidum, total proteins, enzymes activities.
Published in DKUM: 06.07.2022; Views: 1778; Downloads: 39
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Enzymatic fatty ester synthesis
Simona Pečnik, Željko Knez, 1992, original scientific article

Abstract: Fatty ester synthesis with immobilized 1,3-specific lipase from Mucor Miehei is described. 1,2-Isopropylidene glycerol was peoduced by condensation of glycerol with acetone was esterified with oleic acid in the presence of a Mucor Miehei lipaze (Lipozyme TM) to obtain 1,2 isopropylidene- 3-oleoyl glycerol. The effects of various process parameters (temperature and pressure)and various ratios (enzyme/substrate) have been investigated to determine optimal conditions for the esterification process. The highest conversion of oleic acid (80% w/w) was obtained at 55 oC and 57.057 bar, while the optimal addition of lipase to substrate was determined to be 0,096 g per gram of reaction mixture. The esterification can be modelled successfully as a reverse second order reaction. Thermodynamic properties of the reaction system at 55 oC and 0.057 bar were also determined. Activation energy was 20.82 kJ/mole, entropy of activation -0,26 kJ/(Kmole) and free energy of activation was 103.32 kJ/mole.
Keywords: chemical engineering, biotechnology, esterification, syntheses, esters, enzymes, lipase, Mucor miehei, reaction kinetics, reaction thermodynamics, 1, 2-isopropylidene-3-oleoyl glycerol
Published in DKUM: 06.06.2012; Views: 2498; Downloads: 97
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Silica aerogels as support for lipase catalyzed esterifications at sub- and supercritical conditions
Zoran Novak, Maja Leitgeb, Vlasta Krmelj, Željko Knez, 2003, original scientific article

Abstract: The enzymes (lipases from Candida rugosa and porcine pancreas) were immobilized on silica aerogels by sol-gel procedure followed by supercritical drying with CO2. Such immobilized enzymes were used as biocatalysts for esterification in supercritical CO2 and near critical propane at 40 °C and 100 bar. It was found out that the initial reaction rates in propane rose two to three times in comparison with the same reaction, catalyzed by free lipase. SC CO2 deactivated the non-immobilized lipase in reaction mixture while with the immobilized enzyme the conversion was 35%. The initial reaction rates in propane were 20 times higher than in water medium due to the properties of propane as a medium for esterification of fatty acids.
Keywords: chemical processing, biotechnology, esterification, immobilization of enzymes, supercritial CO2, propane, lipases, supercritical CO2 drying
Published in DKUM: 01.06.2012; Views: 1828; Downloads: 29
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Decolorization of textile dyes by whole cultures of Ischnoderma Resinosum and by purified laccase and Mn-peroxidase
Vanja Kokol, Aleš Doliška, Ivana Eichlerová, Petr Baldrian, František Nerud, 2007, original scientific article

Abstract: Ischnoderma resinosum produced extracellular ligninolytic enzymes laccase and MnP. The activity of laccase achieved the maximum on day 10 (29.4 U L-1), the MnP on day 14 (34.5 U L-1). Laccase and Mn-peroxidase were purified from the culture liquid using gel permeation and ion-exchange chromatographies. Purified Mn-peroxidase performed decolorization of all textile dyes tested (Reactive Black 5, Reactive Blue 19, Reactive Red 22 and Reactive Yellow 15). Laccase was inactive with Reactive Black 5 and Reactive Red 22, while all dyes were decolorized after addition of the redox mediators violuric acid (VA) and hydroxybenzotriazole (HBT). The culture liquid from I. resinosum cultures was also able to decolorize all dyes as well as the synthetic dyebaths in the presence of VA and HBT. The highest decolorization rates were detected in acidic pH (3-4).
Keywords: Ischnoderma resinosum, Basidiomycetes, Laccase, Mn-peroxidase, Textile dyes, ligninolytic enzymes
Published in DKUM: 01.06.2012; Views: 1911; Downloads: 88
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The influence of enzymatic treatment on wool fibre properties using PEG-modified proteases
Suzana Jus, Marc Schroeder, Georg M. Gübitz, Elisabeth Heine, Vanja Kokol, 2007, original scientific article

Abstract: The main contribution of the presented work was to introduce the use of proteases modified with the soluble polymer polyethylene glycol (PEG) in the bio-finishing process of wool fibres, to target enzyme action to the outerparts of wool fibres, i.e. to avoid the diffusion and consequent destroying of the inner parts of the wool fibre structure, in the case of native proteases using. Different proteolytic enzymes from Bacillus lentus and Bacillus subtilis in native and PEG-modified forms were investigated and their influence on the modification of wool fibres morphology surface, chemical structure, as well as the hydrolysis of wool proteins, the physico-mechanical properties, and the sorption properties of 1:2 metal complex dye during dyeing were studied. SEM images of wool fibres confirmed smoother and cleaner fibre surfaces without fibre damages using PEG-modified proteases. Modified enzyme products have a benefit effect on the wool fibres felting behaviours (14%) in the case when PEG-modified B. lentus is used, without markedly fibre damage expressed by tensile strength and weight loss ofthe fibre. Meanwhile the dye exhaustion showed slower but comparable level of dye uptake at the end of the dyeing.
Keywords: volnena vlakna, proteolitski encimi, encimske modifikacije, sorpcija barve, morfologija vlaken, wool fibres, proteolytic enzymes, enzyme modification, felting, dye sorption, protein hydrolysis, XPS-analysis, fibre morphology
Published in DKUM: 01.06.2012; Views: 3062; Downloads: 108
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A novel metalloprotease from Bacillus cereus for protein fibre processing
Fernanda de Sousa, Suzana Jus, Anita Erbel, Vanja Kokol, Artur Cavaco-Paulo, Georg M. Gübitz, 2007, original scientific article

Abstract: A novel protease produced by Bacillus cereus grown on wool as carbon and nitrogen source was purified. B. cereus protease is a neutral metalloprotease with a molecular mass of 45.6 kDa. The optimum activity was at 45 °C and pH 7.0. The substrate specificity was assessed using oxidized insulin B-chain and synthetic peptide substrates. The cleavage of the insulin B-chain was determined to be Asn3, Leu6, His10-Leu11, Ala14, Glu21, after 12 h incubation. Among the peptide substrates, the enzyme did not exhibit activity towards ester substrates; with p-nitroanilide, the kinetic data indicate that aliphatic and aromatic amino acids were the preferred residues at the P1 position. For furylacryloyl peptides substrates, which are typical substrates for thermolysin, the enzyme exhibited high hydrolytic activity with a Km values of 0.858 and 2.363 mM for N-(3-[2-Furyl]acryloyl)-Ala-Phe amide and N-(3-[2-Furyl]acryloyl)-Gly-Leu amide, respectively. The purified protease hydrolysed proteins substrates such as azocasein, azocoll, keratin azure and wool.
Keywords: textile finishing, enzymatic modification, wool fibre, enzymes, Bacilus cereus, specificity, kinetics, metalloprotease
Published in DKUM: 01.06.2012; Views: 2448; Downloads: 102
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