Journal articles: 'Transition metals; Hydrolytic enzymes'

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Bautista-Expósito, Sara, Irene Tomé-Sánchez, Ana Belén Martín-Diana, Juana Frias, Elena Peñas, Daniel Rico, María Jesús García Casas, and Cristina Martínez-Villaluenga. "Enzyme Selection and Hydrolysis under Optimal Conditions Improved Phenolic Acid Solubility, and Antioxidant and Anti-Inflammatory Activities of Wheat Bran." Antioxidants 9, no. 10 (October 13, 2020): 984. http://dx.doi.org/10.3390/antiox9100984.

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Valorization of wheat bran (WB) into new high-value products is of great interest within the framework of sustainability and circular economy. In the present study, we utilized a multi-step approach to extract nutraceutical compounds (phenolic acids) from WB and improved its antioxidant and anti-inflammatory properties through using sequential hydrothermal and enzymatic hydrolysis. Thirteen commercial glycosidases differing in their specific activity were screened and compared for hydrolytic efficiency to release monosaccharides, ferulic acid, and diferulic acid. Ultraflo XL was selected as the desired enzyme treatment on the basis of its higher WB solubilization, as well as its monosaccharide and phenolic acids yields. The relationships between better hydrolytic performance of Ultraflo XL and its particular activity profile were established. To determine the optimum conditions for Ultraflo XL treatment, we tested different factors (solvent pH, incubation temperature, and time) under 15 experiments. A multicomponent analysis (MCA), including central composite design, model fitness, regression coefficients, analysis of variance, 3D response curves, and desirability, was used for processing optimization. A beneficial effect of autoclave treatment on the release of phenolic compounds was also evidenced. The results of MCA showed involvement of linear, quadratic, and interactive effects of processing factors, although solvent pH was the main determinant factor, affecting enzymatic extraction of phenolics and bioactivity of hydrolysates. As compared to control WB, under optimized conditions (47 °C, pH = 4.4, and 20.8 h), WB hydrolysates showed 4.2, 1.5, 2, and 3 times higher content of ferulic acid (FA) and capacity to scavenge oxygen radicals, chelate transition metals, and inhibit monocyte chemoattractant protein-1 secretion in macrophages, respectively. These approaches could be applied for the sustainable utilization of WB, harnessing its nutraceutical potential.

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Sugrue, Elena, Nicholas J. Fraser, Davis H. Hopkins, Paul D. Carr, Jeevan L. Khurana, John G. Oakeshott, Colin Scott, and Colin J. Jackson. "Evolutionary Expansion of the Amidohydrolase Superfamily in Bacteria in Response to the Synthetic Compounds Molinate and Diuron." Applied and Environmental Microbiology 81, no. 7 (January 30, 2015): 2612–24. http://dx.doi.org/10.1128/aem.04016-14.

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ABSTRACTThe amidohydrolase superfamily has remarkable functional diversity, with considerable structural and functional annotation of known sequences. In microbes, the recent evolution of several members of this family to catalyze the breakdown of environmental xenobiotics is not well understood. An evolutionary transition from binuclear to mononuclear metal ion coordination at the active sites of these enzymes could produce large functional changes such as those observed in nature, but there are few clear examples available to support this hypothesis. To investigate the role of binuclear-mononuclear active-site transitions in the evolution of new function in this superfamily, we have characterized two recently evolved enzymes that catalyze the hydrolysis of the synthetic herbicides molinate (MolA) and phenylurea (PuhB). In this work, the crystal structures, mutagenesis, metal ion analysis, and enzyme kinetics of both MolA and PuhB establish that these enzymes utilize a mononuclear active site. However, bioinformatics and structural comparisons reveal that the closest putative ancestor of these enzymes had a binuclear active site, indicating that a binuclear-mononuclear transition has occurred. These proteins may represent examples of evolution modifying the characteristics of existing catalysts to satisfy new requirements, specifically, metal ion rearrangement leading to large leaps in activity that would not otherwise be possible.

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Grootveld, Martin, Edward Lynch, Georgina Page, Wyman Chan, Benita Percival, Eugenia Anagnostaki, Valina Mylona, Sonia Bordin-Aykroyd, and Kerry L. Grootveld. "Potential Advantages of Peroxoborates and Their Ester Adducts Over Hydrogen Peroxide as Therapeutic Agents in Oral Healthcare Products: Chemical/Biochemical Reactivity Considerations In Vitro, Ex Vivo And In Vivo." Dentistry Journal 8, no. 3 (August 7, 2020): 89. http://dx.doi.org/10.3390/dj8030089.

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Peroxides present in oral healthcare products generally exert favourable protective activities against the development and progression of tooth decay, plaque, gingivitis, and halitosis, etc. However, despite the high level of research focus on hydrogen and carbamide peroxides as therapeutically active (and tooth-whitening) agents, to date the use of alternative chemical forms of peroxides such as peroxoborates for these purposes has received only scant attention. Intriguingly, peroxoborate and its esters with polyols, such as glycerol, have a very diverse chemistry/biochemistry in aqueous solution, for which there is an increasing amount of evidence that it remains distinctive from that of hydrogen peroxide; such properties include self-associative and hydrolytic equilibria, and their abilities to participate in electrophile- or nucleophile-scavenging, metal ion-complexing, redox and free radical reactions, for example. Therefore, the purpose of this detailed commentary is to evaluate both differences and similarities between the molecular/biomolecular reactivities of peroxoborate species and hydrogen peroxide in vitro, ex-vivo and in vivo. It encompasses brief sectional accounts regarding the molecular heterogeneity of peroxoborates, the release of bioactive agents therefrom, and their oxidative attack on oral cavity biomolecules (the nucleophilic or electrophilic character of these oxidations are discussed). Further areas explored are the abilities of borates and peroxoborates to enhance the solubility of iron ions in aqueous solution, their involvements in free radical biochemistry (particularly the complexation of oxygen radical-promoting transition metal ions by, and antioxidant properties of, peroxoborate-polyol ester adducts), and the specific inhibition of protease enzymes. Further aspects focus on the tooth-whitening, oral malodor neutralizing, and potential mutagenic and genotoxic properties of peroxoborates, along with possible mechanisms for these processes. The abilities of peroxoborates, and peroxides in general, to modulate the activities of inflammatory mediators and vitamins, antioxidant or otherwise, are also explored.

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Purg, Miha, Anna Pabis, Florian Baier, Nobuhiko Tokuriki, Colin Jackson, and Shina Caroline Lynn Kamerlin. "Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 374, no. 2080 (November 13, 2016): 20160150. http://dx.doi.org/10.1098/rsta.2016.0150.

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Diverse organophosphate hydrolases have convergently evolved the ability to hydrolyse man-made organophosphates. Thus, these enzymes are attractive model systems for studying the factors shaping enzyme functional evolution. Methyl parathion hydrolase (MPH) is an enzyme from the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphate, aryl ester and lactone substrates. In addition, MPH demonstrates metal-ion-dependent selectivity patterns. The origins of this remain unclear, but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. Here, we present detailed mechanistic studies of the paraoxonase and arylesterase activities of MPH complexed with five different transition metal ions, and demonstrate that the hydrolysis reactions proceed via similar pathways and transition states. However, while it is possible to discern a clear structural origin for the selectivity between different substrates , the selectivity between different metal ions appears to lie instead in the distinct electrostatic properties of the metal ions themselves, which causes subtle changes in transition state geometries and metal–metal distances at the transition state rather than significant structural changes in the active site. While subtle, these differences can be significant for shaping the metal-ion-dependent activity patterns observed for this enzyme. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’.

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Barrozo, Alexandre, David Blaha-Nelson, Nicholas H. Williams, and Shina C. L. Kamerlin. "The effect of magnesium ions on triphosphate hydrolysis." Pure and Applied Chemistry 89, no. 6 (June 27, 2017): 715–27. http://dx.doi.org/10.1515/pac-2016-1125.

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AbstractThe role of metal ions in catalyzing phosphate ester hydrolysis has been the subject of much debate, both in terms of whether they change the transition state structure or mechanistic pathway. Understanding the impact of metal ions on these biologically critical reactions is central to improving our understanding of the role of metal ions in the numerous enzymes that facilitate them. In the present study, we have performed density functional theory studies of the mechanisms of methyl triphosphate and acetyl phosphate hydrolysis in aqueous solution to explore the competition between solvent- and substrate-assisted pathways, and examined the impact of Mg2+ on the energetics and transition state geometries. In both cases, we observe a clear preference for a more dissociative solvent-assisted transition state, which is not significantly changed by coordination of Mg2+. The effect of Mg2+ on the transition state geometries for the two pathways is minimal. While our calculations cannot rule out a substrate-assisted pathway as a possible solution for biological phosphate hydrolysis, they demonstrate that a significantly higher energy barrier needs to be overcome in the enzymatic reaction for this to be an energetically viable reaction pathway.

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da Silva, Antônio Carlos, S. C. Santos, and Sonia Regina Homem de Mello-Castanho. "Transition Metals in Glass Formation." Materials Science Forum 727-728 (August 2012): 1496–501. http://dx.doi.org/10.4028/www.scientific.net/msf.727-728.1496.

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The structure of silicate glasses gets its charge stability through SiO2, R2O3, R2+and R+groups arrangement. In these glassy structures, transition metals are usually used as dopants in small amounts. However, in soda-lime glass systems, transition metals can take part in the glassy network in larger quantities as secundary former or modifier, insted R2+groups, if the charge balance conditions are made favorable by R2O3groups additions. This paper studies transition metals (Cr, Ni, Fe, Cu, Zn, Pb, Ru) soda-lime-borosilicate glass network incorporation. This process was applied for many kinds of toxic metals containing vitrification waste. The glasses were obtaind by melt at temperature of 1300°C, and characterized by FT-IR and XRD techinics. The chemical stability was evaluated by hydrolytic attack test. The glasses showed a high chemistry and environmental stability like the soda-lime glass.Keywords: glass structure, electroplating waste, e-waste, nanowaste.

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Lemanowicz, Joanna, and Agata Bartkowiak. "Diagnosis of the Content of Selected Heavy Metals in the Soils of the Pałuki Region Against their Enzymatic Activity." Archives of Environmental Protection 39, no. 3 (September 1, 2013): 23–32. http://dx.doi.org/10.2478/aep-2013-0026.

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Abstract The paper presents the research results for the soils sampled from the area located in the eastern part of the Chodzieskie Lakes, between the Middle Noteć River Valley and the Wełna River Valley, the right tributary of the Warta River. The research involved 7 soil samples from the surface horizons, allocated to the cultivation of various plant species (cereals and vegetable crops). The following were determined in the soil material: the content of phytoavailable forms of selected heavy metals Zn, Cu, Pb, Ni, Fe and Mn, active and available to plants phosphorus against the activity of selected oxydo-reduction and hydrolytic enzymes. The soil under the vegetable crops showed a very high richness in phosphorus available to plants, which must have been related to an intensive fertilisation. There were identified relatively low contents of the available forms of the heavy metals investigated, the fact that points to their natural content in soil, which triggered the inhibition of neither the oxydo-reduction nor hydrolytic enzymes.

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Abouhmad, Adel, Ahmed H. Korany, Carl Grey, Tarek Dishisha, and Rajni Hatti-Kaul. "Exploring the Enzymatic and Antibacterial Activities of Novel Mycobacteriophage Lysin B Enzymes." International Journal of Molecular Sciences 21, no. 9 (April 30, 2020): 3176. http://dx.doi.org/10.3390/ijms21093176.

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Mycobacteriophages possess different sets of lytic enzymes for disruption of the complex cell envelope of the mycobacteria host cells and release of the viral progeny. Lysin B (LysB) enzymes are mycolylarabinogalactan esterases that cleave the ester bond between the arabinogalactan and mycolic acids in the mycolylarabinogalactan-peptidoglycan (mAGP) complex in the cell envelope of mycobacteria. In the present study, four LysB enzymes were produced recombinantly and characterized with respect to their enzymatic and antibacterial activities. Examination of the kinetic parameters for the hydrolysis of para-nitrophenyl ester substrates, shows LysB-His6 enzymes to be active against a range of substrates (C4–C16), with a catalytic preference towards p-nitrophenyl laurate (C12). With p-nitrophenyl butyrate as substrate, LysB-His6 enzymes showed highest activity at 37 °C. LysB-His6 enzymes also hydrolyzed different Tween substrates with highest activity against Tween 20 and 80. Metal ions like Ca2+ and Mn2+ enhanced the enzymatic activity of LysB-His6 enzymes, while transition metal ions like Zn2+ and Cu2+ inhibited the enzymatic activity. The mycolylarabinogalactan esterase activity of LysB-His6 enzymes against mAGP complex was confirmed by LC-MS. LysB-His6 enzymes showed marginal antibacterial activity when tested alone against Mycobacterium smegmatis, however a synergetic activity was noticed when combined with outer membrane permealizers. These results confirm that LysB enzymes are lipolytic enzymes with potential application as antimycobacterials.

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Sanyal, Sankar N, Gurdeep Singh, and Shailender S Kanwar. "Thermotropic Lipid Phase Transition and the Behavior of Hydrolytic Enzymes in the Kidney Cortex Brush Border Membrane." Chemistry & Biodiversity 3, no. 10 (October 2006): 1102–15. http://dx.doi.org/10.1002/cbdv.200690112.

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Olin, Magnus, Jonas Carlsson, and Leif Bülow. "Quantitation of Transition Metals Using Genetically Engineered Enzymes Carrying Polyhistidine Tails." Analytical Letters 28, no. 7 (May 1995): 1159–71. http://dx.doi.org/10.1080/00032719508000335.

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DINH, P. M., M. T. EL GIHANI, J. M. J. WILLIAMS, and W. HARRIS. "ChemInform Abstract: Dynamic Kinetic Resolution Using Enzymes and Transition Metals Combination." ChemInform 30, no. 4 (June 17, 2010): no. http://dx.doi.org/10.1002/chin.199904262.

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Hou, S., D. M. Hoyle, C. J. Blackwell, K. Haernvall, V. Perz, G. M. Guebitz, and E. Khosravi. "Hydrolytic degradation of ROMP thermosetting materials catalysed by bio-derived acids and enzymes: from networks to linear materials." Green Chemistry 18, no. 19 (2016): 5190–99. http://dx.doi.org/10.1039/c6gc00378h.

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ROMP thermosetting polymers are degraded by bio-derived acetic and citric acids as well as cutinase from Thermobifida cellulosilytica enzyme becoming soluble in DCM. The degradation process breaks the acetal ester linkages allowing transition to linear thermoplastic polymers.

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Nielsen, Jacob Holm, Gitte Hald, Line Kjeldsen, Henrik J. Andersen, and Henrik Østdal. "Oxidation of Ascorbate in Raw Milk Induced by Enzymes and Transition Metals." Journal of Agricultural and Food Chemistry 49, no. 6 (June 2001): 2998–3003. http://dx.doi.org/10.1021/jf000862j.

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Rai, Rikky, Manish Ranjan, Binod B. Pradhan, and Subhadeep Chatterjee. "Atypical Regulation of Virulence-Associated Functions by a Diffusible Signal Factor in Xanthomonas oryzae pv. oryzae." Molecular Plant-Microbe Interactions® 25, no. 6 (June 2012): 789–801. http://dx.doi.org/10.1094/mpmi-11-11-0285-r.

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In Xanthomonas oryzae pv. oryzae, the bacterial blight pathogen of rice, a secreted fatty acid signaling molecule known as diffusible signal factor (DSF) is required for virulence and growth on low-iron medium. To identify other virulence-associated traits that are regulated by DSF in this pathogen, we have performed microarray analysis of transcriptional changes between the wild type and DSF-deficient mutants of X. oryzae pv. oryzae. Expression of genes that encode secreted hydrolytic enzymes, motility, and chemotaxis functions are negatively regulated by DSF while functions involved in adhesion and biofilm formation are positively regulated. Enzymatic assays for hydrolytic enzymes as well as assays for chemotaxis, motility, attachment, and biofilm formation corroborate these findings. These results demonstrate that, in X. oryzae pv. oryzae, DSF-mediated cell-to-cell signaling coordinates transition from solitary to biofilm lifestyle by promoting expression of attachment functions and negatively regulating expression of motility functions. This is in contrast to X. campestris pv. campestris, a pathogen of crucifers, wherein the DSF system positively regulates motility functions and negatively regulates biofilm formation. These results indicate that virulence-associated functions can be regulated in a completely contrasting fashion by the same signaling system in very closely related bacteria.

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Bosnich, Brice. "Alan McLeod Sargeson FAA. 13 October 1930 — 29 December 2008." Biographical Memoirs of Fellows of the Royal Society 58 (January 2012): 265–82. http://dx.doi.org/10.1098/rsbm.2011.0017.

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Alan Sargeson was an extraordinarily gifted inorganic chemist who consistently made important and lasting contributions to his discipline. His lifelong interests were in the area of coordination chemistry, especially in the stereochemistry and reactivity of complexes involving the transition element cobalt. Notable discoveries included the elucidation of the mechanisms of substitution reactions of cobalt complexes, the demonstration that amino acid amides and their esters and phosphate esters incorporated in properly designed metal complexes could achieve the high rates of hydrolysis displayed by enzyme reactions, and perhaps most notably the discovery of the ready formation of cage complexes in which the metal is fully encapsulated. His impact on his field was far reaching, his achievements were at the highest level and for more than 30 years he was among the few who dominated the field.

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Bosnich, B. "Alan McLeod Sargeson 1930 - 2008." Historical Records of Australian Science 22, no. 2 (2011): 246. http://dx.doi.org/10.1071/hr11011.

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Alan Sargeson was an extraordinarily gifted inorganic chemist who consistently made important and lasting contributions to his discipline. His lifelong interests were in the area of coordination chemistry, especially in the stereochemistry and reactivity of complexes involving the transition element cobalt. Notable discoveries included the elucidation of the mechanisms of substitution reactions of cobalt complexes, and the demonstration that amino acid amides and their esters and phosphate esters incorporated in properly designed metal complexes could achieve the high rates of hydrolysis displayed by enzyme reactions. Perhaps most notable was the discovery of the ready formation of cage complexes where the metal is fully encapsulated. His impact on his field was far-reaching, his achievements were at the highest level and for over thirty years he was among the few who dominated the field.

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Bramasole, Laylan, Abhishek Sinha, Dana Harshuk, Angela Cirigliano, Gurevich Sylvia, Zanlin Yu, Rinat Carmeli, Michael Glickman, Teresa Rinaldi, and Elah Pick. "The Proteasome Lid Triggers COP9 Signalosome Activity during the Transition of Saccharomyces cerevisiae Cells into Quiescence." Biomolecules 9, no. 9 (September 4, 2019): 449. http://dx.doi.org/10.3390/biom9090449.

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The class of Cullin–RING E3 ligases (CRLs) selectively ubiquitinate a large portion of proteins targeted for proteolysis by the 26S proteasome. Before degradation, ubiquitin molecules are removed from their conjugated proteins by deubiquitinating enzymes, a handful of which are associated with the proteasome. The CRL activity is triggered by modification of the Cullin subunit with the ubiquitin-like protein, NEDD8 (also known as Rub1 in Saccharomyces cerevisiae). Cullin modification is then reversed by hydrolytic action of the COP9 signalosome (CSN). As the NEDD8–Rub1 catalytic cycle is not essential for the viability of S. cerevisiae, this organism is a useful model system to study the alteration of Rub1–CRL conjugation patterns. In this study, we describe two distinct mutants of Rpn11, a proteasome-associated deubiquitinating enzyme, both of which exhibit a biochemical phenotype characterized by high accumulation of Rub1-modified Cdc53–Cullin1 (yCul1) upon entry into quiescence in S. cerevisiae. Further characterization revealed proteasome 19S-lid-associated deubiquitination activity that authorizes the hydrolysis of Rub1 from yCul1 by the CSN complex. Thus, our results suggest a negative feedback mechanism via proteasome capacity on upstream ubiquitinating enzymes.

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Kudaibergenov, Sarkyt. "Physicochemical, Complexation and Catalytic Properties of Polyampholyte Cryogels." Gels 5, no. 1 (February 21, 2019): 8. http://dx.doi.org/10.3390/gels5010008.

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Polyampholyte cryogels are a less considered subject in comparison with cryogels based on nonionic, anionic and cationic precursors. This review is devoted to physicochemical behavior, complexation ability and catalytic properties of cryogels based on amphoteric macromolecules. Polyampholyte cryogels are able to exhibit the stimuli-responsive behavior and change the structure and morphology in response to temperature, pH of the medium, ionic strength and water–organic solvents. Moreover, they can uptake transition metal ions, anionic and cationic dyes, ionic surfactants, polyelectrolytes, proteins, and enzymes through formation of coordination bonds, hydrogen bonds, and electrostatic forces. The catalytic properties of polyampholyte cryogels themselves and with immobilized metal nanoparticles suspended are outlined following hydrolysis, transesterification, hydrogenation and oxidation reactions of various substrates. Application of polyampholyte cryogels as a protein-imprinted matrix for separation and purification of biomacromolecules and for sustained release of proteins is demonstrated. Comparative analysis of the behavior of polyampholyte cryogels with nonionic, anionic and cationic precursors is given together with concluding remarks.

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Kumar, Amit, Gopal Raj Periyannan, Beena Narayanan, Aaron W. Kittell, Jung-Ja Kim, and Brian Bennett. "Experimental evidence for a metallohydrolase mechanism in which the nucleophile is not delivered by a metal ion: EPR spectrokinetic and structural studies of aminopeptidase from Vibrio proteolyticus." Biochemical Journal 403, no. 3 (April 12, 2007): 527–36. http://dx.doi.org/10.1042/bj20061591.

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Metallohydrolases catalyse some of the most important reactions in biology and are targets for numerous chemotherapeutic agents designed to combat bacterial infectivity, antibiotic resistance, HIV infectivity, tumour growth, angiogenesis and immune disorders. Rational design of inhibitors of these enzymes with chemotherapeutic potential relies on detailed knowledge of the catalytic mechanism. The roles of the catalytic transition ions in these enzymes have long been assumed to include the activation and delivery of a nucleophilic hydroxy moiety. In the present study, catalytic intermediates in the hydrolysis of L-leucyl-L-leucyl-L-leucine by Vibrio proteolyticus aminopeptidase were characterized in spectrokinetic and structural studies. Rapid-freeze-quench EPR studies of reaction products of L-leucyl-L-leucyl-L-leucine and Co(II)-substituted aminopeptidase, and comparison of the EPR data with those from structurally characterized complexes of aminopeptidase with inhibitors, indicated the formation of a catalytically competent post-Michaelis pre-transition state intermediate with a structure analogous to that of the inhibited complex with bestatin. The X-ray crystal structure of an aminopeptidase–L-leucyl-L-leucyl-L-leucine complex was also analogous to that of the bestatin complex. In these structures, no water/hydroxy group was observed bound to the essential metal ion. However, a water/hydroxy group was clearly identified that was bound to the metal-ligating oxygen atom of Glu152. This water/hydroxy group is proposed as a candidate for the active nucleophile in a novel metallohydrolase mechanism that shares features of the catalytic mechanisms of aspartic proteases and of B2 metallo-β-lactamases. Preliminary studies on site-directed variants are consistent with the proposal. Other features of the structure suggest roles for the dinuclear centre in geometrically and electrophilically activating the substrate.

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Han, Xiao, Zheng Chen, Wenxing Chen, Chunlin Lv, Yongjun Ji, Jing Li, Weng-Chon Cheong, et al. "A general strategy to prepare atomically dispersed biomimetic catalysts based on host–guest chemistry." Chemical Communications 57, no. 15 (2021): 1895–98. http://dx.doi.org/10.1039/d0cc07119f.

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Goedl, Christiane, Richard Griessler, Alexandra Schwarz, and Bernd Nidetzky. "Structure–function relationships for Schizophyllum commune trehalose phosphorylase and their implications for the catalytic mechanism of family GT-4 glycosyltransferases." Biochemical Journal 397, no. 3 (July 13, 2006): 491–500. http://dx.doi.org/10.1042/bj20060029.

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The cDNA encoding trehalose phosphorylase, a family GT-4 glycosyltransferase from the fungus Schizophyllum commune, was isolated and expressed in Escherichia coli to yield functional recombinant protein in its full length of 737 amino acids. Unlike the natural phosphorylase that was previously obtained as a truncated 61 kDa monomer containing one tightly bound Mg2+, the intact enzyme produced in E. coli is a dimer and not associated with metal ions [Eis, Watkins, Prohaska and Nidetzky (2001) Biochem. J. 356, 757–767]. MS analysis of the slow spontaneous conversion of the full-length enzyme into a 61 kDa fragment that is fully active revealed that critical elements of catalysis and specificity of trehalose phosphorylase reside entirely in the C-terminal protein part. Intact and truncated phosphorylases thus show identical inhibition constants for the transition state analogue orthovanadate and α,α-trehalose (Ki≈1 μM). Structure-based sequence comparison with retaining glycosyltransferases of fold family GT-B reveals a putative active centre of trehalose phosphorylase, and results of site-directed mutagenesis confirm the predicted crucial role of Asp379, His403, Arg507 and Lys512 in catalysis and also delineate a function of these residues in determining the large preference of the wild-type enzyme for the phosphorolysis compared with hydrolysis of α,α-trehalose. The pseudo-disaccharide validoxylamine A was identified as a strong inhibitor of trehalose phosphorylase (Ki=1.7±0.2 μM) that displays 350-fold tighter binding to the enzyme–phosphate complex than the non-phosphorolysable substrate analogue α,α-thio-trehalose. Structural and electronic features of the inhibitor that may be responsible for high-affinity binding and their complementarity to an anticipated glucosyl oxocarbenium ion-like transition state are discussed.

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Srivastava, Vartika, Rajeev K. Singla, and Ashok K. Dubey. "Inhibition of Biofilm and Virulence Factors of Candida albicans by Partially Purified Secondary Metabolites of Streptomyces chrestomyceticus Strain ADP4." Current Topics in Medicinal Chemistry 18, no. 11 (August 28, 2018): 925–45. http://dx.doi.org/10.2174/1568026618666180711154110.

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Background: Despite several advancements in antifungal drug discovery, fungal diseases like Invasive Candidiasis (IC) still remain associated with high rates of morbidity and mortality worldwide. Thus there is an enormous need for anti-Candida drugs. Objective: The main objectives of the work included: 1. To investigate therapeutically significant classes of secondary metabolites produced by S. chrestomyceticus strain ADP4. 2. To investigate and analyze inhibition of significant virulence attributes of C. albicans, such as, biofilm and secretory hydrolytic enzymes by ADP4 secondary metabolites. 3. Mechanistic analysis of probable compounds for their site of action on Secretary Aspartyl Proteinase 3 (Sap3). Methods: Metabolite extract-SDB (MESDB) of S. chrestomyceticus strain ADP4 was fractionated on silica gel column chromatography. Fractions were analyzed for anti-Candida activity by disc diffusion assay. Active fractions were further purified by differential solvent treatment. MIC90 values were determined by broth dilution method. MFC was based on counting viable cells. Inhibition of yeast to hyphae transition and that of production of hydrolytic enzymes were estimated by plate assays. GC-MS of MESDB and Partially Purified Metabolite preparations (PPMs) was done. GRIP docking studies with Sap 3 of C. albicans was done using VLife MDS 4.6 software. Results: Chemical profiling showed that ADP4 secondary metabolites contained alkaloids, flavonoids, polyphenols, terpenoids and triterpenes. The MESDB and the PPMs showed low or no cytotoxicity but were able to effectively contain virulence attributes of Candida pathogen. Docking studies revealed that some of the probable compounds have affinity for aspartic acid residue in Sap3 enzyme of C. albicans. Conclusion: Secondary metabolite of strain ADP4 included important classes of therapeutically important compounds. Their anti-Candida activity was mediated by inhibition of critical virulence factors of the pathogen.

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Vaniushenkova, Anna A., Elina E. Dosadina, Sergey V. Kalenov, Nikolay S. Markvichev, and Alexey A. Belov. "Synthesis and study of the properties of composite materials based on cellulose and chitosan containing various therapeutic agents. Part 2. Effect of chitosan on the destruction of cellulosic carriers and the kinetics of release of the therapeutic agent in the model environment." Butlerov Communications 57, no. 3 (March 31, 2019): 105–19. http://dx.doi.org/10.37952/roi-jbc-01/19-57-3-105.

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One of the important directions in the field of creation and research of medicines is the optimization of the therapeutic action of the active substance and the study of the interaction of the drug and its components with the body. Numerous studies have established that a modern wound-healing agent should have the following properties: to sorb purulent discharge and its destruction products, to have cleansing properties (usually due to the introduced proteolytic enzyme), to have biocidal properties (especially with respect to pathogenic microflora and first of all with respect to to Staphylococcus aureus), because wound infection can significantly slow down the healing process, and in some cases contribute to the transition of the wound process to a chronic one and include an antioxidant (especially for the treatment of long-term diseases). The degradation of high-molecular compounds in the body can be biological and non-biological. From the point of view of the destruction of biopolymers, degradation under the influence of external factors existing in the environment of a living organism is of particular interest. The mechanism for the release of a therapeutic agent into a wound occurs due to the destruction of the base and the rupture of various links between the therapeutic agents and the matrix during its use: hydrolytic destruction under the action of the body environment, as well as biological destruction due to the action of various biomolecules in the medium, mainly enzymes. On the basis of our own and literature data, schemes have been proposed for working in a model liquid medium of wound applications, based on dialdehydecellulose and chitosan, containing immobilized therapeutic agents, including enzymes. Chitosan has been shown to stabilize dialdehyde cellulose during hydrolytic degradation. Immobilization in chitosan gel, drying and storing various therapeutic agents and their mixtures in different directions affects the kinetics of drug release.

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Janiszewska, Kamila, Michał Talma, Bartosz Oszywa, Małgorzata Pawełczak, Paweł Kafarski, and Artur Mucha. "N-Benzyl Residues as the P1′ Substituents in Phosphorus-Containing Extended Transition State Analog Inhibitors of Metalloaminopeptidases." Molecules 25, no. 18 (September 22, 2020): 4334. http://dx.doi.org/10.3390/molecules25184334.

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Peptidyl enzyme inhibitors containing an internal aminomethylphosphinic bond system (P(O)(OH)-CH2-NH) can be termed extended transition state analogs by similarity to the corresponding phosphonamidates (P(O)(OH)-NH). Phosphonamidate pseudopeptides are broadly recognized as competitive mechanism-based inhibitors of metalloenzymes, mainly hydrolases. Their practical use is, however, limited by hydrolytic instability, which is particularly restricting for dipeptide analogs. Extension of phosphonamidates by addition of the methylene group produces a P-C-N system fully resistant in water conditions. In the current work, we present a versatile synthetic approach to such modified dipeptides, based on the three-component phospha-Mannich condensation of phosphinic acids, formaldehyde, and N-benzylglycines. The last-mentioned component allowed for simple and versatile introduction of functionalized P1′ residues located on the tertiary amino group. The products demonstrated moderate inhibitory activity towards porcine and plant metalloaminopeptidases, while selected derivatives appeared very potent with human alanyl aminopeptidase (Ki = 102 nM for 6a). Analysis of ligand-protein complexes obtained by molecular modelling revealed canonical modes of interactions for mono-metallic alanyl aminopeptidases, and distorted modes for di-metallic leucine aminopeptidases (with C-terminal carboxylate, not phosphinate, involved in metal coordination). In general, the method can be dedicated to examine P1′-S1′ complementarity in searching for non-evident structures of specific residues as the key fragments of perspective ligands.

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Tomova, Iva, Margarita Stoilova−Disheva, and Evgenia Vasileva−Tonkova. "Characterization of heavy metals resistant heterotrophic bacteria from soils in the Windmill Islands region, Wilkes Land, East Antarctica." Polish Polar Research 35, no. 4 (December 10, 2014): 593–607. http://dx.doi.org/10.2478/popore-2014-0028.

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AbstractIn this study, selected heavy metals resistant heterotrophic bacteria isolated from soil samples at the Windmill Islands region, Wilkes Land (East Antarctica), were characterized. Phylogenetic analysis revealed affiliation of isolates to genera Bacillus, Lysinibacillus, Micrococcus and Stenotrophomonas. The strains were found to be psychrotolerant and halotolerant, able to tolerate up to 10% NaCl in the growth medium. The Minimum Inhibitory Concentration of the seven heavy metals Cr, Cu, Ni, Co, Cd, Zn, and Pb was determined in solid media for each bacterial strain. Gram−positive Vi−2 strain and Gram−negative Vi−4 strain showed highest multiply heavy metals resistance, and Vi−3 and Vi−4 strains showed multi−antibiotic resistance to more than a half of the 13 used antibiotics. Plasmids were detected only in Gram−negative Vi−4 strain. The bacteria were able to produce different hydrolytic enzymes including industrially important proteases, xylanases, cellulases, and β−glucosidases. High heavy metals resistance of the Antarctic bacteria suggests their potential application for wastewater treatment in cold and temperate climates. Highly sensitive to Cd and Co ions Vi−1, Vi−5 and Vi−7 strains would be promising for developing biosensors to detect these most toxic heavy metals in environmental samples.

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Mroczyńska, Martyna, and Anna Brillowska-Dąbrowska. "Virulence of Clinical Candida Isolates." Pathogens 10, no. 4 (April 12, 2021): 466. http://dx.doi.org/10.3390/pathogens10040466.

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The factors enabling Candida spp. infections are secretion of hydrolytic enzymes, adherence to surfaces, biofilm formation or morphological transition, and fitness attributes. The aim of this study was to investigate the correlation between known extracellular virulence factors and survival of Galleria mellonella larvae infected with clinical Candida. The 25 isolates were tested and the activity of proteinases among 24/24, phospholipases among 7/22, esterases among 14/23, hemolysins among 18/24, and biofilm formation ability among 18/25 isolates was confirmed. Pathogenicity investigation using G. mellonella larvae as host model demonstrated that C. albicans isolates and C. glabrata isolate were the most virulent and C. krusei isolates were avirulent. C. parapsilosis virulence was identified as varied, C. inconspicua were moderately virulent, and one C. palmioleophila isolate was of low virulence and the remaining isolates of this species were moderately virulent. According to our study, virulence of Candida isolates is related to the expression of proteases, hemolysins, and esterases.

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Olszowska, Grażyna. "Denoting the intensity of soil biochemical transition according to stand species composition." Forest Research Papers 79, no. 4 (December 1, 2018): 327–34. http://dx.doi.org/10.2478/frp-2018-0033.

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Abstract The aim of this study was to denote biochemical soil activity in pure Scots pine, Norway spruce, silver fir, European larch, European beech and oak stands as well as in mixed fir-pine, beech-pine and fir-beech forests growing on a fertile fresh mixed deciduous site. The field work was carried out in the following Forest Districts: Nowe Ramuki (Mazursko-Podlaska forest region), Płońsk, Jabłonna, Brzeziny Siedlce, Grójec (Mazowiecko-Podlaska forest region) and Skarżysko, Ostrowiec and Marcule (Małopolska forest region). In 2015–2017, sample plots were assigned and chemical as well as soil enzyme activity measurements were made in each forest stand. Samples were taken from the organic (O) and humus (A) layers and for both the acidity (in 1M KCl), content of nitrogen, carbon, sum of exchangeable alkaline cations and hydrolytic acidity were determined. The investigation of soil enzymes included the measurements of urease, asparginase, acid phosphatase and dehydrogenase activity. Coniferous trees, especially fir, spruce or larch, and mixed fir-beech and pine-beech stands were observed to have a very positive influence on the biochemical soil properties. The highest activity of dehydrogenase was observed in soils of spruce and mixed fir-beech stands, whereas it was lower in soils of beech and pine stands, and the lowest in oak stands. Oak stands were furthermore characterized by the lowest soil acidity, lowest concentration of alkaline cations, the lowest nitrogen and carbon content as well as the smallest C/N ratio. In overall, soil enzyme activity showed a significant correlation with chemical soil parameters.

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Sato, Shin, Yoichi Honda, Masaaki Kuwahara, and Takashi Watanabe. "Degradation of Vulcanized and Nonvulcanized Polyisoprene Rubbers by Lipid Peroxidation Catalyzed by Oxidative Enzymes and Transition Metals." Biomacromolecules 4, no. 2 (March 2003): 321–29. http://dx.doi.org/10.1021/bm025683k.

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29

Sharma, Yamini, Sumit Kumar Rastogi, Ahmad Perwez, Moshahid Alam Rizvi, and Nikhat Manzoor. "β-citronellol alters cell surface properties of Candida albicans to influence pathogenicity related traits." Medical Mycology 58, no. 1 (March 6, 2019): 93–106. http://dx.doi.org/10.1093/mmy/myz009.

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Abstract The pathogenicity of Candida albicans, an opportunistic human fungal pathogen, is attributed to several virulence factors. β-citronellol is a monoterpenoid present in several plant essential oils. The present study explores the antifungal potential and mode of action of β-citronellol against C. albicans ATCC 90028 (standard), C. albicans D-27 (FLC-sensitive), and C. albicans S-1 (FLC-resistant). Anti-Candida potential was studied by performing MIC, MFC, growth curves, disc diffusion, spot assay, and WST1 cytotoxic assay. Morphological transition was monitored microscopically in both solid and liquid hyphae inducing media. β-citronellol inhibits yeast to hyphal transition in both liquid and solid hyphae inducing media. It had a significant inhibitory effect on biofilm formation and secretion of extracellular proteinases and phospholipases. We showed that it has an adverse effect on membrane ergosterol levels and modulates expression of related ERG genes. Expression profiles of selected genes associated with C. albicans pathogenicity displayed reduced expression in treated cells. This work suggests that β-citronellol inhibits morphological transition in C. albicans and decreases the secretion of hydrolytic enzymes involved in the early stage of infection as well as modulates the expression of associated genes. Pleiotropic phenotype shown by β-citronellol treated Candida cells suggests various modes of action. Further studies will assess the clinical application of β-citronellol in the treatment of fungal infections.

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Urresti, Saioa, Alan Cartmell, Feng Liu, Paul H. Walton, and Gideon J. Davies. "Structural studies of the unusual metal-ion site of the GH124 endoglucanase from Ruminiclostridium thermocellum." Acta Crystallographica Section F Structural Biology Communications 74, no. 8 (August 1, 2018): 496–505. http://dx.doi.org/10.1107/s2053230x18006842.

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The recent discovery of `lytic' polysaccharide monooxygenases, copper-dependent enzymes for biomass degradation, has provided new impetus for the analysis of unusual metal-ion sites in carbohydrate-active enzymes. In this context, the CAZY family GH124 endoglucanase from Ruminiclostridium thermocellum contains an unusual metal-ion site, which was originally modelled as a Ca2+ site but features aspartic acid, asparagine and two histidine imidazoles as coordinating residues, which are more consistent with a transition-metal binding environment. It was sought to analyse whether the GH124 metal-ion site might accommodate other metals. It is demonstrated through thermal unfolding experiments that this metal-ion site can accommodate a range of transition metals (Fe2+, Cu2+, Mn2+ and Ni2+), whilst the three-dimensional structure and mass spectrometry show that one of the histidines is partially covalently modified and is present as a 2-oxohistidine residue; a feature that is rarely observed but that is believed to be involved in an `off-switch' to transition-metal binding. Atomic resolution (<1.1 Å) complexes define the metal-ion site and also reveal the binding of an unusual fructosylated oligosaccharide, which was presumably present as a contaminant in the cellohexaose used for crystallization. Although it has not been possible to detect a biological role for the unusual metal-ion site, this work highlights the need to study some of the many metal-ion sites in carbohydrate-active enzymes that have long been overlooked or previously mis-assigned.

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31

Mason, Maria G., Andrew S. Ball, Brandon J. Reeder, Gary Silkstone, Peter Nicholls, and Michael T. Wilson. "Extracellular Heme Peroxidases in Actinomycetes: a Case of Mistaken Identity." Applied and Environmental Microbiology 67, no. 10 (October 1, 2001): 4512–19. http://dx.doi.org/10.1128/aem.67.10.4512-4519.2001.

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ABSTRACT Actinomycetes secrete into their surroundings a suite of enzymes involved in the biodegradation of plant lignocellulose; these have been reported to include both hydrolytic and oxidative enzymes, including peroxidases. Reports of secreted peroxidases have been based upon observations of peroxidase-like activity associated with fractions that exhibit optical spectra reminiscent of heme peroxidases, such as the lignin peroxidases of wood-rotting fungi. Here we show that the appearance of the secreted pseudoperoxidase of the thermophilic actinomycete Thermomonospora fusca BD25 is also associated with the appearance of a heme-like spectrum. The species responsible for this spectrum is a metalloporphyrin; however, we show that this metalloporphyrin is not heme but zinc coproporphyrin. The same porphyrin was found in the growth medium of the actinomyceteStreptomyces viridosporus T7A. We therefore propose that earlier reports of heme peroxidases secreted by actinomycetes were due to the incorrect assignment of optical spectra to heme groups rather than to non-iron-containing porphyrins and that lignin-degrading heme peroxidases are not secreted by actinomycetes. The porphyrin, an excretory product, is degraded during peroxidase assays. The low levels of secreted peroxidase activity are associated with a nonheme protein fraction previously shown to contain copper. We suggest that the role of the secreted copper-containing protein may be to bind and detoxify metals that can cause inhibition of heme biosynthesis and thus stimulate porphyrin excretion.

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32

Rizzo, D. M., R. A. Blanchette, and M. A. Palmer. "Biosorption of metal ions by Armillaria rhizomorphs." Canadian Journal of Botany 70, no. 8 (August 1, 1992): 1515–20. http://dx.doi.org/10.1139/b92-190.

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Armillaria rhizomorphs consist of differentiated hyphae with a melanized outer cortex. Melanin is known to prevent lysis of fungal structures by hydrolytic enzymes and may protect against antagonistic microorganisms. Our studies indicate that melanized rhizomorphs also adsorb high concentrations of cations from the surrounding soil environment. Rhizomorphs of four Armillaria species (A. ostoyae (Romagn.) Herink, A. calvescens Bérubé & Dessureault, A. gemina Bérubé & Dessureault, and A. sinapina Bérubé & Dessureault) collected from Minnesota, New Hampshire, and Oregon had substantially elevated levels of metal ions compared with the soil from which they were collected. With some elements, ions were 50–100 times more concentrated on rhizomorphs than in soil. Concentrations of Al, Zn, Fe, Cu, and Pb on rhizomorphs ranged up to 3440, 1930, 1890, 15, and 680 μg/g, respectively. Energy dispersive X-ray microanalysis showed that metal ions were located only on the outer portions of the rhizomorphs and not concentrated in the interior. A coating of metal ions may play a key role in the longevity and survival of rhizomorphs in soil. Key words: Armillaria, rhizomorphs, metals, fungal antagonism.

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Sokurenko, Yulia, Vera Ulyanova, Pavel Zelenikhin, Alexey Kolpakov, Dmitriy Blokhin, Dieter Müller, Vladimir Klochkov, and Olga Ilinskaya. "The Role of Metals in the Reaction Catalyzed by Metal-Ion-Independent Bacillary RNase." Bioinorganic Chemistry and Applications 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/4121960.

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Extracellular enzymes of intestinal microbiota are the key agents that affect functional activity of the body as they directly interact with epithelial and immune cells. Several species of theBacillusgenus, likeBacillus pumilus, a common producer of extracellular RNase binase, can populate the intestinal microbiome as a colonizing organism. Without involving metal ions as cofactors, binase depolymerizes RNA by cleaving the 3′,5′-phosphodiester bond and generates 2′,3′-cyclic guanosine phosphates in the first stage of a catalytic reaction. Maintained in the reaction mixture for more than one hour, such messengers can affect the human intestinal microflora and the human body. In the present study, we found that the rate of 2′,3′-cGMP was growing in the presence of transition metals that stabilized the RNA structure. At the same time, transition metal ions only marginally reduced the amount of 2′,3′-cGMP, blocking binase recognition sites of guanine at N7 of nucleophilic purine bases.

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34

Wang, Xingmin, Rui Song, Hui Ning Bian, Ulf T. Brunk, Ming Zhao, and Ke-seng Zhao. "Polydatin, a natural polyphenol, protects arterial smooth muscle cells against mitochondrial dysfunction and lysosomal destabilization following hemorrhagic shock." American Journal of Physiology-Regulatory, Integrative and Comparative Physiology 302, no. 7 (April 1, 2012): R805—R814. http://dx.doi.org/10.1152/ajpregu.00350.2011.

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The main objective of this study was to investigate the activity of polydatin on mitochondrial dysfunction and lysosomal stability of arteriolar smooth muscle cells (ASMCs) in severe shock. The experimental animals (rats) were divided into five groups: control, hemorrhagic shock, shock + CsA, shock + Res, and shock + PD (exposed to cyclosporin A, resveratrol, or polydatin following induction of hemorrhagic shock, respectively). The calcein-Co2+ technique revealed opening of ASMC mitochondrial permeability transition pores (mPTP) after shock with resulting mitochondrial swelling, decreased mitochondrial membrane potential (ΔΨm), and reduced intracellular ATP levels. These alterations were all inhibited by exposure to PD, which was significantly more effective than CsA and Res. PD also preserved lysosomal stability, suppressed activation of KATP channels, ASMC hyperpolarization, and reduced vasoresponsiveness to norepinephrine that normally follows severe shock. The results demonstrate that exposure to PD after initiation of severe shock effectively preserves ASMC mitochondrial integrity and has a significant therapeutic effect in severe shock. The effects may partially result from lysosomal stabilization against shock-induced oxidative stress and depressed relocation of hydrolytic enzymes and redox-active lysosomal iron that, in turn, may induce mPTP opening.

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35

Mishchenko, Natalya V., Ivan N. Kurochkin, Natalya V. Chugay, and Ekaterina Yu Kulagina. "Assessment of the state of soils of uncultivated agricultural lands by indicators of enzymatic activity, humus and heavy metals." Bulletin of Nizhnevartovsk State University 54, no. 2 (June 19, 2021): 106–11. http://dx.doi.org/10.36906/2311-4444/21-2/14.

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Abstract. Studies were conducted to determine such indicators as humus, heavy metals, and enzymatic activity in the soils of uncultivated farmlands of the Vladimir region located in the Klyazma river basin. In the course of field research in 2018, soil samples were selected at 13 points representing various landscape areas belonging to the Klyazma river basin. According to the results of research, a positive relationship between the activity of soil enzymes and the content of humus was established. In the soils of uncultivated farmland, where there is a high concentration of soil enzymes, a high percentage of humus was found from 2.88% to 3.96%. The dependence between the indicators of activity of soil enzymes and anthropogenic impact was revealed. Thus, the transition from deposits to the meadow, i.e. reduce anthropogenic impact on the soil, there is a sharp increase in the activity of soil invertase, catalase and dehydrogenase, an active process of humification of soil. The detected concentrations of heavy metals in soil samples of uncultivated farmland do not exceed the standards set for the approximate permissible concentrations, but their quantitative content has increased significantly over the past decade, their accumulation occurs and there is a potential danger in the case of secondary input of these soils into agricultural use.

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Hioki, Hideaki, Ryosuke Nishimoto, Kota Kawaguchi, Miwa Kubo, Kenichi Harada, and Yoshiyasu Fukuyama. "Discovery of hydrolytic catalysts in a peptidocalixarene library by binding assay with a transition state analogue for the hydrolysis." Chemical Communications, no. 46 (2009): 7194. http://dx.doi.org/10.1039/b913907a.

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37

Kim, J. Dongun, Stefan Senn, Arye Harel, Benjamin I. Jelen, and Paul G. Falkowski. "Discovering the electronic circuit diagram of life: structural relationships among transition metal binding sites in oxidoreductases." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1622 (July 19, 2013): 20120257. http://dx.doi.org/10.1098/rstb.2012.0257.

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Oxidoreductases play a central role in catalysing enzymatic electron-transfer reactions across the tree of life. To first order, the equilibrium thermodynamic properties of these proteins are governed by protein folds associated with specific transition metals and ligands at the active site. A global analysis of holoenzyme structures and functions suggests that there are fewer than approximately 500 fundamental oxidoreductases, which can be further clustered into 35 unique groups. These catalysts evolved in prokaryotes early in the Earth's history and are largely responsible for the emergence of non-equilibrium biogeochemical cycles on the planet's surface. Although the evolutionary history of the amino acid sequences in the oxidoreductases is very difficult to reconstruct due to gene duplication and horizontal gene transfer, the evolution of the folds in the catalytic sites can potentially be used to infer the history of these enzymes. Using a novel, yet simple analysis of the secondary structures associated with the ligands in oxidoreductases, we developed a structural phylogeny of these enzymes. The results of this ‘composome’ analysis suggest an early split from a basal set of a small group of proteins dominated by loop structures into two families of oxidoreductases, one dominated by α-helices and the second by β-sheets. The structural evolutionary patterns in both clades trace redox gradients and increased hydrogen bond energy in the active sites. The overall pattern suggests that the evolution of the oxidoreductases led to decreased entropy in the transition metal folds over approximately 2.5 billion years, allowing the enzymes to use increasingly oxidized substrates with high specificity.

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38

Milnerowicz, Halina, Katarzyna Kowalska, and Ewelina Socha. "Paraoxonase Activity as a Marker of Exposure to Xenobiotics in Tobacco Smoke." International Journal of Toxicology 34, no. 3 (May 2015): 224–32. http://dx.doi.org/10.1177/1091581815584624.

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The paraoxonase (PON) family is composed of 3 proteins (PON1, PON2, and PON3), each of which plays a crucial role in the body, displaying antioxidant, anti-inflammatory, and antiatherosclerotic properties. The activities and properties of PON proteins can be modulated by a number of environmental factors, including cigarette smoke. In the present article, a review of existing literature is employed to analyze both the direct and the indirect impact of cigarette smoking on the activity of members of the PON family. Cigarette smoking leads to direct inhibition of the hydrolytic activity of PON enzymes by modification of thiol groups, by the reactions of free radicals, or by inhibiting enzyme-active regions with heavy metals. It has been shown that cigarette smoking correlates with a decrease in high-density lipoprotein (HDL) concentration as well as with an increase in other components of the lipid profile (low-density lipoprotein (LDL), triglycerides, and total cholesterol). By decreasing HDL levels, cigarette smoking likely acts indirectly to induce a decline in PON1 activity. Inhibition of PON1 activity by smoking is a reversible process after cessation of exposure to the xenobiotics in tobacco smoke.

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39

Kukric, Zoran, and Mirjana Zabic. "Trypsin inhibition by ferrocene." Acta Periodica Technologica, no. 36 (2005): 203–13. http://dx.doi.org/10.2298/apt0536203k.

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Many transition metals and their complexes show inhibitory effect on someproteolytic enzymes, including trypsin. Their inhibitory activity is based on the direct binding to the active site of trypsin, mimicking formation of a five-coordinate transition state required for the reaction. The influence of ferrocene on trypsin activity using N-?-benzoyl-DL-arginine p-nitroanilide as a substrate was investigated. Ferrocene was selected as a potential inhibitor because it belongs to the family oforganometallic, so called "sandwich " compounds, and its cyclopentadienyl rings might have an appropriate geometry. It was found that ferrocene decreases trypsin activity and the K. for ferrocene was found to be 39.8.

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40

Gayda, Galina Z., Olha M. Demkiv, Yanna Gurianov, Roman Ya Serkiz, Mykhailo V. Gonchar, and Marina Nisnevitch. "“Green” Nanozymes: Synthesis, Characterization, and Application in Amperometric (Bio)sensors." Proceedings 60, no. 1 (November 2, 2020): 58. http://dx.doi.org/10.3390/iecb2020-07072.

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Nanozymes (NZs) are catalytically active nanomaterials that have enzyme-like activity but possess increased stability and greater availability due to the fact of their simpler preparation technologies. Nanozymes as nanoscale artificial enzymes demonstrate various catalytic specificities as oxidoreductases, such as peroxidase, catalase, laccase, and others as well as hydrolases, proteases, endonucleases, DNA-ases, NO synthases, etc. A broad variety of NZs exhibits dual- or multienzyme mimetic activity. Nanozymes as stable, low-cost mimetics of natural enzymes have a high potential for application in different branches of biotechnology including scientific investigations, industry, and ecology. Nanozymes can be applied in medicine as diagnostic tools and components of therapeutic drugs. Since NZs have high catalytic activity and chemical and biological stability, they are very promising in the construction of biosensors and biofuel cells. For these reasons, the search for simple methods of synthesis and characterization of different NZs is a very important and real problem. The “green” synthesis of Prussian blue analogous as peroxidase-like NZs using oxido-reductases is described in this study. The obtained green-synthesized hexacyanoferrates (gHCFs) of transition metals were characterized by structure, size, composition, catalytic properties, electro-mediator activities, and substrate specificity. Copper hexacyanoferrate (gCuHCF) was studied in more detail. When immobilized on a graphite electrode (GE), gCuHCF under special conditions of pH and tension gave amperometric signals on hydrogen peroxide and can be used as a peroxidase mimetic in oxidase-based biosensors. Under other conditions, gCuHCF/GE reacts to other analytes. We propose that gHCFs of transition metals synthesized via enzymes may become prospect platforms for the construction of multi-functional amperometric (bio)sensors.

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41

Shi, Yuqian, Homme W. Hellinga, and Lorena S. Beese. "Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I." Proceedings of the National Academy of Sciences 114, no. 23 (May 22, 2017): 6010–15. http://dx.doi.org/10.1073/pnas.1704845114.

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Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5′-nuclease superfamily. Its dominant, processive 5′–3′ exonuclease and secondary 5′-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5′-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5′ flaps. Their distinctive 5′ ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5′ flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. The striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.

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Phillips, Ana M. F., and Armando J. L. Pombeiro. "Transition Metal-Based Prodrugs for Anticancer Drug Delivery." Current Medicinal Chemistry 26, no. 41 (January 8, 2020): 7476–519. http://dx.doi.org/10.2174/0929867326666181203141122.

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: Transition metal complexes, of which the platinum(II) complex cisplatin is an example, have been used in medicine to treat cancer for more than 40 years. Although many successes have been achieved, there are problems associated with the use of these drugs, such as side effects and drug resistance. Converting them into prodrugs, to make them more inert, so that they can travel to the tumour site unchanged and release the drug in its active form only there, is a strategy which is the subject of much research nowadays. The new prodrugs may be activated and release the cytotoxic agent by differences in oxygen concentration or in pH, by the action of overexpressed enzymes, by differences in metabolic rates, etc., which characteristically distinguish cancer cells from normal ones, or even by the input of radiation, which can be visible light. Converting a metal complex into a prodrug may also be used to improve its pharmacological properties. In some cases, the metal complex is a carrier which transports the active drug as a ligand. Some platinum prodrugs have reached clinical trials. So far platinum, ruthenium and cobalt have been the most studied metals. This review presents the recent developments in this area, including the types of complexes used, the mechanisms of drug action and in some cases the techniques applied to monitor drug delivery to cells.

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Kuznetsova, Alexandra, Olga Fedorova, and Nikita Kuznetsov. "Kinetic Features of 3′-5′ Exonuclease Activity of Human AP-Endonuclease APE1." Molecules 23, no. 9 (August 21, 2018): 2101. http://dx.doi.org/10.3390/molecules23092101.

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Human apurinic/apyrimidinic (AP)-endonuclease APE1 is one of the key enzymes taking part in the repair of damage to DNA. The primary role of APE1 is the initiation of the repair of AP-sites by catalyzing the hydrolytic incision of the phosphodiester bond immediately 5′ to the damage. In addition to the AP-endonuclease activity, APE1 possesses 3′-5′ exonuclease activity, which presumably is responsible for cleaning up nonconventional 3′ ends that were generated as a result of DNA damage or as transition intermediates in DNA repair pathways. In this study, the kinetic mechanism of 3′-end nucleotide removal in the 3′-5′ exonuclease process catalyzed by APE1 was investigated under pre-steady-state conditions. DNA substrates were duplexes of deoxyribonucleotides with one 5′ dangling end and it contained a fluorescent 2-aminopurine residue at the 1st, 2nd, 4th, or 6th position from the 3′ end of the short oligonucleotide. The impact of the 3′-end nucleotide, which contained mismatched, undamaged bases or modified bases as well as an abasic site or phosphate group, on the efficiency of 3′-5′ exonuclease activity was determined. Kinetic data revealed that the rate-limiting step of 3′ nucleotide removal by APE1 in the 3′-5′ exonuclease process is the release of the detached nucleotide from the enzyme’s active site.

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44

Gayda, Galina Z., Olha M. Demkiv, Yanna Gurianov, Roman Ya Serkiz, Halyna M. Klepach, Mykhailo V. Gonchar, and Marina Nisnevitch. "“Green” Prussian Blue Analogues as Peroxidase Mimetics for Amperometric Sensing and Biosensing." Biosensors 11, no. 6 (June 10, 2021): 193. http://dx.doi.org/10.3390/bios11060193.

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Prussian blue analogs (PBAs) are well-known artificial enzymes with peroxidase (PO)-like activity. PBAs have a high potential for applications in scientific investigations, industry, ecology and medicine. Being stable and both catalytically and electrochemically active, PBAs are promising in the construction of biosensors and biofuel cells. The “green” synthesis of PO-like PBAs using oxido-reductase flavocytochrome b2 is described in this study. When immobilized on graphite electrodes (GEs), the obtained green-synthesized PBAs or hexacyanoferrates (gHCFs) of transition and noble metals produced amperometric signals in response to H2O2. HCFs of copper, iron, palladium and other metals were synthesized and characterized by structure, size, catalytic properties and electro-mediator activities. The gCuHCF, as the most effective PO mimetic with a flower-like micro/nano superstructure, was used as an H2O2-sensitive platform for the development of a glucose oxidase (GO)-based biosensor. The GO/gCuHCF/GE biosensor exhibited high sensitivity (710 A M−1m−2), a broad linear range and good selectivity when tested on real samples of fruit juices. We propose that the gCuHCF and other gHCFs synthesized via enzymes may be used as artificial POs in amperometric oxidase-based (bio)sensors.

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45

Pitson, S. M., R. J. Seviour, B. M. McDougall, J. R. Woodward, and B. A. Stone. "Purification and characterization of three extracellular (1→3)-β-d-glucan glucohydrolases from the filamentous fungus Acremonium persicinum." Biochemical Journal 308, no. 3 (June 15, 1995): 733–41. http://dx.doi.org/10.1042/bj3080733.

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Three (1-->3)-beta-D-glucanases (GNs) were isolated from the culture filtrates of the filamentous fungus Acremonium persicinum and purified by (NH4)2SO4 precipitation followed by anion-exchange and gel-filtration chromatography. Homogeneity of the purified proteins was confirmed by SDS/PAGE, isoelectric focusing and N-terminal amino acid sequencing. All three GNs (GN I, II and III) are non-glycosylated, monomeric proteins with apparent molecular masses, estimated by SDS/PAGE, of 81, 85 and 89 kDa respectively. pI values for the three enzymes are 5.3, 5.1, and 4.4 respectively. The pH optimum for GN I is 6.5, and 5.0 for GN II and III. All three purified enzymes displayed stability over the pH range 4.5-10.0. Optimum activities for GN I, II and III were recorded at 65, 55 and 60 degrees C respectively, with both GN II and III having short-term stability up to 50 degrees C and GN I up to 55 degrees C. The purified GNs have high specificity for (1-->3)-beta-linkages and hydrolysed a range of (1-->3)-beta- and (1-->3)(1-->6)-beta-D-glucans, with laminarin from Laminaria digitata being the most rapidly hydrolysed substrate of those tested. K(m) values for GN I, II, and III against L. digitata laminarin were 0.1, 0.23 and 0.22 mg/ml respectively. D-Glucono-1,5-lactone does not inhibit any of the three GNs, some metals ions are mild inhibitors, and N-bromosuccinimide and KMnO4 are strong inhibitors. All three GNs acted in an exo-hydrolytic manner, determined by the release of alpha-glucose as the initial and major product of hydrolysis of (1-->3)-beta-D-glucans, and confirmed by viscometric analysis and the inability to cleave periodate-oxidized laminarin, and may be classified as (1-->3)-beta-D-glucan glucohydrolases (EC 3.2.1.58).

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46

Zverev, Yakov F. "Flavonoids through the eyes of a pharmacologist. Antioxidant and anti-inflammatory activities." Reviews on Clinical Pharmacology and Drug Therapy 15, no. 4 (December 15, 2017): 5–13. http://dx.doi.org/10.17816/rcf1545-13.

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Review discusses the mechanisms of antioxidant and anti-inflammatory actions of flavonoids. In discussing the antioxidant effect detail the mechanisms of scavenging of reactive oxygen species, the chelation of transition metals, the activation of antioxidant enzymes. In consideration of anti-inflammatory action emphasis on the effects of flavonoids on the activity of the transcription factors and pathways involved in the formation of the inflammatory response. (For citation: Zverev YaF. Flavonoids through the eyes of a pharmacologist. Antioxidant and anti-inflammatory activities. Reviews on Clinical Pharmacology and Drug Therapy. 2017;15(4):5-13. doi: 10.17816/RCF1545-13).

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Permyakov, Eugene A. "Metal Binding Proteins." Encyclopedia 1, no. 1 (March 15, 2021): 261–92. http://dx.doi.org/10.3390/encyclopedia1010024.

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Metal ions play several major roles in proteins: structural, regulatory, and enzymatic. The binding of some metal ions increase stability of proteins or protein domains. Some metal ions can regulate various cell processes being first, second, or third messengers. Some metal ions, especially transition metal ions, take part in catalysis in many enzymes. From ten to twelve metals are vitally important for activity of living organisms: sodium, potassium, magnesium, calcium, manganese, iron, cobalt, zinc, nickel, vanadium, molybdenum, and tungsten. This short review is devoted to structural, physical, chemical, and physiological properties of proteins, which specifically bind these metal cations.

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48

POMMER, Ansgar J., Russell WALLIS, Geoffrey R. MOORE, Richard JAMES, and Colin KLEANTHOUS. "Enzymological characterization of the nuclease domain from the bacterial toxin colicin E9 from Escherichia coli." Biochemical Journal 334, no. 2 (September 1, 1998): 387–92. http://dx.doi.org/10.1042/bj3340387.

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The cytotoxicity of the bacterial toxin colicin E9 is due to a non-specific DNase that penetrates the cytoplasm of the infected organism and causes cell death. We report the first enzymological characterization of the overexpressed and purified 15 kDa DNase domain (E9 DNase) from this class of toxin. CD spectroscopy shows the E9 DNase to be structured in solution, and analytical ultracentrifugation data indicate that the enzyme is a monomer. The nuclease activity of the E9 DNase was compared with the well-studied, non-specific DNase I by using a spectrophotometric assay with calf thymus DNA as the substrate. Both enzymes require divalent metal ions for activity but, unlike DNase I, the E9 DNase is not activated by Ca2+ ions. Somewhat surprisingly, the E9 DNase shows optimal activity and linear kinetics in the presence of transition metals such as Ni2+ and Co2+ but displays non-linear kinetics with metals such as Mg2+ and Ca2+. Conversely, Ni2+ and other transition metals showed poor activity in a plasmid-based nicking assay, yielding significant amounts of linearized plasmid, whereas Mg2+ was very active, with the main intermediate being open-circle DNA. The results suggest that, on entry into bacterial cells, the E9 DNase is likely to exhibit primarily Mg2+-dependent nicking activity against chromosomal DNA, although other metals could also be utilized to introduce both single- and double-strand cleavages.

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49

Demkiv, Olha, Nataliya Stasyuk, Roman Serkiz, Galina Gayda, Marina Nisnevitch, and Mykhailo Gonchar. "Peroxidase-Like Metal-Based Nanozymes: Synthesis, Catalytic Properties, and Analytical Application." Applied Sciences 11, no. 2 (January 15, 2021): 777. http://dx.doi.org/10.3390/app11020777.

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Nanozymes (NZs) are nanostructured artificial enzymes that mimic catalytic properties of natural enzymes. The NZs have essential advantages over natural enzymes, namely low preparation costs, stability, high surface area, self-assembling capability, size and composition-dependent activities, broad possibility for modification, and biocompatibility. NZs have wide potential practical applications as catalysts in biosensorics, fuel-cell technology, environmental biotechnology, and medicine. Most known NZs are mimetics of oxidoreductases or hydrolases. The present work aimed to obtain effective artificial peroxidase (PO)-like NZs (nanoPOs), to characterize them, and to estimate the prospects of their analytical application. NanoPOs were synthesized using a number of nanoparticles (NPs) of transition and noble metals and were screened for their catalytic activity in solution and on electrodes. The most effective nanoPOs were chosen as NZs and characterized by their catalytic activity. Kinetic parameters, size, and structure of the best nanoPOs (Cu/CeS) were determined. Cu/CeS-based sensor for H2O2 determination showed high sensitivity (1890 A·M−1·m−2) and broad linear range (1.5–20,000 µM). The possibility to apply Cu/CeS-NZ as a selective layer in an amperometric sensor for hydrogen-peroxide analysis of commercial disinfectant samples was demonstrated.

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Alem, Mamaru Bitew, and Yilkal Bezie Ayele. "Modeling the Transition State Structures of the Reductive-Half Reaction Active Site of Xanthine Oxidase Bound to Guanine Analogues: A Density Functional Theory Approach." International Journal of Chemistry 10, no. 1 (January 28, 2018): 137. http://dx.doi.org/10.5539/ijc.v10n1p137.

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Modeling and characterization the transition state structure of enzyme catalyzed reactions is essential. A DFT method employing B3LYP level of theory with 6-31G (d',p') basis set for non-metals and LanL2DZ basis set for molybdenum have been used. The bond orders of chemical fragments were calculated using AOmix softaware. The effect of chalcogen replacement, amine group and methyl group in the parent structure of xanthine bound to xanthine oxidase active site were compared. The transition state structure of model substrates (2AX, 2A6TP, 2A6SP and 2A6MP) bound to the truncated form of XO active site has been confirmed by the presence of one negative imaginary frequencies (s-1) (-60), (-140), (-230) and (-270), respectively. The corresponding normalized energy barriers (kcal/mol) from pre-transition state to the transition state, respectively, are (13.869), (21.753), (23.109) and (0.212). In this work, 2A6SP and 2A6TP substrates were found to be potential xanthine oxidase inhibitors. The large bond distances and minimum bond order for CRH-HRH bond, and small bond distances and maximum bond order for SMo-HRH bond at the transition state for chalcogen replaced 2AX confirms early transition state structure. Methyl substituted 2AX analog found to have post transition state structure. A potential xanthine oxidase inhibitor can be designed from purine family enzymes using DFT approach.

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Journal articles on the topic 'Transition metals; Hydrolytic enzymes'

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