20 research outputs found

    Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction

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    The comparison of eight tools applicable to ligand-binding site prediction is presented. The methods examined cover three types of approaches: the geometrical (CASTp, PASS, Pocket-Finder), the physicochemical (Q-SiteFinder, FOD) and the knowledge-based (ConSurf, SuMo, WebFEATURE). The accuracy of predictions was measured in reference to the catalytic residues documented in the Catalytic Site Atlas. The test was performed on a set comprising selected chains of hydrolases. The results were analysed with regard to size, polarity, secondary structure, accessible solvent area of predicted sites as well as parameters commonly used in machine learning (F-measure, MCC). The relative accuracies of predictions are presented in the ROC space, allowing determination of the optimal methods by means of the ROC convex hull. Additionally the minimum expected cost analysis was performed. Both advantages and disadvantages of the eight methods are presented. Characterization of protein chains in respect to the level of difficulty in the active site prediction is introduced. The main reasons for failures are discussed. Overall, the best performance offers SuMo followed by FOD, while Pocket-Finder is the best method among the geometrical approaches

    Mangiferin stimulates carbohydrate oxidation and protects against metabolic disorders induced by high-fat diets

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    Excessive dietary fat intake causes systemic metabolic toxicity, manifested in weight gain, hyperglycemia, and insulin resistance. In addition, carbohydrate utilization as a fuel is substantially inhibited. Correction or reversal of these effects during high-fat diet (HFD) intake is of exceptional interest in light of widespread occurrence of diet-associated metabolic disorders in global human populations. Here we report that mangiferin (MGF), a natural compound (the predominant constituent of Mangifera indica extract from the plant that produces mango), protected against HFD-induced weight gain, increased aerobic mitochondrial capacity and thermogenesis, and improved glucose and insulin profiles. To obtain mechanistic insight into the basis for these effects, we determined that mice exposed to an HFD combined with MGF exhibited a substantial shift in respiratory quotient from fatty acid toward carbohydrate utilization. MGF treatment significantly increased glucose oxidation in muscle of HFD-fed mice without changing fatty acid oxidation. These results indicate that MGF redirects fuel utilization toward carbohydrates. In cultured C2C12 myotubes, MGF increased glucose and pyruvate oxidation and ATP production without affecting fatty acid oxidation, confirming in vivo and ex vivo effects. Furthermore, MGF inhibited anaerobic metabolism of pyruvate to lactate but enhanced pyruvate oxidation. A key target of MGF appears to be pyruvate dehydrogenase, determined to be activated by MGF in a variety of assays. These findings underscore the therapeutic potential of activation of carbohydrate utilization in correction of metabolic syndrome and highlight the potential of MGF to serve as a model compound that can elicit fuel-switching effects

    The NAD(+) Precursor Nicotinamide Riboside Enhances Oxidative Metabolism and Protects against High-Fat Diet-Induced Obesity

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    As NAD(+) is a rate-limiting cosubstrate for the sirtuin enzymes, its modulation is emerging as a valuable tool to regulate sirtuin function and, consequently, oxidative metabolism. In line with this premise, decreased activity of PARP-1 or CD38-both NAD(+) consumers-increases NAD(+) bioavailability, resulting in SIRT1 activation and protection against metabolic disease. Here we evaluated whether similar effects could be achieved by increasing the supply of nicotinamide riboside (NR), a recently described natural NAD(+) precursor with the ability to increase NAD(+) levels, Sir2-dependent gene silencing, and replicative life span in yeast. We show that NR supplementation in mammalian cells and mouse tissues increases NAD(+) levels and activates SIRT1 and SIRT3, culminating in enhanced oxidative metabolism and protection against high-fat diet-induced metabolic abnormalities. Consequently, our results indicate that the natural vitamin NR could be used as a nutritional supplement to ameliorate metabolic and age-related disorders characterized by defective mitochondrial function

    Glycerol Steam Reforming for Hydrogen Production over Nickel Supported on Alumina, Zirconia and Silica Catalysts

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    The aim of the work was to investigate the influence of support on the catalytic performance of Ni catalysts for the glycerol steam reforming reaction. Nickel catalysts (8 wt%) supported on Al2O3, ZrO2, SiO2 were prepared by the wet impregnation technique. The catalysts’ surface and bulk properties, at their calcined, reduced and used forms, were determined by ICP, BET, XRD, NH3-TPD, CO2-TPD, TPR, XPS, TEM, TPO, Raman, SEM techniques. The Ni/Si sample, even if it was less active for T <600 °C, produces more gaseous products and reveals higher H2 yield for the whole temperature range. Ni/Zr and Ni/Si catalysts facilitate the WGS reaction, producing a gas mixture with a high H2/CO molar ratio. Ni/Si after stability tests exhibits highest values for total (70%) and gaseous products (45%) glycerol conversion, YH2 (2.5), SH2 (80%), SCO2 (65%), H2/CO molar ratio (6.0) and lowest values for SCO (31%), SCH4 (3.1%), CO/CO2 molar ratio (0.48) among all samples. The contribution of the graphitized carbon formed on the catalysts follows the trend Ni/Si (I D /I G = 1.34) < Ni/Zr (I D /I G = 1.08) < Ni/Al (I D /I G = 0.88) and indicates that the fraction of different carbon types depends on the catalyst’s support nature. It is suggested that the type of carbon is rather more important than the amount of carbon deposited in determining stability. It is confirmed that the nature of the support affects mainly the catalytic performance of the active phase and that Ni/SiO2 can be considered as a promising catalyst for the glycerol steam reforming reaction

    Negative regulators of plant immunity derived from cinnamyl alcohol dehydrogenases are targeted by multiple Phytophthora Avr3a‐like effectors

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    Oomycete pathogens secrete numerous effectors to manipulate host immunity. While some effectors share a conserved structural fold, it remains unclear if any have conserved host targets. Avr3a‐like family effectors, which are related to Phytophthora infestans effector PiAvr3a and are widely distributed across diverse clades of Phytophthora species, were used to study this question. By using yeast‐two‐hybrid, bimolecular fluorescence complementation and co‐immunoprecipitation assays, we identified members of the plant cinnamyl alcohol dehydrogenase 7 (CAD7) subfamily as targets of multiple Avr3a‐like effectors from Phytophthora pathogens. The CAD7 subfamily has expanded in plant genomes but lost the lignin biosynthetic activity of canonical CAD subfamilies. In turn, we identified CAD7s as negative regulators of plant immunity that are induced by Phytophthora infection. Moreover, AtCAD7 was stabilized by Avr3a‐like effectors and involved in suppression of pathogen‐associated molecular pattern‐triggered immunity, including callose deposition, reactive oxygen species burst and WRKY33 expression. Our results reveal CAD7 subfamily proteins as negative regulators of plant immunity that are exploited by multiple Avr3a‐like effectors to promote infection in different host plants
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