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Digital library of scientific journals published by Plovdiv University Paisii Hilendarski.

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Browsing Journals by Subject "3D structure"

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    3D structure prediction of lignolytic enzymes lignin peroxidase and manganese peroxidase based on homology modelling
    (Plovdiv University Press “Paisii Hilendarski”, 2015-11-27) Kale, Swapnil K.; Deshmukh, Amit G.
    Lignolytic enzymes have great biotechnological value in biopulping, biobleaching, and bioremediation. Manganese peroxidase (EC 1:11:1:13) and lignin peroxidase (EC 1:11:1:14) are extracellular and hem-containing peroxidases that catalyze H2O2-dependent oxidation of lignin. Because of their ability to catalyse oxidation of a wide range of organic compounds and even some inorganic compounds, they got tremendous industrial importance. In this study, 3D structure of lignin and manganese peroxidase has been predicted on the basis of homology modeling using Swiss PDB workspace. The physicochemical properties like molecular weight, isoelectric point, Grand average of hydropathy, instability and aliphatic index of the target enzymes were performed using Protparam. The predicted secondary structure of MnP has 18 helices and 6 strands, while LiP has 20 helices and 4 strands. Generated 3D structure was visualized in Pymol. The generated model for MnP and LiP has Z-score Qmean of 0.01 and -0.71, respectively. The predicted models were validated through Ramachandran Plot, which indicated that 96.1 and 95.5% of the residues are in most favored regions for MnP and LiP respectively. The quality of predicted models were assessed and confirmed by VERIFY 3D, PROCHECK and ERRAT. The modeled structure of MnP and LiP were submitted to the Protein Model Database.
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    In silico sequence analysis and homology modeling of predicted beta-amylase 7-like protein in Brachypodium distachyon L.
    (Plovdiv University Press “Paisii Hilendarski”, 2014-01-10) Filiz, Ertuğrul; Koç, Ibrahim
    Beta-amylase (β-amylase, EC 3.2.1.2) is an enzyme that catalyses hydrolysis of glucosidic bonds in polysaccharides. In this study, we analyzed protein sequence of predicted beta-amylase 7-like protein in Brachypodium distachyon. pI (isoelectric point) value was found as 5.23 in acidic character, while the instability index (II) was found as 50.28 with accepted unstable protein. The prediction of subcellular localization was revealed that the protein may reside in chloroplast by using CELLO v.2.5. The 3D structure of protein was performed using comparative homology modeling with SWISS-MODEL. The accuracy of the predicted 3D structure was checked using Ramachandran plot analysis showed that 95.4% in favored region. The results of our study contribute to understanding of β-amylase protein structure in grass species and will be scientific base for 3D modeling of beta-amylase proteins in further studies.