02628nas a2200265   4500008004100000022001400041245019800055210006900253260007400322300001400396490000700410520155800417653003201975653002202007653002602029653002202055100002002077700001802097700001802115700002402133700003202157700002202189700002702211856012402238       2013                        eng d  a0301-485100aFunctional characterization, homology modeling and docking studies of beta-glucosidase responsible for bioactivation of cyanogenic hydroxynitrile glucosides from Leucaena leucocephala (subabul)0 aFunctional characterization homology modeling and docking studie  aVAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDSbSPRINGERcFEB  a1351-13630 v403 a<p>Glycosyl hydrolase family 1 beta-glucosidases are important enzymes that serve many diverse functions in plants including defense, whereby hydrolyzing the defensive compounds such as hydroxynitrile glucosides. A hydroxynitrile glucoside cleaving beta-glucosidase gene (Llbglu1) was isolated from Leucaena leucocephala, cloned into pET-28a (+) and expressed in E. coli BL21 (DE3) cells. The recombinant enzyme was purified by Ni-NTA affinity chromatography. The optimal temperature and pH for this beta-glucosidase were found to be 45 A degrees C and 4.8, respectively. The purified Llbglu1 enzyme hydrolyzed the synthetic glycosides, pNPGlucoside (pNPGlc) and pNPGalactoside (pNPGal). Also, the enzyme hydrolyzed amygdalin, a hydroxynitrile glycoside and a few of the tested flavonoid and isoflavonoid glucosides. The kinetic parameters K (m) and V (max) were found to be 38.59 mu M and 0.8237 mu M/mg/min for pNPGlc, whereas for pNPGal the values were observed as 1845 mu M and 0.1037 mu M/mg/min. In the present study, a three dimensional (3D) model of the Llbglu1 was built by MODELLER software to find out the substrate binding sites and the quality of the model was examined using the program PROCHEK. Docking studies indicated that conserved active site residues are Glu 199, Glu 413, His 153, Asn 198, Val 270, Asn 340, and Trp 462. Docking of rhodiocyanoside A with the modeled Llbglu1 resulted in a binding with free energy change (Delta G) of -5.52 kcal/mol on which basis rhodiocyanoside A could be considered as a potential substrate.</p>10aGlycosyl hydrolase family 110ahomology modeling10aLeucaena leucocephala10aMolecular docking1 aShaik, Noor, M.1 aMisra, Anurag1 aSingh, Somesh1 aFatangare, Amol, B.1 aRamakumar, Suryanarayanarao1 aRawal, Shuban, K.1 aKhan, Bashir, Mohammad  uhttps://library.ncl.res.in/content/functional-characterization-homology-modeling-and-docking-studies-beta-glucosidase-002479nas a2200241   4500008004100000022001400041245010300055210006900158260005700227300000800284490000700292520161300299653002101912653001501933653002201948653003301970653002002003100001902023700001802042700002702060700002202087856012802109       2015                        eng d  a1610-294000aIn silico ligand binding studies of cyanogenic beta-glucosidase, dhurrinase-2 from Sorghum bicolor0 aIn silico ligand binding studies of cyanogenic betaglucosidase d  a233 SPRING ST, NEW YORK, NY 10013 USAbSPRINGERcJUL  a1840 v213 a<p>Dhurrinase, a cyanogenic beta-glucosidase from Sorghum bicolor is the key enzyme responsible for the hydrolysis of dhurrin to produce toxic hydrogen cyanide, as a part of plant defence mechanism. Dhurrinase 1 (SbDhr1) and dhurrinase 2 (SbDhr2), two isozymes have been isolated and characterized from S. bicolor. However, there is no information in the literature about the three dimensional (3D) structure of SbDhr2 and molecular interactions involved between the protein and ligand. In this study, the three dimensional structure of SbDhr2 was built based on homology modeling by using the X-ray crystallographic structure of its close homologue SbDhr1 as the template. The generated 3D model was energy minimized and the quality was validated by Ramachndran plot, various bioinformatic tools and their relevant parameters. Stability, folding-unfolding and flexibility of the modeled SbDhr2 was evaluated on the basis of RMSD, radius of gyration (R-g) and RMSF values respectively, obtained through molecular dynamic (MD) simulation. Further, molecular docking was performed with its natural substrate dhurrin, one substrate analogue, three un-natural substrates, and one inhibitor. Analysis of molecular interactions in the SbDhr2-ligand complexes revealed the key amino acid residues responsible to stabilize the ligands within the binding pocket through non-bonded interactions and some of them were found to be conserved (Glu239, Tyr381, Trp426, Glu454, Trp511). Reasonably broader substrate specificity of SbDhr2 was explained through the wider entrance passage observed in comparison to SbDhr1.</p>10abeta-Glucosidase10aDhurrinase10aMolecular docking10aMolecular dynamic simulation10aSorghum bicolor1 aMahajan, Chavi1 aPatel, Krunal1 aKhan, Bashir, Mohammad1 aRawal, Shuban, S.  uhttps://library.ncl.res.in/content/silico-ligand-binding-studies-cyanogenic-beta-glucosidase-dhurrinase-2-sorghum-bicolor-1