title: In silico ligand binding studies of cyanogenic β-glucosidase, dhurrinase-2 from Sorghum bicolor.
abstract: Dhurrinase, a cyanogenic β-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 (Rg) 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.
authors.affiliation: Arya Hybrid Seeds Ltd., Chitengaon, Aurangabad, Maharashtra, 4311005, India.
authors.forename: Chavi
authors.initials: C
authors.lastname: Mahajan
authors.forename: Krunal
authors.initials: K
authors.lastname: Patel
authors.forename: Bashir M
authors.initials: BM
authors.lastname: Khan
authors.forename: Shuban S
authors.initials: SS
authors.lastname: Rawal
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D065089:Glycoside Hydrolase Inhibitors / Q000737:chemistry*; D007700:Kinetics; D008024:Ligands; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009570:Nitriles / Q000737:chemistry*; D010940:Plant Proteins / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D055550:Protein Stability; D016415:Sequence Alignment; D045868:Sorghum / Q000737:chemistry* / Q000201:enzymology; D040681:Structural Homology, Protein; D013379:Substrate Specificity; D013816:Thermodynamics; D001617:beta-Glucosidase / Q000737:chemistry*
chemical_list: D065089:Glycoside Hydrolase Inhibitors; D008024:Ligands; D009570:Nitriles; D010940:Plant Proteins; C411650:Dhr1 protein, Sorghum; C021514:cyanogenic beta-glucosidase; D001617:beta-Glucosidase; C011220:dhurrin