Dhurrinase, a cyanogenic β-glucosidase from Sorghum bicolor is the key enzyme responsible for the... more 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.
Spodoptera litura (Lepidoptera: Noctuidae), commonly known as tobacco cutworm or cotton leafworm,... more Spodoptera litura (Lepidoptera: Noctuidae), commonly known as tobacco cutworm or cotton leafworm, is a polyphagous pest which causes considerable damage to cotton (Gossypium hirsutum) and other crops. Herbivore-induced defence response is activated in plants against chewing pests, in which plant secondary metabolites play an important role. Dhurrinase2 (SbDhr2), a cyanogenic β-glucosidase from Sorghum bicolor, is the key enzyme responsible for the hydrolysis of dhurrin (cyanogenic β-glucosidic substrate) to p-hydroxymandelonitrile. Hydroxynitrile lyase (MeHNL) from Mannihot esculanta catalyses the dissociation of cyanohydrins to hydrogen cyanide and corresponding carbonyl compound, both enzymes play a pivotal role in plant defence mechanism. SbDhr2 and MeHNL genes were expressed individually and co-expressed transiently in cotton leaves. We examined the feeding response of S. litura to leaves in the choice assay. The S. litura population used in this study showed better feeding dete...
BIOINFOLET - A Quarterly Journal of Life Sciences, 2019
Hydroxynitrile lyase (HNL) plays significant role in plant defence mechanism, through the synthes... more Hydroxynitrile lyase (HNL) plays significant role in plant defence mechanism, through the synthesis of chiral cyanohydrins, which act as antifeedants. Present investigation was undertaken on hydroxynitrile lyase from Manihot esculenta, in order to increase its efficiency through mutagenesis. For this purpose, six amino acid (Trp-128, Leu-149, Leu-158, Leu-179, Ile-210 and Phe-210) residues were selected for ‘in silico ’mutagenesis with hydrophobic amino acids to generate 25single-mutants. These ‘in silico ’mutants were analysed for protein-ligand interactions and binding affinity. Mutants with proper orientation of the substrate were identified. To improve binding affinity, double-point ‘in silico ’mutations were carried out. In addition, stability of these mutants was evaluated through molecular dynamic (MD) simulation studies.
Dhurrinase, a cyanogenic β-glucosidase from Sorghum bicolor is the key enzyme responsible for the... more 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.
Spodoptera litura (Lepidoptera: Noctuidae), commonly known as tobacco cutworm or cotton leafworm,... more Spodoptera litura (Lepidoptera: Noctuidae), commonly known as tobacco cutworm or cotton leafworm, is a polyphagous pest which causes considerable damage to cotton (Gossypium hirsutum) and other crops. Herbivore-induced defence response is activated in plants against chewing pests, in which plant secondary metabolites play an important role. Dhurrinase2 (SbDhr2), a cyanogenic β-glucosidase from Sorghum bicolor, is the key enzyme responsible for the hydrolysis of dhurrin (cyanogenic β-glucosidic substrate) to p-hydroxymandelonitrile. Hydroxynitrile lyase (MeHNL) from Mannihot esculanta catalyses the dissociation of cyanohydrins to hydrogen cyanide and corresponding carbonyl compound, both enzymes play a pivotal role in plant defence mechanism. SbDhr2 and MeHNL genes were expressed individually and co-expressed transiently in cotton leaves. We examined the feeding response of S. litura to leaves in the choice assay. The S. litura population used in this study showed better feeding dete...
BIOINFOLET - A Quarterly Journal of Life Sciences, 2019
Hydroxynitrile lyase (HNL) plays significant role in plant defence mechanism, through the synthes... more Hydroxynitrile lyase (HNL) plays significant role in plant defence mechanism, through the synthesis of chiral cyanohydrins, which act as antifeedants. Present investigation was undertaken on hydroxynitrile lyase from Manihot esculenta, in order to increase its efficiency through mutagenesis. For this purpose, six amino acid (Trp-128, Leu-149, Leu-158, Leu-179, Ile-210 and Phe-210) residues were selected for ‘in silico ’mutagenesis with hydrophobic amino acids to generate 25single-mutants. These ‘in silico ’mutants were analysed for protein-ligand interactions and binding affinity. Mutants with proper orientation of the substrate were identified. To improve binding affinity, double-point ‘in silico ’mutations were carried out. In addition, stability of these mutants was evaluated through molecular dynamic (MD) simulation studies.
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