caa a22 4500 605511411 CHVBK 20210128100650.0 cr unu---uuuuu 210128e20150701xx s 000 0 eng 10.1007/s00894-015-2730-1 doi (NATIONALLICENCE)springer-10.1007/s00894-015-2730-1 In silico ligand binding studies of cyanogenic β -glucosidase, dhurrinase-2 from Sorghum bicolor [Elektronische Daten] [Chavi Mahajan, Krunal Patel, Bashir Khan, Shuban Rawal] 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. Springer-Verlag Berlin Heidelberg, 2015 β -Glucosidase nationallicence Dhurrinase nationallicence Molecular docking nationallicence Molecular dynamic simulation nationallicence Sorghum bicolor nationallicence Mahajan Chavi Arya Hybrid Seeds Ltd., Chitengaon, 4311005, Aurangabad, Maharashtra, India aut Patel Krunal Arya Hybrid Seeds Ltd., Chitengaon, 4311005, Aurangabad, Maharashtra, India aut Khan Bashir Plant Tissue Culture Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, Maharashtra, India aut Rawal Shuban Arya Hybrid Seeds Ltd., Chitengaon, 4311005, Aurangabad, Maharashtra, India aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/7(2015-07-01), 1-11 1610-2940 21:7<1 2015 21 894 https://doi.org/10.1007/s00894-015-2730-1 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2730-1 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Mahajan Chavi Arya Hybrid Seeds Ltd., Chitengaon, 4311005, Aurangabad, Maharashtra, India aut NATIONALLICENCE 700 1- Patel Krunal Arya Hybrid Seeds Ltd., Chitengaon, 4311005, Aurangabad, Maharashtra, India aut NATIONALLICENCE 700 1- Khan Bashir Plant Tissue Culture Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, Maharashtra, India aut NATIONALLICENCE 700 1- Rawal Shuban Arya Hybrid Seeds Ltd., Chitengaon, 4311005, Aurangabad, Maharashtra, India aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/7(2015-07-01), 1-11 1610-2940 21:7<1 2015 21 894