title: In silico mutagenesis and docking study of Ralstonia solanacearum RSL lectin: performance of docking software to predict saccharide binding.
abstract: In this study, in silico mutagenesis and docking in Ralstonia solanacearum lectin (RSL) were carried out, and the ability of several docking software programs to calculate binding affinity was evaluated. In silico mutation of six amino acid residues (Agr17, Glu28, Gly39, Ala40, Trp76, and Trp81) was done, and a total of 114 in silico mutants of RSL were docked with Me-α-L-fucoside. Our results show that polar residues Arg17 and Glu28, as well as nonpolar amino acids Trp76 and Trp81, are crucial for binding. Gly39 may also influence ligand binding because any mutations at this position lead to a change in the binding pocket shape. The Ala40 residue was found to be the most interesting residue for mutagenesis and can affect the selectivity and/or affinity. In general, the docking software used performs better for high affinity binders and fails to place the binding affinities in the correct order.
authors.affiliation: Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
authors.forename: Sushil Kumar
authors.initials: SK
authors.lastname: Mishra
authors.forename: Jan
authors.initials: J
authors.lastname: Adam
authors.forename: Michaela
authors.initials: M
authors.lastname: Wimmerová
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Koča
mesh_terms: D001665:Binding Sites; D002240:Carbohydrate Sequence; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D037102:Lectins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016296:Mutagenesis; D043368:Ralstonia solanacearum / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D011956:Receptors, Cell Surface / Q000737:chemistry*; D012984:Software
chemical_list: D037102:Lectins; D011956:Receptors, Cell Surface; C055213:saccharide-binding proteins