In silico mutagenesis and docking study of Ralstonia solanacearum RSL lectin: performance of docking software to predict saccharide binding
Language English Country United States Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't
PubMed
22506916
DOI
10.1021/ci200529n
Knihovny.cz E-resources
- MeSH
- Crystallography, X-Ray MeSH
- Lectins chemistry genetics metabolism MeSH
- Models, Molecular MeSH
- Molecular Sequence Data MeSH
- Mutagenesis MeSH
- Computer Simulation * MeSH
- Ralstonia solanacearum chemistry genetics metabolism MeSH
- Receptors, Cell Surface chemistry MeSH
- Carbohydrate Sequence MeSH
- Software * MeSH
- Binding Sites MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Names of Substances
- Lectins MeSH
- Receptors, Cell Surface MeSH
- saccharide-binding proteins MeSH Browser
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.
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