Journal
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Volume 52, Issue 5, Pages 1250-1261Publisher
AMER CHEMICAL SOC
DOI: 10.1021/ci200529n
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Funding
- Ministry of Education of the Czech Republic [ME08008]
- Grant Agency of the Czech Republic [303/09/1168, 301/09/H004]
- CEITEC - Central European Institute of Technology [CZ.1.05/1.1.00/02.0068]
- Ministry of Education, Youth, and Sports of the Czech Republic [LM2010005]
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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-alpha-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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