In Silico Mutagenesis
and Docking Study of <i>Ralstonia solanacearum</i> RSL Lectin:
Performance
of Docking Software To Predict Saccharide Binding
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Abstract
In this study, in silico mutagenesis and docking in <i>Ralstonia
solanacearum</i> 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