Central European Institute of Technology, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
J Chem Inf Model. 2012 May 25;52(5):1250-61. doi: 10.1021/ci200529n. Epub 2012 May 11.
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.
本研究对茄果胶杆菌凝集素（RSL）进行了计算机诱变和对接，并评估了几种对接软件程序计算结合亲和力的能力。对六个氨基酸残基（Agr17、Glu28、Gly39、Ala40、Trp76 和 Trp81）进行了计算机诱变，共对接了 114 种 RSL 计算机突变体与 Me-α-L-岩藻糖苷。我们的结果表明，极性残基 Arg17 和 Glu28 以及非极性氨基酸 Trp76 和 Trp81 对结合至关重要。Gly39 也可能影响配体结合，因为该位置的任何突变都会导致结合口袋形状发生变化。Ala40 残基被发现是最有趣的突变位点，可影响选择性和/或亲和力。一般来说，使用的对接软件对高亲和力配体的表现更好，无法正确排列结合亲和力的顺序。
