Mishra, Sushil Kumar, Johan Sund, Johan Åqvist, and Jaroslav Koča. 2012. “Computational Prediction of Monosaccharide Binding Free Energies to Lectins With Linear Interaction Energy Models.”. Journal of Computational Chemistry 33 (29): 2340-50.
Abstract
The linear interaction energy (LIE) method to compute binding free energies is applied to lectin-monosaccharide complexes. Here, we calculate the binding free energies of monosaccharides to the Ralstonia solanacearum lectin (RSL) and the Pseudomonas aeruginosa lectin-II (PA-IIL). The standard LIE model performs very well for RSL, whereas the PA-IIL system, where ligand binding involves two calcium ions, presents a major challenge. To overcome this, we explore a new variant of the LIE model, where ligand-metal ion interactions are scaled separately. This model also predicts the saccharide binding preference of PA-IIL on mutation of the receptor, which may be useful for protein engineering of lectins.