Publication details

Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models

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MISHRA Sushil Kumar SUND Johan AQVIST Johan KOČA Jaroslav

Year of publication 2012
Type Article in Periodical
Magazine / Source Journal of Computational Chemistry
MU Faculty or unit

Central European Institute of Technology

Field Physical chemistry and theoretical chemistry
Keywords free energy; saccharides; linear interaction energy; molecular dynamics; Ralstonia solanacearum lectin; Pseudomonas aeruginosa lectin-II
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Description 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.
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