期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 33, 期 29, 页码 2340-2350出版社
WILEY-BLACKWELL
DOI: 10.1002/jcc.23081
关键词
free energy; saccharides; linear interaction energy; molecular dynamics; Ralstonia solanacearum lectin; Pseudomonas aeruginosa lectin-II
资金
- Ministry of Education of the Czech Republic [ME08008, LM2010005]
- Grant Agency of the Czech Republic [301/09/H004]
- EU [CZ.1.05/1.1.00/02.0068]
- Capacities Specific Programme [286154]
- Swedish Research Council (VR)
- eSSENCE e-Science Initiative
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 ligandmetal 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. (c) 2012 Wiley Periodicals, Inc.
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