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Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations |
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| Authors: | Navnit Kumar Mishra Michaela Wimmerová Jaroslav Ko?a |
| Institution: | a National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlá?ská 2, 611 37 Brno, Czech Republic b Department of Biochemistry, Faculty of Science, Masaryk University, Kotlá?ská 2, 611 37 Brno, Czech Republic c Department of Chemistry, Faculty of Science, Masaryk University, Kotlá?ská 2, 611 37 Brno, Czech Republic |
| Abstract: | In this study, interactions of selected monosaccharides with the Pseudomonas aeruginosa Lectin II (PA-IIL) are analyzed in detail. An interesting feature of the PA-IIL binding is that the monosaccharide is interacting via two calcium ions and the binding is unusually strong for protein-saccharide interaction. We have used Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) and normal mode analysis to calculate the free energy of binding. The impact of intramolecular hydrogen bond network for the lectin/monosaccharide interaction is also analyzed. |
| Keywords: | MMPBSA Molecular Mechanics Poisson-Boltzmann Surface Area PA-IIL Pseudomonas aeruginosa Lectin II FUC l-fucopyranose" target="_blank">α-l-fucopyranose Me-FUC l-fucopyranoside" target="_blank">Me-α-l-fucopyranoside MAN d-mannopyranose" target="_blank">α-d-mannopyranose FRU d-fructopyranose" target="_blank">β-d-fructopyranose l-GAL" target="_blank">l-GAL l-galactopyranose" target="_blank">α-l-galactopyranose Me-ARA d-arabinopyranoside" target="_blank">Me-β-d-arabinopyranoside GLC d-glucopyranose" target="_blank">β-d-glucopyranose |
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