title: Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations.
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.
authors.affiliation: National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlárská 2, 611 37 Brno, Czech Republic.
authors.forename: Navnit Kumar
authors.initials: NK
authors.lastname: Mishra
authors.forename: Zdenek
authors.initials: Z
authors.lastname: Kríz
authors.forename: Michaela
authors.initials: M
authors.lastname: Wimmerová
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Koca
mesh_terms: D018829:Adhesins, Bacterial / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D002236:Carbohydrate Conformation; D019277:Entropy; D006860:Hydrogen Bonding; D037102:Lectins / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009005:Monosaccharides / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011487:Protein Conformation; D011550:Pseudomonas aeruginosa; D055672:Static Electricity
chemical_list: D018829:Adhesins, Bacterial; D037102:Lectins; D009005:Monosaccharides; C038692:adhesin, Pseudomonas; D002118:Calcium