Role of Water Molecules in Structure and Energetics of Pseudomonas Aeruginosa Pa-il Lectin Interacting with Disaccharides

The calcium-dependent lectin I from Pseudomonas aeruginosa (PA-IL) binds specifically to oligosaccharides presenting an -galactose residue at their non-reducing end, such as the disaccharides Gal1-2GalOMe, Gal1-3GalOMe and Gal1-4GalOMe. This provides a unique model for studying the effect of the glycosidic linkage of the ligands on structure and thermodynamics of the complexes by means of experimental and theoretical tools. The structural features of PA-IL in complex with the three disaccharides were established by docking and molecular dynamics (MD) simulations and compared to those observed in available crystal structures, including PA-IL/Gal12GalOMe complex, that was solved at 2.4 Å resolution and reported herein. The role of a structural bridge water molecule in the binding site of -PAIL was also elucidated through MD simulations and molecular mechanics Poisson-Bolzmann surface area MM-PBSA approach. This water molecule establishes three very stable hydrogen bonds with O6 of non-reducing galactose, oxygen from Pro51 main chain and nitrogen from Gln53 main chain of the lectin binding site. Binding free energies for PA-IL in complex with the three disaccharides were investigated and the results were compared with the experimental data determined by titration microcalorimetry. When the bridge water molecule was included in the MM-PBSA calculations, the simulations predicted the correct binding affinity trends with the 1-2 linked disaccharide presenting three times stronger affinity ligand than the two other ones. These results highlight the role of the water molecule in the binding site of PA-IL and indicate that it should be taken into account when designing glycoderivatives active against P. aeruginosa adhesion.