Induction of rare conformation of oligosaccharide by binding to calcium-dependent bacterial lectin: X-ray crystallography and modelling study

• DOI: 10.1016/j.ejmech.2019.05.049
• Publication Date: 2019-05-18T23:00:01Z
• Authors: Martin Lepsik; Roman Sommer; Sakonwan Kuhaudom...; Mickaël Lelimousin; Emanuele Paci; Annabelle Varrot; Alexander Titz; Anne Imberty
• Keywords: Glucosamine; Carbohydrate; Binding Sites; Calcium ion; Carbohydrate; Lectin; Molecular dynamics; N-Acetyl; Quantum effect; Molecular Conformation; 610; Oligosaccharides; 500; Molecular Dynamics Simulation; Molecular dynamics; 540; Crystallography, X-Ray; Ligands; Quantum effect; 3. Good health; [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry; Lectins; Mutation; Pseudomonas aeruginosa; Calcium ion; [CHIM]Chemical Sciences; Calcium; Lectin; N-Acetyl; Protein Binding

ABSTRACTPathogenic micro-organisms utilize protein receptors in adhesion to host tissues, a process that in some cases relies on the interaction between lectin and human glycoconjugates. Oligosaccharide epitopes are recognized through their three-dimensional structure and their flexibility is a key issue in specificity. In this paper, we analyse by X-ray crystallography the structures of the lectin LecB from two strains of Pseudomonas aeruginosa in complex with Lewis x oligosaccharide present on cell surfaces of human tissues. An unusual conformation of the glycan was observed in all binding sites with a non-canonical syn orientation of the N-acetyl group of N-acetyl-glucosamine. A PDB-wide search revealed that such an orientation occurs only in 2% of protein/carbohydrate complexes. Theoretical chemistry calculations showed that the observed conformation is unstable in solution but stabilised by the lectin. A reliable description of LecB/Lewis x complex by force field-based methods had proven as especially challenging due to the special feature of the binding site, two closely apposed Ca2+ ions which induce strong charge delocalisation. By comparing various force-field parametrisations, we design general protocols which will be useful in near future for designing carbohydrate-based ligands (glycodrugs) against other calcium-dependent protein receptors.