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3D structures of putative heparanase-binding oligosaccharides and the model of oligosaccharide-protein complex

Molecular modelling studies of interactions between two heparanase binding domains, Lys158-Asp171 and Q270-V289, with seven different oligosaccharides were performed. The results of these studies enabled detailed characterization of 3D structures of intermolecular complexes between the target oligosaccharides and heparanase binding domains.

Furthermore, the effects of two factors, counter-ions and substituents, that influence the interactions between ligands and receptors, were also analyzed. The data, for the first time, characterize the heparanase binding domain-heparin oligosaccharide complexes at the molecular level and can be used to help to design the heparanase inhibitors.

Modeling of interactions between the heparanase binding domain Lys158-Asp171 and seven different pentasaccharides have been performed by both molecular mechanics and Monte Carlo conformational search. Results of these calculations permitted to identify specific sulfate groups of the pentasaccharide that interact with specific aminoacid residues of the peptide.

Reported by

Institute of Chemistry, Slovak Academy of Sciences
Dubravska cesta 9
84538 Bratislava
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