Effect of the hyaluronidase microe nvironment on the enzyme structure–function relationship and computational study of the in silico molecular docking of chondroitin sulfate and heparin short fragments to hyaluronidase

Abstract

The review addresses the biochemical interactions of hyaluronidases with components of the natural microenvironment. The effect of subtle structural differences between ligands on the enzyme structure–function relationship regulation is noted. Docking of chondroitin sulfate (CS) trimers (hexasaccharides) and heparin tetramers (octasaccharides) to the 3D model of the bovine testicular hyaluronidase (BTH) was performed by computational chemistry methods in order to elucidate the mechanism of regulation of the enzyme functioning in the body (using virtual screening, molecular dynamics, and calculation of surface electrostatic potential of protein complexes). Several binding sites for glycosaminoglycan (GAG) ligands were found to occur on the hyaluronidase surface. They are identical for CS trimers and heparin tetramers. The calculations showed the possibility of both reversible and irreversible conformational changes of the 3D structure of BTH, depending on the arrangement of negatively charged ligands on its globule. When the changes are irreversible, Glu-149 and Asp-147, which are key amino acid residues for the catalytic activity of BTH, can migrate from the vicinity of the native enzyme active site to the periphery of the protein molecule, thus inducing enzyme inactivation. The interaction of the GAG ligands with the BTH active site is mainly caused by electrostatic forces. Four or five binding sites of the chondroitin sulfate trimer proved to be critical for stabilization of the enzyme structure. Their occupation was sufficient for preventing irreversible deformation of the BTH molecule upon the insertion of the heparin ligand into the active site cavity. Protein stabilization is accompanied by the formation of a particular form of the surface electrostatic potential.