Modelling β-1,3-exoglucanase–saccharide interactions: Structure of the enzyme–substrate complex and enzyme binding to the cell wall

Abstract

Glycoside hydrolases are a class of enzymes that break/form the bond between sugar monomers (monosaccharides). Candida albicans's β-1,3-exoglucanase (Exg), a family 5 glycosidase, belongs to this class of enzymes. This small protein is an ideal computational model for its family of enzymes and was used here to create several enzyme–substrate models starting from a crystallographic glucanase-inhibitor structure. A series of enzyme–substrate complexes were generated using molecular docking, ranging from Exg–glucose (Exg–1Glc) to Exg–laminarihexaose (Exg–6Glc). Structure optimizations followed by molecular dynamics provided a picture of the way the enzyme and substrates interact. Molecular dynamics was conducted for each complex to assess the flexibility of the substrate, of the enzyme as a whole, and of enzyme–substrate interactions. The enzyme overall conformation was found to be quite rigid, although most enzyme residues increase mobility upon substrate binding. However, two surface loops stand out by having large fluctuations and becoming less flexible when the substrates were bound. These data point to a possible biological role for the mentioned loops, corresponding to amino acids 36–47 and 101–106. We propose that these loops could bind the enzyme to a glucan chain in the cell wall. The polysaccharide and enzyme structures have very complementary shapes and form numerous interactions; so it appears likely that the flexible loops connect the enzyme to the cell wall and allow it to navigate the wall to shape glucan structure.