Binding Site Flexibility in the CD44:Hyaluronan Protein:Carbohydrate Interaction

Abstract

The CD44:hyaluronan protein:carbohydrate binding interaction is an important component of inflammation and cancer cell invasiveness and metastasis. Association of a key arginine sidechain in the beta1-alpha1 loop of the binding site with the carbohydrate ligand has been postulated to lead to a high-affinity state of the complex based on atomic-resolution x-ray crystal studies. NMR studies point to coupling between an order-to-disorder transition of the beta9-alpha3 region of the CD44 protein, which is distant from the binding site, and the formation of the high-affinity state; however, this region of the protein is well-ordered in all crystal structures. All-atom explicit-solvent molecular dynamics simulations of the CD44:hyaluronan complex revealed beta1-alpha1 loop backbone instability when arginine is in close association with hyaluronan, whereas the loop was stable in the absence of sidechain association. Additionally, a conformational transition in the backbone phi angle of a single residue in the beta1-alpha1 loop was demonstrated to be sufficient to induce reversible arginine sidechain:hyaluronan association, leading to the description of a molecular switching mechanism. The instability of the beta1-alpha1 loop in the context of a well-ordered beta9-alpha3 region suggests possible allosteric coupling between the binding site conformation and the order-to-disorder transition.