Computational Analysis of Integrin Subunit Glycosylation: Investigations on its Role in Orienting Ligand-Receptor Interaction

Abstract

Integrins serve as the primary mediators of cellular adhesion to the extracellular matrix (ECM). Several cellular processes (e.g. apoptosis) are controlled through their interactions with ligands in the ECM. Integrins bind to their ECM ligands through their head domains. The crystal structure of an integrin heterodimer (αVβ3) reveals the location of the ECM ligand binding site. Integrin function may be altered by the disruption of the ligand binding site either through changes in protein conformation or heterodimer binding orientation. Previous studies have suggested a link between disruptions of integrin function to changes in glycosylation. This study focuses on characterizing the effect of altering individual glycosylation sites on the interaction between integrin head domains. Part of the analysis was conducted using the molecular soft docking program, BiGGER (Krippahl, 2003). Docking simulations were done using structure files generated from integrin subunit head domain entries in the Protein Data Bank (www.pdb.org). Dock assessment involved the measurement of subunit orientations based on user-defined anchor residues in the interacting subunits. Initial analysis was conducted on the Integrin αVβ3 heterodimer. The integrin αVβ3 head domain has four glycosylation sites, three for the αV beta propeller and one for the β3 A-domain. Sugar residues were iteratively removed from each of these glycosylation sites to determine their effects on integrin subunit interaction. Our results suggest the importance of glycosylation at αV N266 for the formation of the ligand binding site. Removal of these sugar residues resulted in the greatest deviation in predicted docking orientation. A ∼90° rotation, counter-clockwise from the reference position, was predicted for the docking of the β3 subunit to the N266-deglycosylated αV subunit. This altered conformation is predicted to effectively destroy the ligand binding site and thus, disrupt integrin αVβ3 function.