Predicted Structure and Binding Motifs of Collagen a1(Xi)
The amino propeptide of collagen a1(XI) (NPP) has been shown to bind glycosaminoglycans and to form a dimer. While these are independent biochemical events, it is likely that dimerization facilitates the interaction with glycosaminoglycans or alternatively, that glycosaminoglycan interaction facilitates the formation of an NPP:NPP dimer. The computer program MODELLER was used to generate a homology model of the collagen a1(XI) NPP monomer using the crystal structure of the closely related noncollagenous-4 (NC4) domain of collagen a1(IX) (PDB:2UUR) as the template. Additionally, a dimer model of collagen a1(XI) NPP domain was created based upon the thrombospondin dimer template (PDB:1Z78). The structure of the dimer created in MODELLER was validated by comparison to a dimer model generated by docking two monomers of PDB:2UUR using ClusPro. Calculations of relative binding energy for the interaction between each collagen 1(XI) NPP model and glycosaminoglycans as ligands was performed using AutoDock4. Computational results support a higher affinity between heparan sulfate and a dimer compared to a monomer. These findings are supported by affinity chromatography experiments in which distinct monomer and dimer peaks were observed. Sequentialvpoint mutation studies of the putative binding site (147-KKKITK-152) indicated the importance of the basic lysine residue for binding to heparan sulfate. Two orders of magnitude change in binding affinity was predicted when comparing wild type to the mutation K152A. Experimental data supports the predicted change in affinity.
Oxford, Julia; McDougal, Owen; Warner, Lisa; and Mallory, Chris. (2011). "Predicted Structure and Binding Motifs of Collagen a1(Xi)". Journal on Bioinformatics and Biotechnology, 1(1), 46-51.