PREDICTED STRUCTURE AND BINDING MOTIFS OF COLLAGEN a1(XI)

Abstract

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. Sequential
point 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.