Herein we report the establishment of the 3D structure of the biglycan core protein, using conventional homology molecular modelling techniques. The 3D model has been structurally optimised via molecular dynamics. It was found that the final model of biglycan resembles in structure its template protein bearing a set of distinct parallel β-sheet structure patterns. The biglycan model bears a very hydrophobic amino acid region towards its inner cavity that acquires an arc-like structure. The external domain of the biglycan model is made up of hydrophilic residues that are exposed to the water solvent. It is those hydrophilic residues that are responsible for their interaction with polysaccharide polymers. Overall comparison of the model of biglycan to the recently determined x-ray structure of the same protein returns a very low Root Mean Square Deviation (RMSD), which confirms the viability of the model and its reliability as a platform for the study biglycan interactions.
