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K.M. Meek, C. Knupp, D. Vlachakis, M.E. Boulton, C.S. Kamma; Homology–Based Molecular Modelling of the Bovine Corneal Biglycan Core Protein: Implications for Structure and Function . Invest. Ophthalmol. Vis. Sci. 2006;47(13):3000.
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© ARVO (1962-2015); The Authors (2016-present)
The establishment of the 3D structure of bovine corneal biglycan by means of homology–based molecular modelling and the molecular optimisation of the model using molecular dynamics
Molecular modelling experiments were done on a Linux P4 workstation using Molecular Operating Environment (MOE) software. The initial DNA sequence of the gene encoding for bovine corneal biglycan was downloaded from GenBank. The DNA sequences were translated to protein and the blast–P search revealed that the best template was decorin, which has been determined by X–ray crystallography (res. 2.5Å, PDB entry: 1XKU). The pair–wise alignment was performed using ClustalX and revealed 55% homology identity between the model and the template. The alignment was repeated and manually adjusted within MOE. The homology algorithm of MOE produced a total of 10 different models that were scored and in silico evaluated for their reliability. The best one (as proposed by the MOE algorithm) was further structurally optimised by undergoing molecular dynamics at 300K, 1 atm for 1000 ps with 1 fs per step. The results of the molecular dynamics simulation were collected into a trajectory database by MOE for further analysis. The model was evaluated with Procheck and 95% of its residues were found in the core regions and another 5% in the allowed regions of the Ramachandran plot.
The final model of biglycan was structurally similar to the template protein, since it had all of its secondary elements conserved (e.g. the distinct parallel ß–sheet pattern). The core protein was a horse shoe shaped molecule, with patches of hydrophobic amino acids in its inner cavity. The outer part of the protein consisted mainly of hydrophilic amino acids and exposed polar amino acids providing interaction sites to water molecules and polysaccharide polymers, respectively.
The relatively high homology between the decorin and biglycan core proteins confirms that the proposed molecular model for biglycan is reliable. The hydrophilic and hydrophobic patches that were found in the biglycan protein suggest possible interaction sites with water molecules and collagen fibrils in the corneal stroma.
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