Almora Barrios, N.; (2010) A computational investigation of the interaction of the collagen molecule with hydroxyapatite. Doctoral thesis , UCL (University College London).

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Abstract

This thesis presents the results of computer simulation studies of the interaction of the predominant molecules in the collagen protein with the hydroxyapatite mineral. Using a combination of computational techniques, quantum-mechanical methods based on the density functional theory (DFT) and molecular dynamics simulations based on interatomic potentials, we have investigated the interface between the collagen protein and the apatite mineral. First we have employed electronic structure techniques (DFT) to study a range of different binding modes of the amino acids glycine, proline and hydroxyproline, which are major constituents of the collagen I protein, at two important hydroxyapatite surfaces, (0001) and (0110) . We have performed full geometry optimizations of the hydroxyapatite surface with adsorbed amino acid molecules to obtain the optimum substrate/adsorbate structures and interaction energies. We have also used DFT to investigate the binding of a series of representative peptides containing hydrophobic side groups (proline), uncharged polar side groups (glycine and hydroxyproline), and charged polar side groups (lysine and hydroxylysine) to the hydroxyapatite (0001) and (0110) surfaces. This selection of adsorbates has given us the opportunity to study separately the interactions of the carboxylic acid and amine functional groups, as well as the effect of hydroxylation and the charges of the side group, on the strength of interaction with the surfaces. We have also investigated the same systems in an aqueous environment using classical molecular dynamics simulation, where we have calculated the energies and geometries of adsorption of the peptide at the surfaces of hydroxyapatite in competition with pre-adsorbed water. Finally, we have studied the onset of nucleation of the hydroxyapatite mineral at an entire collagen molecule in aqueous solution.

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