Atomistic Simulations of Collagen Fibrils

Abstract

Computational molecular dynamics simulations are used to investigate the supramolecular structure of a collagen fibril at an atomistic scale of resolution. The simulations use a newly developed protocol that allows the overall fibrillar structure of collagen to be studied, rather than only providing data on individual, fully solvated proteins. The data generated provide new information regarding the arrangement of collagen proteins and water molecules within a fibril, and the nature of the inter-protein attractions that are responsible for the process of fibrillogenesis. It is anticipated that this new approach to modelling a fibril will lead to a better understanding of how collagen’s material properties depend on the dynamic behaviour of the underlying proteins and water molecules.