Abstract

The pathway for protein self-assembly is determined by the free energy landscape coded in the noncovalent interactions between the building blocks. We use this basic principle to develop a model that describes the mechanisms involved in the staggering of collagen molecules in fibrillar assemblies. In this work we present a simple, parameter-free model for collagen fibril design that allows us to predict the structure of self-assembling collagen fibers on the basis of the amino acid sequence of the constituent alpha-chain subunits. We develop a classification algorithm and use it to scan through large data sets of collagen molecules to predict the periodicity of the resulting assemblies. We argue that, with our model, it becomes possible to design tailor-made, periodic collagen structures, thereby enabling the design of novel biomimetic materials based on collagen-mimetic trimers.