Protein Non-Folding: A Molecular Simulation Study of the Structure and Self-Aggregation of Elastin

Elastin is the protein responsible for the elastic recoil of skin, arteries, and lungs. In order to function, elastin, as well as other self-assembling elastomeric proteins, must remain disordered even when aggregated, and must therefore avoid the formation of amyloid fibrils. Elastin undergoes phase separation and self-organization into a fibrillar structure upon increasing temperature. In order to investigate the molecular basis for elastin self-aggregation, we performed extensive atomistic molecular dynamics simulations of both monomers and aggregates. To obtain statistical convergence of average structural properties, it was necessary to use massive sampling in combination with simulated tempering distributed replica sampling. The development and testing of this method is an important contribution of this thesis. The first key finding of this thesis is that the sequences of all known rubber-like elastomeric proteins are separated from amyloidogenic sequences by a threshold in the combined content of proline and glycine. Our results suggest that avoiding the formation of a water-excluding core involving extensive self-interactions is not only a fundamental requirement, but may very well constitute the single most essential design principle of self-assembling elastomeric proteins. The conformational ensemble of an elastin-like aggregate resembles that of a polymer melt. In the aggregate, individual chains retain significant hydration and do not form a water-excluding hydrophobic core, but are also completely entangled with each other and form significant intermolecular interactions. As a result, the overall chain dimensions approach the expected dimensions of chains in an ideal solvent, a state in which chain entropy is maximized. This is the prediction of the Flory theorem for generic polymer chains within a polymer melt, but has never, to our knowledge, been observed before for an aggregate of polypeptide chains in atomistic detail. Finally, we note that our results are not consistent with the current model of elastin self-aggregation, which involves a conformational transition of a monomer towards a more ordered, aggregation-prone state. Instead, we propose a model in which both the hydrophobic effect and the enhanced chain entropy afforded by the interactions with other peptides within the aggregate favour elastin self-aggregation.Ph