What a physicist can do on protein aggregation and amyloid fibril form…

Protein aggregation is associated with serious and eventually-fatal neuro-degenerative diseases including Alzheimer’s and Parkinson’s. While atomic resolution molecular dynamics simulations have been useful in this regard, they are limited to the examination of either oligomer formation by a small number of peptides or the analysis of the stability of a moderate number of peptides placed in trial or known experimental structures. We describe large scale intermediate-resolution molecular dynamics simulations of the spontaneous formation of fibrils by a system containing 48 Aβ16-22 peptides. We are able, for the first time, to trace out the aggregation process of a large system of non-trivial peptides along the entire fibrillization pathway, from an initial configuration of random coils to twisted proto-filaments with cross-β structures, and to demonstrate how kinetics dictates the structural details of the fully formed fibril. Fibrillization kinetics depends strongly on the temperature. Nucleation and templated growth via monomer addition occur at and near a transition temperature above which fibrils are unlikely to form. Oligomeric merging and structural rearrangement are observed at lower temperatures. Multi-layer fibrillar structures are formed with perfectly anti-parallel β-strands and inter-digitating side chains analogous to a “steric zipper” interface. Structural details including intra-strand and inter-sheet distance and dependence of twist on the number of layers are consistent with those from experiments.