Molecular Dynamics Studies of the Process of Amyloid Aggregation of Peptide Fragments of Transthyretin

It has been shown recently that an 11-residue peptide fragment of transthyretin, TTR(105–115), can form amyloid fibrils in vitro by adopting an extended β-strand conformation. We used molecular dynamics simulations on systems of TTR(105–115) peptides, for a total length of about 5 μs, to explore the process of self-assembly and the structures of the resulting aggregates. Our results suggest that an antiparallel association of the β-strands is more probable than a parallel one and that the central residues (T106-L111) in a β-strand have a high propensity to form inter-peptide hydrogen bonds. The study of the dynamics of self-association indicated that, for this peptide, trajectories leading to conformations with high α-helical content are off-pathway from those leading to aggregates with high β-structure content. We also show that the diverse oligomeric structures that form spontaneously in the molecular dynamics simulations are, to a large extent, compatible with solid-state NMR experimental measurements, including chemical shifts, on fully formed fibrils. The strategy that we present may therefore be used in the design of new experiments to determine the structure of amyloid fibrils, such as those involving site-specific isotope labelling schemes to measure key inter-atomic distances.