Primary Nucleation Kinetics of Short Fibril-Forming Amyloidogenic Peptides

The primary nucleation step in amyloid fibril formation can, depending on the nature of peptide sequence, occur in one step, straight from a dilute solution, or in multiple steps, via oligomers or disordered aggregates. The precise kinetic pathways of these processes are poorly understood. Employing forward flux sampling and a midresolution coarse-grained force field, we analyzed the reactive pathways from the solvated state to the fibril nucleus for a system of 12 amyloidogenic peptides. In line with previous work, increasing the overall side-chain hydrophobicity switches the fibrillization mechanism from one- to two-step nucleation. Overall, in this mechanism, peptides first form dimers and trimers, which then grow into a β-sheet. This sheet serves as a template for nucleation of additional β sheets until the fibril nucleus is fully formed. Our simulations indicate that the presence of the recently predicted polymerized phase in the nucleation pathway of intermediately hydrophobic peptides slows down the dynamics of fibril formation considerably, which may influence the time scale on which toxic early oligomers exist. The structure of the amyloid fibrils was found to be strongly dependent on the relative hydrophobic strength of side chains along the sequence: β sheets in the fibril are oriented such that a core of the relative strongest hydrophobic residues is formed along the fibril axis.