Aggregation of amphipathic peptides into amyloid-like fibrils

In aqueous solution, amphipathic peptides aggregate into amyloid-like fibrils that are being considered for several biomedical applications due to their mechanical properties and biocompatibility. Here, we perform all-atom molecular dynamics simulations in explicit solvent to study the aggregation of amphipathic peptides. We study systems containing more than 200,000 atoms, which are simulated for up to 14 μs for six different peptide sequences. We show that peptide sequences that do not form fibrils in experiments show a low propensity to form hydrogen bonds and β-structures in our simulations, and vice-versa. Simulations are also performed at different temperatures to highlight the importance of hydrophobic interactions on aggregation. The aggregation rate in our simulations increases with increasing temperature for highly hydrophobic amphipathic peptides. This is related to the strength of hydrophobic interactions that is enhanced with increasing temperature. We also observe coassembly process of peptides composed of L- and D-handed peptides.