Helical intermediate formation and its role in amyloids of an amphibian antimicrobial peptide

Helical intermediates appear to be crucial in the amyloid formation of several amyloidogenic peptides, including Aβ, that are implicated in different neurodegenerative diseases. Intermediate species of amyloid formation have been reported to be more toxic than mature amyloid fibrils. Hence, the current work focuses on understanding the mechanistic roles of the helical intermediates in the early stages of amyloid self-assembly in amyloidogenic peptides. Molecular dynamics (MD) simulations and the adaptive biasing force (ABF) method were utilized to investigate structural changes that lead to amyloid formation in amphibian peptide uperin-3.5 (U3.5), an antimicrobial and amyloidogenic peptide. Microsecond time-scale MD simulations revealed that peptide aggregation, into β-sheet dominated aggregates, is centred on two important factors; evolution of α-helical intermediates and the critical role of local peptide concentration inside these aggregates. Electrostatic attraction between the oppositely charged aspartate (D) and arginine (R) residues located near the N-terminus induced hydrogen bonding resulting in the formation of precursor 3₁₀-helices close to the N-terminus. The 3₁₀-helices transitioned into α-helices, thereby imparting partial helical conformations to the peptides. In the initial stages of aggregation, U3.5 peptides with amphipathic, partial helices were driven closer by hydrophobic interactions to form small clusters of helical intermediates. These helices imparted stability to the helical intermediates, which promoted the growth of clusters by further addition of peptides. This led to an increase in the local peptide concentration, which enabled stronger peptide-peptide interactions and triggered a β-sheet transition in these aggregates. Thus, this study emphasized that the helical intermediates may be crucial to the evolution of β-sheet-rich amyloid structures.