Helical Intermediate Formation and Its Role in Amyloid of an Amphibian Antimicrobial Peptide

Abstract

Helical intermediates appear to be crucial in amyloid formation of several amyloidogenic peptides, including A{beta}, that are implicated in different neurodegenerative diseases. Intermediate species have been reported to be more toxic than mature amyloid fibrils. Hence, the focus of the current work is to understand both structural and mechanistic role of 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 {beta}-sheet dominated aggregates, is centred on two important factors; evolution of -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 formation of precursor 310-helices close to the N-terminus. The 310-helices transitioned into -helices, thereby imparting partial helical conformations to the peptides. In the initial stages of aggregation, U3.5 peptides with amphipathic, partial helices aggregated to form small clusters of helical intermediates directed via hydrophobic interactions. These helices imparted stability to the helical intermediates, which promoted 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 {beta}-sheet transition in these aggregates. Thus, the study emphasized that stabilisation of peptide helical content may be crucial to the evolution of {beta}-sheet-rich amyloid structures.