Sequence and Structure Analysis of Parallel β Helices: Implication for Constructing Amyloid Structural Models

SummaryIncreasing evidence suggests that amyloids and parallel β helices may share similar motifs. A systemic analysis of β helices is performed to examine their sequence and structural characteristics. Ile prefers to occur in β strands. In contrast, Pro is disfavored, compatible with the underlying assumption in Pro-scanning mutagenesis. Cys, Asn, and Phe form significant homostacking (identical amino acid interactions). Asn is highly conserved in the high-energy, left-handed α-helical conformation, where it frequently forms amide stacking. Based on the observed prominent stacking of chemically similar residues in parallel β helices, we propose that within the “cross-β” framework, amyloids with longer peptide chains may have common structural features of in-register, parallel alignment, with the side chains forming identical amino acid ladders. The requirement of ladder formation limits the combinations of side chain interactions. Such a limit combined with environmental conditions (e.g., pH, concentration) could be a major reason for the ability of most polypeptides to form amyloids.