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

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