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Sequence and structure analysis of parallel beta helices: Implication for constructing amyloid structural models

  1. Author:
    Tsai, H. H.
    Gunasekaran, K.
    Nussinov, R.

  2. Author Address

    Natl Cent Univ, Dept Chem, Chungli 32001, Taiwan. NCI, Ctr Canc Res Nanobiol Program, SAIC Frederick Inc, Basic Res Program, Frederick, MD 21702 USA. Tel Aviv Univ, Sackler Fac Med, Sackler Inst Mol Med, Dept Human Genet, IL-69978 Tel Aviv, Israel.;Tsai, HH, Natl Cent Univ, Dept Chem, Chungli 32001, Taiwan.;hhtsai@cc.ncu.edu.tw guna@ncifcrf.gov ruthn@ncifcrf.gov
    1. Year: 2006
    2. Date: Jun
  2. Journal: Structure
    1. 14
    2. 6
    3. Pages: 1059-1072
  4. Type of Article: Article
  5. ISSN: 0969-2126
  1. Abstract:

    Increasing evidence suggests that amyloids and parallel beta helices may share similar motifs. A systemic analysis of beta helices is performed to examine their sequence and structural characteristics. lie prefers to occur in beta 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 alpha-helical conformation, where it frequently forms amide stacking. Based on the observed prominent stacking of chemically similar residues in parallel beta helices, we propose that within the "cross-beta" 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.

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External Sources

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  2. DOI: 10.1016/j.str.2006.03.015
  3. View record in Web of Science®
  4. WOS: 000238730300014

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