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Short peptide amyloid organization: Stabilities and conformations of the islet amyloid peptide NFGAIL

  1. Author:
    Zanuy, D.
    Ma, B. Y.
    Nussinov, R.

  2. Author Address

    NCI Frederick, Lab Expt & Computat Biol, Canc Res & Dev Ctr, Bldg 469,Rm 151, Ft Detrick, MD 21702 USA NCI Frederick, Lab Expt & Computat Biol, Canc Res & Dev Ctr, Ft Detrick, MD 21702 USA NCI Frederick, Lab Expt & Computat Biol, Intramural Res Support Program, Sci Applicat Int Corp, Ft Detrick, MD 21702 USA Tel Aviv Univ, Sackler Fac Med, Dept Human Genet, Sackler Inst Mol Med, IL-69978 Tel Aviv, Israel Nussinov R NCI Frederick, Lab Expt & Computat Biol, Canc Res & Dev Ctr, Bldg 469,Rm 151, Ft Detrick, MD 21702 USA
    1. Year: 2003
  2. Journal: Biophysical Journal
    1. 84
    2. 3
    3. Pages: 1884-1894
  4. Type of Article: Article
  1. Abstract:

    Experimentally, short peptides have been shown to form amyloids similar to those of their parent proteins. Consequently, they present useful systems for studies of amyloid conformation. Here we simulate extensively the NFGAIL peptide, derived from the human islet amyloid polypeptide (residues 22-27). We simulate different possible strand/sheet organizations, from dinners to nonamers. Our simulations indicate that the most stable conformation is an antiparallel strand orientation within the sheets and parallel between sheets. Consistent with the alanine mutagenesis, we find that the driving force is the hydrophobic effect. Whereas the NFGAIL forms stable oligomers, the NAGAIL oligomer is unstable, and disintegrates very quickly after the beginning of the simulation. The simulations further identify a minimal seed size. Combined with our previous simulations of the prion-derived AGAAAAGA peptide, AAAAAAAA, and the Alzheimer Abeta fragments 16-22, 24-36,16-35, and 10- 35, and the solid-state NMR data for Abeta fragments 16-22,10- 35, and 1-40, some insight into the length and the sequence matching effects may be obtained.

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