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In Alzheimer's disease and spongiform encephalopathies proteins transform from their native states into fibrils. We find that several amyloid-forming proteins harbor an α-helix in a polypeptide segment that should form a β-strand according to secondary structure predictions. In 1324 nonredundant protein structures, 37 β-strands with ≥7 residues were predicted in segments where the experimentally determined structures show helices. These discordances include the prion protein (helix 2, positions 179–191), the Alzheimer amyloid β-peptide (Aβ, positions 16–23), and lung surfactant protein C (SP-C, positions 12–27). In addition, human coagulation factor XIII (positions 258–266), triacylglycerol lipase from Candida antarctica (positions 256–266), andd-alanyl-d-alanine transpeptidase fromStreptomyces R61 (positions 92–106) contain a discordant helix. These proteins have not been reported to form fibrils but in this …