Effect of Amino Acid Sequence Rearrangment on Prion Aggregation: Molecular Dynamics Simulations of an Amyloid-forming peptide from the Yeast Prion Sup35p

In order to explore the effects of amino acid sequence rearrangement on prion aggregation, 20 ns molecular dynamic simulations of 9 sequence rearranged 7-residue peptides aligned to a 3*3*3 matrix were performed in this study. It was found that the sequence rearrangement did not affect the 7-residue peptide's aggregation behavior, but changed their stabilities of aggregate complexes, especially their typical amyloid characters. Furthermore, our results suggested that the Q-N-Y sequence at the C terminal of 7-residue peptide and the N-X-Q-X-N zipper structure might be related to the aggregation rates and typical amyloid characters, respectively.