Molecular-dynamics simulations for amyloid beta 1-42 monomer with D-aspartic acid residues using continuous solvent.

Molecular-dynamics simulations of amyloid-beta(1-42) peptides including D-aspartic acid residues were performed, and their three-dimensional structures were compared. The simulations were performed in an aqueous environment using a continuous solvent model. In the structures obtained from simulations, the occurrence ratio of beta-extended structures for the peptide that included D-Asp23 was larger than that for the wild-type peptide. These beta-extended structures appeared in the C-terminal region of the peptide, and the alpha-helix structures of the region were lost. On the other hand, for the peptide that included the stereo-inverted form of Asp1 as well as D-Asp23, the occurrence ratio of beta-extended structures in the C-terminal region was lower than that of the peptide including only D-Asp23.