© 2004 The Japanese Biochemical Society
BIOCHEMISTRY |
General Dynamic Properties of Aß12–36 Amyloid Peptide Involved in Alzheimer’s Disease from Unfolding Simulation
1 Laboratory of Bioinformatics, School of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo, 192-0392; 2 Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; and 3 BIRD, JST (Japan Science and Technology Corporation)
To study the folding/unfolding properties of a ß-amyloid peptide Aß12–36 of Alzheimer’s disease, five molecular dynamics simulations of Aß12–36 in explicit water were done at 450 K starting from a structure that is stable in trifluoroethanol/water at room temperature with two 
-helices. Due to high temperature, the initial helical structure unfolded during the simulation. The observed aspects of the unfolding were as follows. 1) One helix (helix 1) had a longer life than the other (helix 2), which correlates well with the theoretically computed 
values. 2) Temporal prolongation of helix 1 was found before unfolding. 3) Hydrophobic cores formed frequently with rearrangement of amino-acid residues in the hydrophobic cores. The formation and rearrangement of the hydrophobic cores may be a general aspect of this peptide in the unfolded state, and the structural changes accompanied by the hydrophobic-core rearrangement may lead the peptide to the most stable structure. 4) Concerted motions (collective modes) appeared to unfold helix 1. The collective modes were similar with those observed in another simulation at 300 K. The analysis implies that the conformation moves according to the collective modes when the peptide is in the initial stage of protein unfolding and in the final stage of protein folding.
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