Effects of zinc binding on the conformational distribution of the Amyloid-b peptide based on molecular dynamics simulations

A number of experiments suggested that metal binding can promote the aggregation of the amyloid-â peptide. In this work, the effects of the zinc binding on the conformational distributions of the full length amyloid-â peptide are investigated on the basis of extensive molecular dynamics simulations. By comparing the conformational distributions of the apo-peptide and the holo-peptide, we show that the zinc binding can affect the conformational distribution of the amyloid-â monomer dramatically. Compared with the apo-peptide, the holo-peptide samples more â-strand conformation for the central hydrophobic cluster 17-21. Meanwhile, the formation probabilities of the salt bridge Asp23-Lys28 and the turn comprising 23-28 are also increased significantly at room temperature. Since these local structures are essential for the amyloid-â aggregation, the observed effects of the zinc binding indicate that the metal induced conformational change of the monomer is one of the possible mechanisms for the metal promoted aggregation of the amyloid-â peptide. I