The study of the interaction between amyloid beta protein and zinc ion and its role in Alzheimer's disease

In this study, the effect of zinc ion binding on the structural changes and the stability of Amyloid beta protein on the incidence of Alzheimer's disease at the molecular level was investigated. This study was done by molecular dynamics simulation computations, using Gromacs 4.6.1 software and Amber03 force field and SPC216 water solvent model. By Root-mean-square-deviation (RMSD), the precision of simulation was investigated; and by means of other different analysis (e.g. DSSP, Hydrogen Bond numbers and Radius of Gyration), we found that in the presence of zinc ions before and after binding, the structure of this protein was significantly changed. The data analysis by DSSP indicated that Amyloid beta peptide loses much percentage of its helical structure as a result of binding with zinc ion’s. With increasing radius of gyration after binding metal ion, the protein loses its global structure and will be changed unfold. Also, the number of hydrogen bonds in amyloid beta peptide in the presence of zinc ions, is less than in the its absence. All of these results are strong reason for the less stability of the protein structure in the presence of zinc ions and it's decomposition in the brain (preventing of aggregation of Amyloid beta peptide) and dealying Alzheimer's disease, consequently.