Molecular dynamics simulations of Aβ (1-42) and Aβ (1-40): A comparative study to determine their role in the development of Alzheimer's disease

Aim and Pathological studies have suggested that formation of fibrous plaques and accumulated masses of amyloid beta peptides in central nervous system is one of the causes to Alzheimer's disease. Since these diseases depend on conformational structure of protein, we investigate initial conformational changes of Aβ (1-42) and Aβ (1-40 by molecular dynamic simulations in this paper.
The solution NMR structures of Aβ (1-42) and Aβ (1-40) (protein data bank: 1IYT &1BA4) was chosen as a template for comparative modeling. All simulations and data analysis were performed by GROMACS program with the united-atom protein force field. The final sampling simulations were 20-ns MD simulations, 310K and constant pressure (1 bar).
The results of RMSD, radius of gyration and solvent accessible surface area showed that structural changes, flexibility and the propensity to aggregation of Aβ (1-42) is more than Aβ (1-40).
The solvent accessible surface area show the hydrophobicity interaction have important role in aggregation and creation of deformed structures. Our data showed that Aβ (1-42) have critical role in the development of Alzheimer's disease