Molecular dynamics folding simulation of amyloid a4 peptide in implicit solvent

Abstract

The objectives of this study is to investigate the pathway of Amyloid A4 peptide (Pdb id: 1AML) folding and to study the interactions involved during the process. The folding process was performed using molecular dynamics (MD) simulation in implicit solvent method. This protein was simulated up to 350 ns. The trajectories of the folded protein were analyzed based on RMSD, hydrogen bond formation and secondary structure evolution. The results showed that there were a few crucial interactions involved in the folding process and important residues that stabilized the folded peptide were also identified.