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.

Index Terms—Molecular dynamics simulation, protein folding, amyloid A4 peptide.

Nurul Bahiyah Ahmad Khairudin is with Malaysia Japan International Institute of Technology, Universiti Teknologi Malaysia Kuala Lumpur, 54100 Kuala Lumpur, Malaysia (e-mail: nurulbahiyah@ic.utm.my).
Fatahiya Mohamed Tap is with the Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi, Malaysia, Johor, Malaysia (e-mail: fatahiyamohdtap@yahoo.com).

Cite: Nurul Bahiyah Ahmad Khairudin and Fatahiya Mohamed Tap, "Molecular Dynamics Folding Simulation of Amyloid A4 Peptide in Implicit Solvent," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 4, no. 5, pp. 351-354, 2014.