In Silico Protein Folding Simulation of Amyloid A4 Peptide


  • Fatahiya Mohamed Tap
  • Nurul Bahiyah Ahmad Khairudin



Amyloid A4 peptide, Molecular Dynamics, Protein folding,


The objective of this study is to investigate the folding pathways of Amyloid A4 peptide (PDB ID: 1AML). The structure and trajectories of this protein has been studied using Molecular Dynamics (MD) simulation. The simulation was run at 300K for 50nsec. The model at 2nsec was aligned to the Nuclear Magnetic Resonance (NMR) structure with the RMSD value of 7.85Å for the overall structure. It was found that the 3_10_helix started to form (ILE32 GLY33 LEU34 MET35) at 4nsec until 7nsec.


A.R. Leach, Molecular Modelling: Principle and application, 2nd edition. Pearson Education, 2001.

E. L. Kavraki., Protein folding, unpublished.

D.Bratko, T. Cellemer, J.M. Prausnitz, and H.W. Blanch., Biotechnology and Bioengineering, 9 2007,1-8.

C.B. Anfinsen, Science, 181 (1973), 223-230.

N. Ferguson, and A.R. Fersht, Elsevier,13 (2003), 75-81.

H. Stricht, P. Bayer, D. Willbold, S. Dames, C. Hilbich, K. Beyreuther, W.R.Frank, and P. Rosch , Eur. J. Biochem, 233 (1995), 293-298.

K. Wataba, T. Segawa, K. Nakamura, M. Kodaka, T. Konakahara, and H. Okuni, J. Peptide Res., 58 (2001), 342-346.

D.A Case, T.A Darden, T.E. Cheatham, III, C.L Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvary, K.F. Wong, F. Paesani, J. Vanicek, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A Kollman, Amber 11, University of California, San Francisco, 2010.

D.A. Case, T. cheatham, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr.,A. Onufriev, C. Simmerling, B. Wang and R. Woods, J. Computat. Chem, 26 (2005), 1668-1688.

V. Tsui, and A.D. Case, Biopolymers (Nucleic Acid Sciences), 56 (2001), 275-291.

D.J. Sindhikara, S. Kim, A.F. Voter, and A.E Roitberg, J. chem.. Theory. Comput.,5 (2009), 1624-1631.

J.P. Ryckppaert, G. Ciccotti, and H.J.C Berendsen, J. Comput. Phys., 23 (1977), 327-341.