Molecular Dynamics Folding Simulation of β-hairpin Protein (1E0Q)

The structure and trajectories of the mutant peptide of ubiquitin (PDB ID: 1E0Q) has been studied using Molecular Dynamics (MD) simulation. The simulation was performed using AMBER 11 utilizing force field 99 for 50 ns at constant temperature 325 K. The purpose of this study is to investigate the protein folding pathway of protein 1E0Q. In this simulation, the protein 1E0Q has folded into its near native β-hairpin structure within 5 ns. The RMSD value as compared to the NMR structure from the first residue to 17 residues is 2.17 Å. It has been observed that Gly 10 had been responsible to promote β-turn which caused the structure to turn into β-hairpin. In secondary structure analysis, it is shown that the residue from Thr 6 to Lys 11 has formed a bend in the structure. Two beta strands has also been found comprising residues Glu 2 to Lys 5 and Ile 13 to Glu 16.