Title :
Molecular dynamics folding simulation of β-hairpins from protein G
Author :
Tap, Fatahiya Mohamed ; Ishak, Ameera ; Hussam, Ragheed ; Khairudin, Nurul Bahiyah Ahmad
Author_Institution :
Bioprocess Dept., Univ. Teknol. Malaysia, Skudai, Malaysia
Abstract :
The structure and trajectories of the 41-56 β-hairpins from the protein G (PDB ID: 1GB1) has been studied using Molecular Dynamics (MD) simulation. The purpose of this project is to investigate the pathway of the folding process. The simulation was run at 325 K for 50ns. The linear chain of the protein sequence became completely folded to β-hairpin structure at nearly 40ns. There were 18 interactions of hydrogen Bonds involved in the model. The model was aligned to the Nuclear Magnetic Resonance (NMR) structure with the RMSD value of 3.05 Å for overall structure and 1.04 Å for the turning part. The values of RMSD showed the comparison of the model and the native structure.
Keywords :
biothermics; hydrogen bonds; molecular biophysics; molecular configurations; molecular dynamics method; nuclear magnetic resonance; proteins; NMR structure; beta-hairpin folding simulation; beta-hairpin structure; beta-hairpin trajectory; hydrogen bond interactions; molecular dynamics simulation; nuclear magnetic resonance structure; protein G; protein sequence linear chain; temperature 325 K; Bonding; Color; Hydrogen; Nuclear magnetic resonance; Protein engineering; Proteins; Solvents; Molecular Dynamics; protein G; protein folding;
Conference_Titel :
Biomedical Engineering (ICoBE), 2012 International Conference on
Conference_Location :
Penang
Print_ISBN :
978-1-4577-1990-5
DOI :
10.1109/ICoBE.2012.6178968
