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

fYear

2012

Firstpage

123

Lastpage

128

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;

fLanguage

English

Publisher

ieee

Conference_Titel

Biomedical Engineering (ICoBE), 2012 International Conference on

Conference_Location

Penang

Print_ISBN

978-1-4577-1990-5

Type

conf

DOI

10.1109/ICoBE.2012.6178968

Filename

6178968