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Molecular dynamics folding simulation of ß-hairpins from protein G

The structure and trajectories of the 41-56 -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 prote...

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Main Authors: Tap, F. M., Ishak, A., Hussam, R., Ahmad Khairudin, Nurul Bahiyah
Format: Book Section
Published: IEEE 2012
Subjects:
Q Science (General)
Online Access:http://eprints.utm.my/id/eprint/35721/
http://dx.doi.org/10.1109/ICoBE.2012.6178968
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spelling my.utm.357212017-02-04T06:17:34Z http://eprints.utm.my/id/eprint/35721/ Molecular dynamics folding simulation of ß-hairpins from protein G Tap, F. M. Ishak, A. Hussam, R. Ahmad Khairudin, Nurul Bahiyah Q Science (General) The structure and trajectories of the 41-56 -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 -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 for overall structure and 1.04 for the turning part. The values of RMSD showed the comparison of the model and the native structure. IEEE 2012 Book Section PeerReviewed Tap, F. M. and Ishak, A. and Hussam, R. and Ahmad Khairudin, Nurul Bahiyah (2012) Molecular dynamics folding simulation of ß-hairpins from protein G. In: 2012 International Conference on Biomedical Engineering, ICoBE 2012. IEEE, New York, USA, pp. 123-128. ISBN 978-145771989-9 http://dx.doi.org/10.1109/ICoBE.2012.6178968 DOI:10.1109/ICoBE.2012.6178968
institution Universiti Teknologi Malaysia
building UTM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Teknologi Malaysia
content_source UTM Institutional Repository
url_provider http://eprints.utm.my/
topic Q Science (General)
spellingShingle Q Science (General)
Tap, F. M.
Ishak, A.
Hussam, R.
Ahmad Khairudin, Nurul Bahiyah
Molecular dynamics folding simulation of ß-hairpins from protein G
description The structure and trajectories of the 41-56 -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 -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 for overall structure and 1.04 for the turning part. The values of RMSD showed the comparison of the model and the native structure.
format Book Section
author Tap, F. M.
Ishak, A.
Hussam, R.
Ahmad Khairudin, Nurul Bahiyah
author_facet Tap, F. M.
Ishak, A.
Hussam, R.
Ahmad Khairudin, Nurul Bahiyah
author_sort Tap, F. M.
title Molecular dynamics folding simulation of ß-hairpins from protein G
title_short Molecular dynamics folding simulation of ß-hairpins from protein G
title_full Molecular dynamics folding simulation of ß-hairpins from protein G
title_fullStr Molecular dynamics folding simulation of ß-hairpins from protein G
title_full_unstemmed Molecular dynamics folding simulation of ß-hairpins from protein G
title_sort molecular dynamics folding simulation of ß-hairpins from protein g
publisher IEEE
publishDate 2012
url http://eprints.utm.my/id/eprint/35721/
http://dx.doi.org/10.1109/ICoBE.2012.6178968
_version_ 1643649820446949376
score 13.160551

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