The investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation

The objective of this study is to investigate the folding pathway of Trp-cage miniprotein. The structure and trajectories of this protein has been studied using Molecular Dynamics (MD) simulation. The simulation was run at 300K for 250ns. Clustering analysis was conducted to group the trajectories...

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Main Authors:	Ahmad Khairudin, Nurul Bahiyah, Mohamed Tap, Fatahiya
Format:	Conference or Workshop Item
Language:	English
Published:	2015
Subjects:	QD Chemistry
Online Access:	http://eprints.utm.my/id/eprint/61209/1/NurulbahiyahAhmadKhairudin2015_TheInvestigationoftheFoldingPathwayofTrp-CageMiniprotein.pdf http://eprints.utm.my/id/eprint/61209/
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Institution:	Universiti Teknologi Malaysia
Language:	English

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spelling	my.utm.612092017-08-02T01:38:43Z http://eprints.utm.my/id/eprint/61209/ The investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation Ahmad Khairudin, Nurul Bahiyah Mohamed Tap, Fatahiya QD Chemistry The objective of this study is to investigate the folding pathway of Trp-cage miniprotein. The structure and trajectories of this protein has been studied using Molecular Dynamics (MD) simulation. The simulation was run at 300K for 250ns. Clustering analysis was conducted to group the trajectories according to the RMSD value and six clusters were generated. From this, the best conformation was identified to best represent the Trp-cage miniprotein. The formation of the hydrogen bond that involved Gly11-Ser14 assisted the formation of 3 10 -helix. In this study, it is strongly suggested that the hydrogen bond interactions determined the formation of secondary structures. 2015 Conference or Workshop Item PeerReviewed application/pdf en http://eprints.utm.my/id/eprint/61209/1/NurulbahiyahAhmadKhairudin2015_TheInvestigationoftheFoldingPathwayofTrp-CageMiniprotein.pdf Ahmad Khairudin, Nurul Bahiyah and Mohamed Tap, Fatahiya (2015) The investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation. In: 3rd International Conference on Computational and Social Sciences (ICCSS-15), 25-27 Aug, 2015, Johor Bahru, Malaysia.
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/
language	English
topic	QD Chemistry
spellingShingle	QD Chemistry Ahmad Khairudin, Nurul Bahiyah Mohamed Tap, Fatahiya The investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation
description	The objective of this study is to investigate the folding pathway of Trp-cage miniprotein. The structure and trajectories of this protein has been studied using Molecular Dynamics (MD) simulation. The simulation was run at 300K for 250ns. Clustering analysis was conducted to group the trajectories according to the RMSD value and six clusters were generated. From this, the best conformation was identified to best represent the Trp-cage miniprotein. The formation of the hydrogen bond that involved Gly11-Ser14 assisted the formation of 3 10 -helix. In this study, it is strongly suggested that the hydrogen bond interactions determined the formation of secondary structures.
format	Conference or Workshop Item
author	Ahmad Khairudin, Nurul Bahiyah Mohamed Tap, Fatahiya
author_facet	Ahmad Khairudin, Nurul Bahiyah Mohamed Tap, Fatahiya
author_sort	Ahmad Khairudin, Nurul Bahiyah
title	The investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation
title_short	The investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation
title_full	The investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation
title_fullStr	The investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation
title_full_unstemmed	The investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation
title_sort	investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation
publishDate	2015
url	http://eprints.utm.my/id/eprint/61209/1/NurulbahiyahAhmadKhairudin2015_TheInvestigationoftheFoldingPathwayofTrp-CageMiniprotein.pdf http://eprints.utm.my/id/eprint/61209/
_version_	1643655102754455552

The investigation of the folding pathway of trp-cage miniprotein using explicit solvent molecular dynamics simulation

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