Molecular dynamics folding simulation of amyloid A4 peptide in implicit solvent

The objectives of this study is to investigate the pathway of Amyloid A4 peptide (Pdb id: 1AML) folding and to study the interactions involved during the process. The folding process was performed using molecular dynamics (MD) simulation in implicit solvent method. This protein was simulated up to 3...

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Main Authors:	Ahmad Khairudin, Nurulbahiyah, Tap, Fatahiya Mohamed
Format:	Article
Published:	IACSIT Press 2014
Subjects:	Q Science (General)
Online Access:	http://eprints.utm.my/id/eprint/59844/ http://dx.doi.org/10.7763/IJBBB.2014.V4.369
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Institution:	Universiti Teknologi Malaysia

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spelling	my.utm.598442022-01-03T08:52:43Z http://eprints.utm.my/id/eprint/59844/ Molecular dynamics folding simulation of amyloid A4 peptide in implicit solvent Ahmad Khairudin, Nurulbahiyah Tap, Fatahiya Mohamed Q Science (General) The objectives of this study is to investigate the pathway of Amyloid A4 peptide (Pdb id: 1AML) folding and to study the interactions involved during the process. The folding process was performed using molecular dynamics (MD) simulation in implicit solvent method. This protein was simulated up to 350 ns. The trajectories of the folded protein were analyzed based on RMSD, hydrogen bond formation and secondary structure evolution. The results showed that there were a few crucial interactions involved in the folding process and important residues that stabilized the folded peptide were also identified. IACSIT Press 2014-09 Article PeerReviewed Ahmad Khairudin, Nurulbahiyah and Tap, Fatahiya Mohamed (2014) Molecular dynamics folding simulation of amyloid A4 peptide in implicit solvent. International Journal Of Bioscience, Biochemistry And Bioinformatics, 4 (5). pp. 351-354. ISSN 2010-3638 http://dx.doi.org/10.7763/IJBBB.2014.V4.369 DOI:10.7763/IJBBB.2014.V4.369
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) Ahmad Khairudin, Nurulbahiyah Tap, Fatahiya Mohamed Molecular dynamics folding simulation of amyloid A4 peptide in implicit solvent
description	The objectives of this study is to investigate the pathway of Amyloid A4 peptide (Pdb id: 1AML) folding and to study the interactions involved during the process. The folding process was performed using molecular dynamics (MD) simulation in implicit solvent method. This protein was simulated up to 350 ns. The trajectories of the folded protein were analyzed based on RMSD, hydrogen bond formation and secondary structure evolution. The results showed that there were a few crucial interactions involved in the folding process and important residues that stabilized the folded peptide were also identified.
format	Article
author	Ahmad Khairudin, Nurulbahiyah Tap, Fatahiya Mohamed
author_facet	Ahmad Khairudin, Nurulbahiyah Tap, Fatahiya Mohamed
author_sort	Ahmad Khairudin, Nurulbahiyah
title	Molecular dynamics folding simulation of amyloid A4 peptide in implicit solvent
title_short	Molecular dynamics folding simulation of amyloid A4 peptide in implicit solvent
title_full	Molecular dynamics folding simulation of amyloid A4 peptide in implicit solvent
title_fullStr	Molecular dynamics folding simulation of amyloid A4 peptide in implicit solvent
title_full_unstemmed	Molecular dynamics folding simulation of amyloid A4 peptide in implicit solvent
title_sort	molecular dynamics folding simulation of amyloid a4 peptide in implicit solvent
publisher	IACSIT Press
publishDate	2014
url	http://eprints.utm.my/id/eprint/59844/ http://dx.doi.org/10.7763/IJBBB.2014.V4.369
_version_	1724073247229607936

Molecular dynamics folding simulation of amyloid A4 peptide in implicit solvent

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