Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein

Replica exchange molecular dynamics (REMD) simulation provides an efficient conformational sampling tool for the study of protein folding. In this study, we explore the mechanism directing the structure variation from α/4β-fold protein to 3α-fold protein after mutation by conducting REMD simulation...

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Main Authors: Lazim, Raudah, Mei, Ye, Zhang, Dawei
Other Authors: School of Physical and Mathematical Sciences
Format: Article
Language:English
Published: 2013
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Online Access:https://hdl.handle.net/10356/98098
http://hdl.handle.net/10220/17485
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Institution: Nanyang Technological University
Language: English
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spelling sg-ntu-dr.10356-980982020-03-07T12:34:44Z Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein Lazim, Raudah Mei, Ye Zhang, Dawei School of Physical and Mathematical Sciences DRNTU::Science::Chemistry::Biochemistry Replica exchange molecular dynamics (REMD) simulation provides an efficient conformational sampling tool for the study of protein folding. In this study, we explore the mechanism directing the structure variation from α/4β-fold protein to 3α-fold protein after mutation by conducting REMD simulation on 42 replicas with temperatures ranging from 270 K to 710 K. The simulation began from a protein possessing the primary structure of GA88 but the tertiary structure of GB88, two G proteins with “high sequence identity.” Albeit the large Cα-root mean square deviation (RMSD) of the folded protein (4.34 Å at 270 K and 4.75 Å at 304 K), a variation in tertiary structure was observed. Together with the analysis of secondary structure assignment, cluster analysis and principal component, it provides insights to the folding and unfolding pathway of 3α-fold protein and α/4β-fold protein respectively paving the way toward the understanding of the ongoings during conformational variation. 2013-11-08T06:28:46Z 2019-12-06T19:50:31Z 2013-11-08T06:28:46Z 2019-12-06T19:50:31Z 2011 2011 Journal Article Lazim, R., Mei, Y., & Zhang, D. (2011). Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein. Journal of molecular modeling, 18(3), 1087-1095. https://hdl.handle.net/10356/98098 http://hdl.handle.net/10220/17485 10.1007/s00894-011-1147-8 en Journal of molecular modeling
institution Nanyang Technological University
building NTU Library
country Singapore
collection DR-NTU
language English
topic DRNTU::Science::Chemistry::Biochemistry
spellingShingle DRNTU::Science::Chemistry::Biochemistry
Lazim, Raudah
Mei, Ye
Zhang, Dawei
Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein
description Replica exchange molecular dynamics (REMD) simulation provides an efficient conformational sampling tool for the study of protein folding. In this study, we explore the mechanism directing the structure variation from α/4β-fold protein to 3α-fold protein after mutation by conducting REMD simulation on 42 replicas with temperatures ranging from 270 K to 710 K. The simulation began from a protein possessing the primary structure of GA88 but the tertiary structure of GB88, two G proteins with “high sequence identity.” Albeit the large Cα-root mean square deviation (RMSD) of the folded protein (4.34 Å at 270 K and 4.75 Å at 304 K), a variation in tertiary structure was observed. Together with the analysis of secondary structure assignment, cluster analysis and principal component, it provides insights to the folding and unfolding pathway of 3α-fold protein and α/4β-fold protein respectively paving the way toward the understanding of the ongoings during conformational variation.
author2 School of Physical and Mathematical Sciences
author_facet School of Physical and Mathematical Sciences
Lazim, Raudah
Mei, Ye
Zhang, Dawei
format Article
author Lazim, Raudah
Mei, Ye
Zhang, Dawei
author_sort Lazim, Raudah
title Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein
title_short Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein
title_full Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein
title_fullStr Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein
title_full_unstemmed Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein
title_sort replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein
publishDate 2013
url https://hdl.handle.net/10356/98098
http://hdl.handle.net/10220/17485
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