Solvent effect on the folding dynamics and structure of E6-associated protein characterized from Ab initio protein folding simulations
Solvent effect on protein conformation and folding mechanism of E6-associated protein (E6ap) peptide are investigated using a recently developed charge update scheme termed as adaptive hydrogen bond-specific charge (AHBC). On the basis of the close agreement between the calculated helix contents fro...
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sg-ntu-dr.10356-952432023-02-28T19:29:33Z Solvent effect on the folding dynamics and structure of E6-associated protein characterized from Ab initio protein folding simulations Xu, Zhijun Lazim, Raudah Sun, Tiedong Mei, Ye Zhang, Dawei School of Physical and Mathematical Sciences DRNTU::Science::Biological sciences Solvent effect on protein conformation and folding mechanism of E6-associated protein (E6ap) peptide are investigated using a recently developed charge update scheme termed as adaptive hydrogen bond-specific charge (AHBC). On the basis of the close agreement between the calculated helix contents from AHBC simulations and experimental results, we observed based on the presented simulations that the two ends of the peptide may simultaneously take part in the formation of the helical structure at the early stage of folding and finally merge to form a helix with lowest backbone RMSD of about 0.9 Å in 40% 2,2,2-trifluoroethanol solution. However, in pure water, the folding may start at the center of the peptide sequence instead of at the two opposite ends. The analysis of the free energy landscape indicates that the solvent may determine the folding clusters of E6ap, which subsequently leads to the different final folded structure. The current study demonstrates new insight to the role of solvent in the determination of protein structure and folding dynamics. Published version 2013-03-05T04:10:47Z 2019-12-06T19:11:08Z 2013-03-05T04:10:47Z 2019-12-06T19:11:08Z 2012 2012 Journal Article Xu, Z., Lazim, R., Sun, T., Mei, Y., & Zhang, D. (2012). Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations. The Journal of Chemical Physics, 136(13), 135102. 0021-9606 https://hdl.handle.net/10356/95243 http://hdl.handle.net/10220/9339 10.1063/1.3698164 en The journal of chemical physics © 2012 American Institute of Physics. This paper was published in The Journal of Chemical Physics and is made available as an electronic reprint (preprint) with permission of American Institute of Physics. The paper can be found at the following official DOI: [http://dx.doi.org/10.1063/1.3698164]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law. application/pdf |
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DRNTU::Science::Biological sciences Xu, Zhijun Lazim, Raudah Sun, Tiedong Mei, Ye Zhang, Dawei Solvent effect on the folding dynamics and structure of E6-associated protein characterized from Ab initio protein folding simulations |
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Solvent effect on protein conformation and folding mechanism of E6-associated protein (E6ap) peptide are investigated using a recently developed charge update scheme termed as adaptive hydrogen bond-specific charge (AHBC). On the basis of the close agreement between the calculated helix contents from AHBC simulations and experimental results, we observed based on the presented simulations that the two ends of the peptide may simultaneously take part in the formation of the helical structure at the early stage of folding and finally merge to form a helix with lowest backbone RMSD of about 0.9 Å in 40% 2,2,2-trifluoroethanol solution. However, in pure water, the folding may start at the center of the peptide sequence instead of at the two opposite ends. The analysis of the free energy landscape indicates that the solvent may determine the folding clusters of E6ap, which subsequently leads to the different final folded structure. The current study demonstrates new insight to the role of solvent in the determination of protein structure and folding dynamics. |
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School of Physical and Mathematical Sciences |
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School of Physical and Mathematical Sciences Xu, Zhijun Lazim, Raudah Sun, Tiedong Mei, Ye Zhang, Dawei |
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Article |
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Xu, Zhijun Lazim, Raudah Sun, Tiedong Mei, Ye Zhang, Dawei |
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Xu, Zhijun |
title |
Solvent effect on the folding dynamics and structure of E6-associated protein characterized from Ab initio protein folding simulations |
title_short |
Solvent effect on the folding dynamics and structure of E6-associated protein characterized from Ab initio protein folding simulations |
title_full |
Solvent effect on the folding dynamics and structure of E6-associated protein characterized from Ab initio protein folding simulations |
title_fullStr |
Solvent effect on the folding dynamics and structure of E6-associated protein characterized from Ab initio protein folding simulations |
title_full_unstemmed |
Solvent effect on the folding dynamics and structure of E6-associated protein characterized from Ab initio protein folding simulations |
title_sort |
solvent effect on the folding dynamics and structure of e6-associated protein characterized from ab initio protein folding simulations |
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2013 |
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https://hdl.handle.net/10356/95243 http://hdl.handle.net/10220/9339 |
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1759858117147885568 |