Direct folding simulation of a long helix in explicit water
A recently proposed Polarizable Hydrogen Bond (PHB) method has been employed to simulate the folding of a 53 amino acid helix (PDB ID 2KHK) in explicit water. Under PHB simulation, starting from a fully extended structure, the peptide folds into the native state as confirmed by measured time evoluti...
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sg-ntu-dr.10356-981472023-02-28T19:40:50Z Direct folding simulation of a long helix in explicit water Zhang, John Z. H. Gao, Ya Lu, Xiaoliang Duan, Lili Zhang, Dawei Mei, Ye School of Physical and Mathematical Sciences A recently proposed Polarizable Hydrogen Bond (PHB) method has been employed to simulate the folding of a 53 amino acid helix (PDB ID 2KHK) in explicit water. Under PHB simulation, starting from a fully extended structure, the peptide folds into the native state as confirmed by measured time evolutions of radius of gyration, root mean square deviation (RMSD), and native hydrogen bond. Free energy and cluster analysis show that the folded helix is thermally stable under the PHB model. Comparison of simulation results under, respectively, PHB and standard nonpolarizable force field demonstrates that polarization is critical for stable folding of this long α-helix. Published version 2013-09-04T07:31:40Z 2019-12-06T19:51:23Z 2013-09-04T07:31:40Z 2019-12-06T19:51:23Z 2013 2013 Journal Article Gao, Y., Lu, X., Duan, L., Zhang, D., Mei, Y.,& Zhang, J. Z. H. (2013). Direct folding simulation of a long helix in explicit water. Applied Physics Letters, 102(19), 193706. 0003-6951 https://hdl.handle.net/10356/98147 http://hdl.handle.net/10220/13304 10.1063/1.4807145 en Applied physics letters © 2013 AIP Publishing LLC. This paper was published in Applied Physics Letters and is made available as an electronic reprint (preprint) with permission of AIP Publishing LLC. The paper can be found at the following official DOI: [http://dx.doi.org/10.1063/1.4807145]. 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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A recently proposed Polarizable Hydrogen Bond (PHB) method has been employed to simulate the folding of a 53 amino acid helix (PDB ID 2KHK) in explicit water. Under PHB simulation, starting from a fully extended structure, the peptide folds into the native state as confirmed by measured time evolutions of radius of gyration, root mean square deviation (RMSD), and native hydrogen bond. Free energy and cluster analysis show that the folded helix is thermally stable under the PHB model. Comparison of simulation results under, respectively, PHB and standard nonpolarizable force field demonstrates that polarization is critical for stable folding of this long α-helix. |
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School of Physical and Mathematical Sciences |
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School of Physical and Mathematical Sciences Zhang, John Z. H. Gao, Ya Lu, Xiaoliang Duan, Lili Zhang, Dawei Mei, Ye |
| format |
Article |
| author |
Zhang, John Z. H. Gao, Ya Lu, Xiaoliang Duan, Lili Zhang, Dawei Mei, Ye |
| spellingShingle |
Zhang, John Z. H. Gao, Ya Lu, Xiaoliang Duan, Lili Zhang, Dawei Mei, Ye Direct folding simulation of a long helix in explicit water |
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Zhang, John Z. H. |
| title |
Direct folding simulation of a long helix in explicit water |
| title_short |
Direct folding simulation of a long helix in explicit water |
| title_full |
Direct folding simulation of a long helix in explicit water |
| title_fullStr |
Direct folding simulation of a long helix in explicit water |
| title_full_unstemmed |
Direct folding simulation of a long helix in explicit water |
| title_sort |
direct folding simulation of a long helix in explicit water |
| publishDate |
2013 |
| url |
https://hdl.handle.net/10356/98147 http://hdl.handle.net/10220/13304 |
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1759858029511049216 |