Direct folding simulation of a long helix in explicit water

Ya Gao; Xiaoliang Lu; Lili Duan; Dawei Zhang; Ye Mei; John Z.H. Zhang

doi:10.1063/1.4807145

Direct folding simulation of a long helix in explicit water

Ya Gao, Xiaoliang Lu, Lili Duan, Dawei Zhang, Ye Mei, John Z.H. Zhang

Chemistry

Research output: Contribution to journal › Article › peer-review

Abstract

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.

Original language	English (US)
Article number	193706
Journal	Applied Physics Letters
Volume	102
Issue number	19
DOIs	https://doi.org/10.1063/1.4807145
State	Published - May 13 2013

ASJC Scopus subject areas

Physics and Astronomy (miscellaneous)

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10.1063/1.4807145

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title = "Direct folding simulation of a long helix in explicit water",

abstract = "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.",

author = "Ya Gao and Xiaoliang Lu and Lili Duan and Dawei Zhang and Ye Mei and Zhang, {John Z.H.}",

note = "Funding Information: This work was supported by the National Science Foundation of China (Grant Nos. 20933002, 21173082, and 11147026), Shanghai PuJiang program (09PJ1404000), Shanghai Rising-Star program (Grant No. 11QA1402000) and Tier 1 RG58/11 of Nanyang Technological University. We also thank the High Performance Computer Center of East China Normal University for CPU time support. ",

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doi = "10.1063/1.4807145",

language = "English (US)",

volume = "102",

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T1 - Direct folding simulation of a long helix in explicit water

AU - Gao, Ya

AU - Lu, Xiaoliang

AU - Duan, Lili

AU - Zhang, Dawei

AU - Mei, Ye

AU - Zhang, John Z.H.

N1 - Funding Information: This work was supported by the National Science Foundation of China (Grant Nos. 20933002, 21173082, and 11147026), Shanghai PuJiang program (09PJ1404000), Shanghai Rising-Star program (Grant No. 11QA1402000) and Tier 1 RG58/11 of Nanyang Technological University. We also thank the High Performance Computer Center of East China Normal University for CPU time support.

PY - 2013/5/13

Y1 - 2013/5/13

N2 - 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.

AB - 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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Direct folding simulation of a long helix in explicit water

Abstract

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