Direct folding simulation of a long helix in explicit water

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

Research output: Contribution to journalArticle

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 languageEnglish (US)
Article number193706
JournalApplied Physics Letters
Volume102
Issue number19
DOIs
StatePublished - May 13 2013

Fingerprint

helices
folding
hydrogen bonds
water
simulation
cluster analysis
gyration
field theory (physics)
peptides
amino acids
free energy
deviation
radii
polarization

ASJC Scopus subject areas

  • Physics and Astronomy (miscellaneous)

Cite this

Direct folding simulation of a long helix in explicit water. / Gao, Ya; Lu, Xiaoliang; Duan, Lili; Zhang, Dawei; Mei, Ye; Zhang, John.

In: Applied Physics Letters, Vol. 102, No. 19, 193706, 13.05.2013.

Research output: Contribution to journalArticle

Gao, Ya ; Lu, Xiaoliang ; Duan, Lili ; Zhang, Dawei ; Mei, Ye ; Zhang, John. / Direct folding simulation of a long helix in explicit water. In: Applied Physics Letters. 2013 ; Vol. 102, No. 19.
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