Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds: Study in explicit water

Li L. Duan, Ya Gao, Ye Mei, Qing G. Zhang, Bo Tang, John Zhang

Research output: Contribution to journalArticle

Abstract

Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M) using a polarized charge scheme that includes electronic polarization of backbone hydrogen bonds. Starting from an extended conformation, the 17-residue peptide was successfully folded into the native structure (α-helix) between 80 and 130 ns with a root-mean-square deviation of ∼1.0 Å. Analysis of the time-dependent trajectories revealed that helix formation of the peptide started at the terminals and progressed toward the center of the peptide. For comparison, MD trajectories generated under various versions of standard AMBER force fields failed to show any significant or stable helix formation in our simulation. Our result shows clear evidence that the electronic polarization of backbone hydrogen bonds energetically stabilizes the helix formation and is critical to the stable folding of the short helix structure.

Original languageEnglish (US)
Pages (from-to)3430-3435
Number of pages6
JournalJournal of Physical Chemistry B
Volume116
Issue number10
DOIs
StatePublished - Mar 15 2012

Fingerprint

helices
folding
Peptides
Hydrogen bonds
Trajectories
Polarization
hydrogen bonds
Molecular dynamics
Water
polarization
water
peptides
trajectories
Conformations
molecular dynamics
Computer simulation
electronics
field theory (physics)
simulation
deviation

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films

Cite this

Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds : Study in explicit water. / Duan, Li L.; Gao, Ya; Mei, Ye; Zhang, Qing G.; Tang, Bo; Zhang, John.

In: Journal of Physical Chemistry B, Vol. 116, No. 10, 15.03.2012, p. 3430-3435.

Research output: Contribution to journalArticle

Duan, Li L. ; Gao, Ya ; Mei, Ye ; Zhang, Qing G. ; Tang, Bo ; Zhang, John. / Folding of a helix is critically stabilized by polarization of backbone hydrogen bonds : Study in explicit water. In: Journal of Physical Chemistry B. 2012 ; Vol. 116, No. 10. pp. 3430-3435.
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