Reactive molecular dynamics study of the pH-dependent dynamic structure of α-helix

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

We have studied the α-helix to random coil transition using ReaxFF reactive molecular dynamics as a function of pH. Urea binding to peptides and associated interference with backbone H-bonds and charged side chains interactions, which can both denature the helices, have been studied previously using nonreactive force fields (Topol, I. A. J. Am. Chem. Soc. 2001, 123, 6054-6060). This study reveals new proton-transfer mechanisms related to the denaturation of α-helical structures, which cannot be captured by nonreactive molecular dynamics. In addition, we show that proton transfer between the solution and the peptide can break the α-helix hydrogen bonds, and consequently, at extreme pHs, a significant amount of helix will unravel. We also compare the effects of temperature in the denaturation mechanism. The ReaxFF findings are in significantly better agreement with ab initio calculations than previous nonreactive force field results, indicating the relevance of the reactive component on helical loss. (Chemical Equation Presented).

Original languageEnglish (US)
Pages (from-to)13498-13504
Number of pages7
JournalJournal of Physical Chemistry B
Volume118
Issue number47
DOIs
StatePublished - Nov 26 2014

Fingerprint

Denaturation
Proton transfer
helices
Peptides
Molecular dynamics
molecular dynamics
biopolymer denaturation
Urea
field theory (physics)
peptides
Hydrogen bonds
protons
ureas
coils
hydrogen bonds
interference
Temperature
interactions
temperature

All Science Journal Classification (ASJC) codes

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

Cite this

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title = "Reactive molecular dynamics study of the pH-dependent dynamic structure of α-helix",
abstract = "We have studied the α-helix to random coil transition using ReaxFF reactive molecular dynamics as a function of pH. Urea binding to peptides and associated interference with backbone H-bonds and charged side chains interactions, which can both denature the helices, have been studied previously using nonreactive force fields (Topol, I. A. J. Am. Chem. Soc. 2001, 123, 6054-6060). This study reveals new proton-transfer mechanisms related to the denaturation of α-helical structures, which cannot be captured by nonreactive molecular dynamics. In addition, we show that proton transfer between the solution and the peptide can break the α-helix hydrogen bonds, and consequently, at extreme pHs, a significant amount of helix will unravel. We also compare the effects of temperature in the denaturation mechanism. The ReaxFF findings are in significantly better agreement with ab initio calculations than previous nonreactive force field results, indicating the relevance of the reactive component on helical loss. (Chemical Equation Presented).",
author = "M. Golkaram and {Kyung Shin}, Yun and {Van Duin}, Adri",
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Reactive molecular dynamics study of the pH-dependent dynamic structure of α-helix. / Golkaram, M.; Kyung Shin, Yun; Van Duin, Adri.

In: Journal of Physical Chemistry B, Vol. 118, No. 47, 26.11.2014, p. 13498-13504.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Reactive molecular dynamics study of the pH-dependent dynamic structure of α-helix

AU - Golkaram, M.

AU - Kyung Shin, Yun

AU - Van Duin, Adri

PY - 2014/11/26

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N2 - We have studied the α-helix to random coil transition using ReaxFF reactive molecular dynamics as a function of pH. Urea binding to peptides and associated interference with backbone H-bonds and charged side chains interactions, which can both denature the helices, have been studied previously using nonreactive force fields (Topol, I. A. J. Am. Chem. Soc. 2001, 123, 6054-6060). This study reveals new proton-transfer mechanisms related to the denaturation of α-helical structures, which cannot be captured by nonreactive molecular dynamics. In addition, we show that proton transfer between the solution and the peptide can break the α-helix hydrogen bonds, and consequently, at extreme pHs, a significant amount of helix will unravel. We also compare the effects of temperature in the denaturation mechanism. The ReaxFF findings are in significantly better agreement with ab initio calculations than previous nonreactive force field results, indicating the relevance of the reactive component on helical loss. (Chemical Equation Presented).

AB - We have studied the α-helix to random coil transition using ReaxFF reactive molecular dynamics as a function of pH. Urea binding to peptides and associated interference with backbone H-bonds and charged side chains interactions, which can both denature the helices, have been studied previously using nonreactive force fields (Topol, I. A. J. Am. Chem. Soc. 2001, 123, 6054-6060). This study reveals new proton-transfer mechanisms related to the denaturation of α-helical structures, which cannot be captured by nonreactive molecular dynamics. In addition, we show that proton transfer between the solution and the peptide can break the α-helix hydrogen bonds, and consequently, at extreme pHs, a significant amount of helix will unravel. We also compare the effects of temperature in the denaturation mechanism. The ReaxFF findings are in significantly better agreement with ab initio calculations than previous nonreactive force field results, indicating the relevance of the reactive component on helical loss. (Chemical Equation Presented).

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