Quantum chemical analysis of the unfolding of a penta-glycyl 3 10-helix initiated by HO, HO2 , and O2-•

Michael C. Owen, B. Viskolcz, I. Csizmadia

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Abstract

In this study, the thermodynamic functions of hydrogen abstraction from the C and amide nitrogen of Gly3 in a homo-pentapeptide (N-Ac-GGGGG-NH2; G5) by HO, HO2 , and O2-• were computed using the Becke three-parameter Lee-Yang-Parr (B3LYP) density functional. The thermodynamic functions, standard enthalpy (H), Gibbs free energy (G), and entropy (S), of these reactions were computed with G5 in the 3 10-helical (G5Hel) and fully-extended (G5Ext) conformations at the B3LYP6-31G(d) and B3LYP6-311G(d,p) levels of theory, both in the gas phase and using the conductor-like polarizable continuum model implicit water model. H abstraction is more favorable at the C than at the amide nitrogen. The secondary structure of G5 affects the bond dissociation energy of the H-C, but has a negligible effect on the dissociation energy of the H-N bond. The HO radical is the strongest hydrogen abstractor, followed by HO2, and finally O2 -•. The secondary structure elements, such as H-bonds in the 310-helix, protect the peptide from radical attack by disabling the potential electron delocalization at the C, which is possible when G5 is in the extended conformation. The unfolding of the peptide radicals is more favorable than the unfolding of G5Hel; however, only the HO can initiate the unfolding of G5Hel and the formation of G5 Ext+. These results are relevant to peptides that are prone to undergoing transitions from helical structures to -sheets in the cellular condition known as oxidative stress and the results are discussed in this context.

Original languageEnglish
Article number035101
JournalThe Journal of Chemical Physics
Volume135
Issue number3
DOIs
Publication statusPublished - Jul 21 2011

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chemical analysis
helices
peptides
Amides
Peptides
amides
Conformations
Hydrogen
Nitrogen
Chemical analysis
Thermodynamics
dissociation
nitrogen
thermodynamics
Oxidative stress
hydrogen
Gibbs free energy
attack
Enthalpy
Entropy

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

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title = "Quantum chemical analysis of the unfolding of a penta-glycyl 3 10-helix initiated by HO•, HO2 •, and O2-•",
abstract = "In this study, the thermodynamic functions of hydrogen abstraction from the C and amide nitrogen of Gly3 in a homo-pentapeptide (N-Ac-GGGGG-NH2; G5) by HO•, HO2 •, and O2-• were computed using the Becke three-parameter Lee-Yang-Parr (B3LYP) density functional. The thermodynamic functions, standard enthalpy (H), Gibbs free energy (G), and entropy (S), of these reactions were computed with G5 in the 3 10-helical (G5Hel) and fully-extended (G5Ext) conformations at the B3LYP6-31G(d) and B3LYP6-311G(d,p) levels of theory, both in the gas phase and using the conductor-like polarizable continuum model implicit water model. H abstraction is more favorable at the C than at the amide nitrogen. The secondary structure of G5 affects the bond dissociation energy of the H-C, but has a negligible effect on the dissociation energy of the H-N bond. The HO• radical is the strongest hydrogen abstractor, followed by HO2•, and finally O2 -•. The secondary structure elements, such as H-bonds in the 310-helix, protect the peptide from radical attack by disabling the potential electron delocalization at the C, which is possible when G5 is in the extended conformation. The unfolding of the peptide radicals is more favorable than the unfolding of G5Hel; however, only the HO• can initiate the unfolding of G5Hel and the formation of G5 Ext+. These results are relevant to peptides that are prone to undergoing transitions from helical structures to -sheets in the cellular condition known as oxidative stress and the results are discussed in this context.",
author = "Owen, {Michael C.} and B. Viskolcz and I. Csizmadia",
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AU - Owen, Michael C.

AU - Viskolcz, B.

AU - Csizmadia, I.

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Y1 - 2011/7/21

N2 - In this study, the thermodynamic functions of hydrogen abstraction from the C and amide nitrogen of Gly3 in a homo-pentapeptide (N-Ac-GGGGG-NH2; G5) by HO•, HO2 •, and O2-• were computed using the Becke three-parameter Lee-Yang-Parr (B3LYP) density functional. The thermodynamic functions, standard enthalpy (H), Gibbs free energy (G), and entropy (S), of these reactions were computed with G5 in the 3 10-helical (G5Hel) and fully-extended (G5Ext) conformations at the B3LYP6-31G(d) and B3LYP6-311G(d,p) levels of theory, both in the gas phase and using the conductor-like polarizable continuum model implicit water model. H abstraction is more favorable at the C than at the amide nitrogen. The secondary structure of G5 affects the bond dissociation energy of the H-C, but has a negligible effect on the dissociation energy of the H-N bond. The HO• radical is the strongest hydrogen abstractor, followed by HO2•, and finally O2 -•. The secondary structure elements, such as H-bonds in the 310-helix, protect the peptide from radical attack by disabling the potential electron delocalization at the C, which is possible when G5 is in the extended conformation. The unfolding of the peptide radicals is more favorable than the unfolding of G5Hel; however, only the HO• can initiate the unfolding of G5Hel and the formation of G5 Ext+. These results are relevant to peptides that are prone to undergoing transitions from helical structures to -sheets in the cellular condition known as oxidative stress and the results are discussed in this context.

AB - In this study, the thermodynamic functions of hydrogen abstraction from the C and amide nitrogen of Gly3 in a homo-pentapeptide (N-Ac-GGGGG-NH2; G5) by HO•, HO2 •, and O2-• were computed using the Becke three-parameter Lee-Yang-Parr (B3LYP) density functional. The thermodynamic functions, standard enthalpy (H), Gibbs free energy (G), and entropy (S), of these reactions were computed with G5 in the 3 10-helical (G5Hel) and fully-extended (G5Ext) conformations at the B3LYP6-31G(d) and B3LYP6-311G(d,p) levels of theory, both in the gas phase and using the conductor-like polarizable continuum model implicit water model. H abstraction is more favorable at the C than at the amide nitrogen. The secondary structure of G5 affects the bond dissociation energy of the H-C, but has a negligible effect on the dissociation energy of the H-N bond. The HO• radical is the strongest hydrogen abstractor, followed by HO2•, and finally O2 -•. The secondary structure elements, such as H-bonds in the 310-helix, protect the peptide from radical attack by disabling the potential electron delocalization at the C, which is possible when G5 is in the extended conformation. The unfolding of the peptide radicals is more favorable than the unfolding of G5Hel; however, only the HO• can initiate the unfolding of G5Hel and the formation of G5 Ext+. These results are relevant to peptides that are prone to undergoing transitions from helical structures to -sheets in the cellular condition known as oxidative stress and the results are discussed in this context.

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