Carbinolamine formation and dehydration in a dna repair enzyme active site

M. L. Dodson, Ross C. Walker, Robert (Stephen) Lloyd

Research output: Contribution to journalArticle

Abstract

In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics-molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with and without a water molecule restrained to remain within the active site quantum region. We recovered potentials of mean force (PMF) from thirty replicate reaction trajectories using Jarzynski averaging. We demonstrated feasible pathways involving water, as well as those independent of water participation. The water-independent enzyme-catalyzed reaction had a bias-corrected Jarzynski-average barrier height of approximately 6:5 kcal mol -1(27:2 kJ mol -1) for the carbinolamine formation reaction and 44:5 kcal mol -11(186 kJ mol -11) for the reverse reaction at this level of representation. When the proton transfer was facilitated with an intrinsic quantum water, the barrier height was approximately 15 kcal mol -11(62:8 kJ mol -11) in the forward (formation) reaction and 19 kcal mol -11(79:5 kJ mol -11) for the reverse. In addition, two modes of unsteered (free dynamics) carbinolamine dehydration were observed: in one, the quantum water participated as an intermediate proton transfer species, and in the other, the active site protonated glutamate hydrogen was directly transferred to the carbinolamine oxygen. Water-independent unforced proton transfer from the protonated active site glutamate carboxyl to the unprotonated N-terminal amine was also observed. In summary, complex proton transfer events, some involving water intermediates, were studied in QM/MM simulations of T4PDG bound to a DNA abasic site. Imine carbinolamine formation was characterized using steered QM/MM molecular dynamics. Dehydration of the carbinolamine intermediate to form the final imine product was observed in free, unsteered, QM/MM dynamics simulations, as was unforced acid-base transfer between the active site carboxylate and the N-terminal amine.

Original languageEnglish (US)
Article numbere31377
JournalPLoS One
Volume7
Issue number2
DOIs
StatePublished - Feb 22 2012

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Mechanics
Dehydration
active sites
Catalytic Domain
Repair
Molecular mechanics
Proton transfer
Water
Quantum theory
Enzymes
enzymes
mechanics
protons
Protons
water
glycosylases
Pyrimidine Dimers
Imines
molecular dynamics
pyrimidines

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Carbinolamine formation and dehydration in a dna repair enzyme active site. / Dodson, M. L.; Walker, Ross C.; Lloyd, Robert (Stephen).

In: PLoS One, Vol. 7, No. 2, e31377, 22.02.2012.

Research output: Contribution to journalArticle

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abstract = "In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics-molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with and without a water molecule restrained to remain within the active site quantum region. We recovered potentials of mean force (PMF) from thirty replicate reaction trajectories using Jarzynski averaging. We demonstrated feasible pathways involving water, as well as those independent of water participation. The water-independent enzyme-catalyzed reaction had a bias-corrected Jarzynski-average barrier height of approximately 6:5 kcal mol -1(27:2 kJ mol -1) for the carbinolamine formation reaction and 44:5 kcal mol -11(186 kJ mol -11) for the reverse reaction at this level of representation. When the proton transfer was facilitated with an intrinsic quantum water, the barrier height was approximately 15 kcal mol -11(62:8 kJ mol -11) in the forward (formation) reaction and 19 kcal mol -11(79:5 kJ mol -11) for the reverse. In addition, two modes of unsteered (free dynamics) carbinolamine dehydration were observed: in one, the quantum water participated as an intermediate proton transfer species, and in the other, the active site protonated glutamate hydrogen was directly transferred to the carbinolamine oxygen. Water-independent unforced proton transfer from the protonated active site glutamate carboxyl to the unprotonated N-terminal amine was also observed. In summary, complex proton transfer events, some involving water intermediates, were studied in QM/MM simulations of T4PDG bound to a DNA abasic site. Imine carbinolamine formation was characterized using steered QM/MM molecular dynamics. Dehydration of the carbinolamine intermediate to form the final imine product was observed in free, unsteered, QM/MM dynamics simulations, as was unforced acid-base transfer between the active site carboxylate and the N-terminal amine.",
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