Energetic preference of 8-oxoG eversion pathways in a DNA glycosylase

J Am Chem Soc. 2011 Sep 21;133(37):14504-6. doi: 10.1021/ja205142d. Epub 2011 Aug 25.

Abstract

Base eversion is a fundamental process in the biochemistry of nucleic acids, allowing proteins engaged in DNA repair and epigenetic modifications to access target bases in DNA. Crystal structures reveal end points of these processes, but not the pathways involved in the dynamic process of base recognition. To elucidate the pathway taken by 8-oxoguanine during base excision repair by Fpg, we calculated free energy surfaces during eversion of the damaged base through the major and minor grooves. The minor groove pathway and free energy barrier (6-7 kcal/mol) are consistent with previously reported results (Qi, Y.; Spong, M. C.; Nam, K.; Banerjee, A.; Jiralerspong, S.; Karplus, M.; Verdine, G. L. Nature 2009, 462, 762.) However, eversion of 8-oxoG through the major groove encounters a significantly lower barrier (3-4 kcal/mol) more consistent with experimentally determined rates of enzymatic sliding during lesion search (Blainey, P. C.; van Oijent, A. M.; Banerjee, A.; Verdine, G. L.; Xie, X. S. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 5752.). Major groove eversion has been suggested for other glycosylases, suggesting that in addition to function, dynamics of base eversion may also be conserved.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • DNA Glycosylases / chemistry
  • DNA Glycosylases / metabolism*
  • DNA Repair
  • DNA-Formamidopyrimidine Glycosylase / chemistry
  • DNA-Formamidopyrimidine Glycosylase / metabolism
  • Guanine / analogs & derivatives*
  • Guanine / chemistry
  • Guanine / metabolism
  • Humans
  • Molecular Dynamics Simulation
  • Prokaryotic Cells / enzymology
  • Thermodynamics

Substances

  • 8-hydroxyguanine
  • Guanine
  • DNA Glycosylases
  • DNA-Formamidopyrimidine Glycosylase