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

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.

Figure 1

Base eversion paths from NEB calculations. Paths are indicated by snapshots, with major groove shown in purple and minor groove in green. Intrahelical 8-oxoG:C base pair is shown in yellow, extrahelical 8-oxoG:C base pair, in red, catalytic loop, in cyan.

Figure 2

Free energy pathways of base eversion via the major (top) and minor (bottom left) grooves. The initial intrahelical state I is in the middle, and the final extrahelical state E is reached on both the right and left sides of the graph. Free energies are given in kcal/mol.