Free Energy Landscape of Lesion Recognition by Human 8-Oxoguanine DNA N-Glycosylase 1: Mechanistic Insights into Detection and Processing of 8-Oxoguanine in DNA

Abstract

Human 8-oxoguanine DNA N-glycosylase 1 (hOGG1) is an essential enzyme in DNA repair, responsible for recognizing and excising 8-oxoguanine (8OG), the lesion resulting from oxidative damage to guanine (G). By removing 8OG, hOGG1 prevents mutations like G-to-T transversions, maintains genomic stability, and reduces the risk of cancer and other diseases. Structural studies of hOGG1 bound to DNA have shown that lesion recognition occurs through base eversion from the DNA helix and hOGG1 finger residue insertion into the DNA helix. To better understand this complex process, enhanced sampling molecular dynamics simulations were used to map two-dimensional free energy surfaces that describe lesion recognition in terms of base eversion and finger residue insertion. The resulting free energy profiles reveal one major SN2-like and two minor SN1-like pathways for 8OG and normal G and show that hOGG1 has kinetic and thermodynamic advantages in terms of recognizing 8OG over G. Based on these data, simple kinetic models were utilized to provide a quantitative view of lesion recognition kinetics of 8OG versus G. The most favorable kinetic scenario identified was that the scanning rate of hOGG1 falls between the initial interrogation rates of 8OG and G. According to this scenario, hOGG1 rapidly scans normal Gs at its intrinsic diffusion speed, bypassing unnecessary interrogations. However, when hOGG1 encounters 8OG, the enzyme significantly slows down during lesion recognition until the damaged base is excised from its catalytic pocket. This highly selective mechanism ensures that hOGG1 efficiently repairs oxidative DNA damage by carefully regulating how it scans the DNA, thus optimizing the balance between speed and accuracy during the scanning process.