Investigating AGT-DNA covalent and non-covalent interactions in methyl-induced DNA damage repair

Methylation induced DNA base-pairing damage, one of the major causes of cancer, can be repaired by O6-alkylguanine-DNA alkyltransferase (AGT). During this process, AGT forms a transient covalent bonding with DNA and then transfers the methyl group from the methylated GUA7 to CYS145. Herein, we modeled the covalent complex of the AGT-DNA system and then investigated structural features of the complex using molecular dynamics (MD) simulations. Utilizing the umbrella sampling method, we also investigated the free energy change between the non-covalent complexes before (pre-repair complex) and after (post-repair complex) the methyl transfer. Our analysis shows that residues THR95, TYR114, and SER151 in AGT consistently form hydrogen bonding with THY9, THY23, and methylated GUA7 (or repaired GUA7) in DNA suggesting the importance of these residues/nucleotides in the AGT-DNA complex formation. In addition, calculation of change in free energies also shows that the pre-transfer complex with methylated GUA7 is more favorable in the catalytic cavity compared to the post-transfer complex with repaired Guanine (GUA7). Our process will not only helpful in computational studies of DNA repair mechanism but also in exploration of cancer therapeutics targeting the AGT-DNA complexes.