Insights into Damaged Base Detection by DNA Glycosylases: A Computational Study of AlkD

Abstract

In order to protect the cellular genome from damage, a wide array of proteins known as DNA repair enzymes must be able to rapidly locate nucleic acid modifications. The first step of the base excision repair pathway is the removal of modified nucleotides, which requires that DNA glycosylases be able to efficiently detect their target. Once located, most DNA glycosylases utilize the base-flipping mechanism to flip damaged nucleobases into a binding pocket on the protein. Recent crystallization studies show that there is at least one exception, AlkD, which repairs methylated DNA without forcing the damaged nucleobase out of its base pair. The unique nature of AlkD allows us to investigate the ways in which DNA glycosylases locate modified DNA. Using microsecond MD simulations, we demonstrate that AlkD is able to stabilize a dramatically contorted DNA structure by promoting localized B-to-A-DNA transitions in the methylated DNA. On the contrary, non-methylated DNA is found to unbind from the putative binding region in order to form a more linear B-DNA type conformation. These observations are further supported by computing the free energy of binding for methylated and non-methylated DNA sequences.