Applying computational methods in the study of biomolecular systems: The recognition mechanism of DNA repair enzyme Fpg

8-oxo-guanine (8OG) is one of the most prevalent forms of oxidative DNA Failure to repair 8OG will lead to cancer and many age-related diseases. For studying pathophysiology of these diseases, it is essential to understand the repair mechanism 8OG in healthy cells. In bacteria, 8OG is excised by formamidopyrimidine glycosylase Fpg) as the initial step in base excision repair. To efficiently excise this lesion, Fpg discriminate between 8OG and an excess of guanine in duplex DNA. We computational methods studying the structural basis underlying this high degree selectivity.;FapydG is another common oxidative DNA lesion involving opening of the imidazole ring. It has similar structure and shares the same precursor with 8OGG and can be excised by the same enzymes as 8OG. We examined the current force field parameters for FapydG and found that the energy barrier of the rotational bond C5-N7 is overestimated. New parameters were calculated and simulations with them can well reproduce the x-ray structures.;DNA sliding and base flipping are two essential motions in DNA lesion searching and recognition. We used targeted MD, umbrella sampling, and long MD simulations (1.6 ms in total) to simulate these two processes. We observed the sliding motions and base pair breaking in our long MD simulations. In the targeted MD simulations, after the forced conformational changes occurred, we observed that the structures of several key residues changed from the original conformations to the new ones, which reproduced the structural differences between x-ray structures at different stages.;In first study free energy calculation methods and point mutation studies have been performed on the comparison of the two binding mode of 8OG. Two different binding modes of 8OG in Fpg/DNA complex have been shown in different structural studies. Our all-atom simulations are consistent with both structures. The syn conformation observed in the crystallographic structure of Fpg obtained from B. stearothermophilus is stabilized through interaction with E77, a non-conserved residue. Replacement of E77 by Ser, creating the Fpg sequence found in E. coli and other bacteria, results in preferred binding of 8OG in the anti conformation.