High-energy ultraviolet radiation damages DNA through the formation of cyclobutane pyrimidine dimers and causes replication to stall. Human DNA polymerase η rescues these stalled replication forks, especially at thymine-thymine dimers (TTDs), by extending the primer with the correct complementary bases opposite the damaged site. We performed extensive molecular dynamics simulations to explore the structural and dynamical effects of four different Pol η complexes with or without a TTD and with either dATP or dGTP as the incoming deoxyribose nucleotide triphosphate. Only minor differences in the overall structures and equilibrium dynamics were detected among the four systems, suggesting that the differences in local interactions in the binding regions predominantly dictate the specificity of this enzyme. In particular, the TTD was found to adopt a more rigid and specific orientation through a more extensive hydrogen-bonding network with its environment. Moreover, two strictly conserved amino acids across the Pol η family, Q38 and R61, were found to establish persistent hydrogen-bonding interactions with the TTD and cation-π interactions with the free base, respectively. We also calculated relative binding free energies of dATP or dGTP to Pol η complexed with undamaged or TTD-containing DNA. The calculations indicate that the binding of dATP to the enzyme-DNA complex is thermodynamically favored for TTD-containing DNA over undamaged DNA. The binding of dATP was also determined to be thermodynamically favored over the binding of dGTP at both thymine positions of the TTD. The insights provided by these calculations are relevant to drug design efforts aimed at modifying the binding properties of this enzyme for potentiating cancer chemotherapy.

Clues for fidelity and overall efficiency of human DNA polymerase η

251st National Meeting (2016)

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