Relative Binding Free Energies of Adenine and Guanine to Damaged and Undamaged DNA in Human DNA Polymerase聽畏: Clues for Fidelity and Overall Efficiency

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• 作者：Melek N. Ucisik ; Sharon Hammes-Schiffer
• 刊名：Journal of the American Chemical Society
• 出版年：2015
• 出版时间：October 21, 2015
• 年：2015
• 卷：137
• 期：41
• 页码：13240-13243
• 全文大小：368K
• ISSN：1520-5126

文摘

Human DNA polymerase 畏 (Pol聽畏) plays an essential protective role against skin cancer caused by cyclobutane thymine鈥搕hymine dimers (TTDs), a frequent form of DNA damage arising from exposure to the sun. This enzyme rescues stalled replication forks at the TTDs by inserting bases opposite these DNA defects. Herein we calculate binding free energies for a free deoxyribose nucleotide triphosphate, dATP or dGTP, to Pol聽畏 complexed with undamaged or damaged DNA. The calculations indicate that the binding of dATP to the enzyme鈥揇NA complex is thermodynamically favored for TTD-containing DNA over undamaged DNA, most likely because of more extensive hydrogen-bonding interactions between the TTD and the enzyme that hold the TTD more rigidly in place. The calculations also illustrate that dATP binding is thermodynamically favored over dGTP binding at both thymine positions of the TTD, most likely due to more persistent and stable hydrogen-bonding interactions between the TTD and dATP than between the TTD and dGTP. This free energy difference is slightly greater for binding at the 5鈥?thymine position than at the 3鈥?thymine position, presumably because of stabilization arising from the A:T base pair formed at the 3鈥?position of the TTD in the previous step of Pol聽畏 function. All of these trends in binding free energies are consistent with experimental measurements of binding strength, fidelity, processivity, and overall efficiency. The insights gained from this analysis have implications for drug design efforts aimed at modifying the binding properties of this enzyme for improving cancer chemotherapy treatments.