Structural and Dynamic Characterization of Polymerase 魏鈥檚 Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity

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• 作者：Lee Lior-Hoffmann ; Shuang Ding ; Nicholas E. Geacintov ; Yingkai Zhang ; Suse Broyde
• 刊名：Biochemistry
• 出版年：2014
• 出版时间：September 9, 2014
• 年：2014
• 卷：53
• 期：35
• 页码：5683-5691
• 全文大小：529K
• ISSN：1520-4995

文摘

DNA lesion bypass polymerases process different lesions with varying fidelities, but the structural, dynamic, and mechanistic origins of this phenomenon remain poorly understood. Human DNA polymerase 魏 (Pol魏), a member of the Y family of lesion bypass polymerases, is specialized to bypass bulky DNA minor groove lesions in a predominantly error-free manner, by housing them in its unique gap. We have investigated the role of the unique Pol魏 gap and N-clasp structural features in the fidelity of minor groove lesion processing with extensive molecular modeling and molecular dynamics simulations to pinpoint their functioning in lesion bypass. Here we consider the N²-dG covalent adduct derived from the carcinogenic aromatic amine, 2-acetylaminofluorene (dG-N²-AAF), that is produced via the combustion of kerosene and diesel fuel. Our simulations reveal how the spacious gap directionally accommodates the lesion aromatic ring system as it transits through the stages of incorporation of the predominant correct partner dCTP opposite the damaged guanine, with preservation of local active site organization for nucleotidyl transfer. Furthermore, flexibility in Pol魏鈥檚 N-clasp facilitates the significant misincorporation of dTTP opposite dG-N²-AAF via wobble pairing. Notably, we show that N-clasp flexibility depends on lesion topology, being markedly reduced in the case of the benzo[a]pyrene-derived major adduct to N²-dG, whose bypass by Pol魏 is nearly error-free. Thus, our studies reveal how Pol魏鈥檚 unique structural and dynamic properties can regulate its bypass fidelity of polycyclic aromatic lesions and how the fidelity is impacted by lesion structures.