Nucleotide Excision Repair Lesion-Recognition Protein Rad4 Captures a Pre-Flipped Partner Base in a Benzo[a]pyrene-Derived DNA Lesion: How Structure Impacts the Binding Pathway.
Nucleotide Excision Repair Lesion-Recognition Protein Rad4 Captures a Pre-Flipped Partner Base in a Benzo[a]pyrene-Derived DNA Lesion: How Structure Impacts the Binding Pathway.
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DOI：
10.1021/acs.chemrestox.7b00074
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发表时间：
2017-06-19
影响因子：
4.1
通讯作者：
Broyde S
中科院分区：
文献类型：
--
作者：
Mu H;Geacintov NE;Min JH;Zhang Y;Broyde S
着色性干皮病 C 蛋白复合物 (XPC) 可识别各种环境诱导的 DNA 损伤，并且是通过核苷酸切除修复 (NER) 途径启动其修复的关键。当与病变结合时，XPC 会将包含病变的两个核苷酸对翻转出 DNA 双链体，产生有效结合的复合物，从而成功切除病变。有趣的是，NER 的效率在不同病变之间差异很大，影响其毒性和细胞致突变性。尽管 XPC 结合的差异可能会影响 NER 效率，但尚不清楚 XPC 是否利用不同的机制来实现与不同病变的有效结合。在这里，我们研究了修复良好的 10R-(+)-cis-抗苯并[a]芘-N2-dG (cis-B[a]P-dG) DNA 加合物，该加合物在含有正常伴侣 C 的双链体中与病变相对。该加合物源自环境致癌物质苯并[a]芘，很可能被细胞中的 NER 遇到。我们使用伞式采样、受限分子动力学模拟和自由能计算，广泛研究了它与酵母 XPC 直系同源物 Rad4 的结合。双链体 DNA 中该损伤的 NMR 溶液结构表明，在不存在 XPC 的情况下，与加合 dG 互补的 dC 从 DNA 双链体中翻转出来。不过，目前尚不清楚“预翻转”的碱基是否会在其获得XPC的认可中发挥作用。我们的结果表明，Rad4 首先捕获移位的 dC，然后是紧密耦合的病变挤出途径以进行有效的结合。该结合路径与针对与错配胸腺嘧啶相对的小顺式-顺式环丁烷嘧啶二聚体损伤推断的结合路径显着不同[,(),((),),-]。导致与 XPC 有效结合的多种路径的可能性与成功 NER 所需的 XPC 多功能病变识别一致。
The xeroderma pigmentosum C protein complex (XPC) recognizes a variety of environmentally induced DNA lesions and is the key in initiating their repair by the nucleotide excision repair (NER) pathway. When bound to a lesion, XPC flips two nucleotide pairs that include the lesion out of the DNA duplex, yielding a productively bound complex that can lead to successful lesion excision. Interestingly, the efficiencies of NER vary greatly among different lesions, influencing their toxicity and mutagenicity in cells. Though differences in XPC binding may influence NER efficiency, it is not understood whether XPC utilizes different mechanisms to achieve productive binding with different lesions. Here, we investigated the well-repaired 10R-(+)-cis-anti-benzo[a]pyrene-N2-dG (cis-B[a]P-dG) DNA adduct in a duplex containing normal partner C opposite the lesion. This adduct is derived from the environmental pro-carcinogen benzo[a]pyrene and is likely to be encountered by NER in the cell. We have extensively investigated its binding to the yeast XPC orthologue, Rad4, using umbrella sampling with restrained molecular dynamics simulations and free energy calculations. The NMR solution structure of this lesion in duplex DNA has shown that the dC complementary to the adducted dG is flipped out of the DNA duplex in the absence of XPC. However, it is not known whether the “pre-flipped” base would play a role in its recognition by XPC. Our results show that Rad4 first captures the displaced dC, which is followed by a tightly coupled lesion-extruding pathway for productive binding. This binding path differs significantly from the one deduced for the small cis-syn cyclobutane pyrimidine dimer lesion opposite mismatched thymines [, () , ( (), ), −]. The possibility of multiple paths that lead to productive binding to XPC is consistent with the versatile lesion recognition by XPC that is required for successful NER.