Metal binding mediated conformational change of XPA protein:a potential cytotoxic mechanism of nickel in the nucleotide excision repair.
Metal binding mediated conformational change of XPA protein:a potential cytotoxic mechanism of nickel in the nucleotide excision repair.
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DOI：
10.1007/s00894-016-3017-x
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发表时间：
2016-07
影响因子：
2.2
通讯作者：
Xie XQ
中科院分区：
文献类型：
--
作者：
Hu J;Hu Z;Zhang Y;Gou X;Mu Y;Wang L;Xie XQ
核苷酸切除修复（Nucleotide excision repair，NER）是修复由化学物质、金属离子、辐射等因素引起的DNA核苷酸错配的重要生命过程。作为NER的起始步骤，着色性干皮病互补组A蛋白（XPA）识别受损的DNA分子，并招募复制蛋白A（RPA），这是NER过程中的另一个重要参与者。XPA中心核心部分的Zn 2+螯合的Zn指结构域（即，XPA 98 -210）是其生物功能的基础，而有毒金属离子（如Ni 2+，一种已知的人类致癌物和过敏原）对Zn 2+的置换可能会削弱NER的有效性，从而增加致癌的机会。在本研究中，我们首先计算了XPA 98 -210体系金属中心的键合模型的力场参数，表明计算结果，包括电荷、键、角度等，与以前报道的光谱实验和量子化学计算结果一致。利用这些参数进行比较分子动力学模拟，揭示了Ni 2+取代Zn 2+后XPA 98 -210锌指结构的构象和运动模式的变化。结果表明，Ni 2+显著破坏了锌指结构中四个Cys残基的相对位置，迫使它们从四面体坍塌成几乎平面的结构。最后，通过分子对接和结构比对，获得了XPA 98 -210与其配体RPA 70 N和DNA的结合模式。我们发现XPA 98 -210的锌指结构域主要与RPA 70 N中的V形裂缝结合，而其C端亚结构域中的阳离子带参与识别受损的DNA。此外，这篇文章揭示了XPA，DNA和其他NER相关蛋白（即，RPA 70 N、RPA 70 A、RPA 70 B、RPA 70 C、RPA 32和RPA 14）基于之前报告的结构生物学信息。因此，我们推导出了一种与镍离子相关的推定细胞毒性机制，其中Ni 2+破坏了XPA锌指的构象，直接削弱了其与RPA 70 N的相互作用，从而降低了NER过程的有效性。总之，这项工作不仅提供了一个理论上的洞察，在NER过程中涉及的多蛋白质相互作用和潜在的细胞毒性机制与Ni 2+结合在XPA，但也可能有助于合理的抗癌药物设计的基础上NER机制。
Nucleotide excision repair (NER) is a pivotal life process for repairing DNA nucleotide mismatch caused by chemicals, metal ions, radiation, and other factors. As the initiation step of NER, the xeroderma pigmentosum complementation group A protein (XPA) recognizes damaged DNA molecules, and recruits the replication protein A (RPA), another important player in the NER process. The stability of the Zn2+-chelated Zn-finger domain of XPA center core portion (i.e., XPA98–210) is the foundation of its biological functionality, while the displacement of the Zn2+ by toxic metal ions (such as Ni2+, a known human carcinogen and allergen) may impair the effectiveness of NER and hence elevate the chance of carcinogenesis. In this study, we first calculated the force field parameters for the bonded model in the metal center of the XPA98–210 system, showing that the calculated results, including charges, bonds, angles etc., are congruent with previously reported results measured by spectrometry experiments and quantum chemistry computation. Then, comparative molecular dynamics simulations using these parameters revealed the changes in the conformation and motion mode of XPA98–210 Zn-finger after the substitution of Zn2+ by Ni2+. The results showed that Ni2+ dramatically disrupted the relative positions of the four Cys residues in the Zn-finger structure, forcing them to collapse from a tetrahedron into an almost planar structure. Finally, we acquired the binding mode of XPA98–210 with its ligands RPA70N and DNA based on molecular docking and structural alignment. We found that XPA98–210’s Zn-finger domain primarily binds to a V-shaped cleft in RPA70N, while the cationic band in its C-terminal subdomain participates in the recognition of damaged DNA. In addition, this article sheds light on the multi-component interaction pattern among XPA, DNA, and other NER-related proteins (i.e., RPA70N, RPA70A, RPA70B, RPA70C, RPA32, and RPA14) based on previously reported structural biology information. Thus, we derived a putative cytotoxic mechanism associated with the nickel ion, where the Ni2+ disrupts the conformation of the XPA Zn-finger, directly weakening its interaction with RPA70N, and thus lowering the effectiveness of the NER process. In sum, this work not only provides a theoretical insight into the multi-protein interactions involved in the NER process and potential cytotoxic mechanism associated with Ni2+ binding in XPA, but may also facilitate rational anti-cancer drug design based on the NER mechanism.