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中国物理学会期刊

p53活性四聚体全原子分子动力学分析

CSTR: 32037.14.aps.73.20231515

Full-atomistic molecular dynamics analysis of p53 active tetramer

CSTR: 32037.14.aps.73.20231515
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  • p53是一种肿瘤抑制蛋白, 对阻碍癌症发展、维持遗传完整性起着至关重要的作用. 在细胞核内, 4个p53分子通过高度协同的方式、通过DNA结合域与DNA结合, 形成稳定的四聚体活性结构, 并转录激活或抑制其靶向基因. 然而, 大多数肿瘤细胞中存在大量p53的突变, 其中绝大部分突变发生在p53的DNA结合域, 而p53的DNA结合域又是p53形成四聚体活性结构、调控下游靶基因转录的重要区域. 本文通过全原子分子动力学模拟, 研究了野生型p53四聚体内分子间的相互作用机制. 结果表明, 位于DNA两侧的对称二聚体是一个稳定的二聚体, 在与DNA结合前后都能维持稳定的结构. 位于DNA同侧的两个单体依靠两个接触面提供的蛋白-蛋白相互作用和DNA的骨架作用使四聚体活性结构保持稳定, 这些相互作用为四聚体的形成机制提供了重要支撑. 该工作厘清了p53四聚体在动力学过程中的内部相互作用机制和关键残基, 揭示了四聚化过程中各个相互作用界面的关键位点, 对于理解p53的抑癌机制、探索有效治癌策略、发展治癌药物具有重要意义.

     

    p53 is a tumor suppressor protein that plays a crucial role in inhibiting cancer development and maintaining the genetic integrity. Within the cell nucleus, four p53 molecules constitute a stable tetrameric active structure through highly cooperative interactions, bind to DNA via its DNA-binding domain, and transcriptionally activate or inhibit their target genes. However, in most human tumor cells, there are numerous p53 mutations. The majority of these mutations are formed in the p53 DNA-binding domain, importantly, the p53 DNA-binding domain is critical for p53 to form the tetrameric active structures and to regulate the transcription of its downstream target genes. In this work, the all-atom molecular dynamics simulation is conducted to investigate the mechanism of interaction within the wild-type p53 tetramers. This study indicates that the symmetric dimers on either side of the DNA are stable ones, keeping stable structures before and after DNA binding. The binding of two monomers on the same side of the DNA depends on protein-protein interaction provided by two contact surfaces. DNA scaffold stabilizes the tetrameric active structure. Such interactions crucially contribute to the tetramer formation. This study clarifies the internal interactions and key residues within the p53 tetramer in dynamic process, as well as the critical sites at various interaction interfaces. The findings of this study may provide a significant foundation for us to further understand the p53’s anticancer mechanisms, to explore the effective cancer treatment strategies, and in near future, to develop the effective anti-cancer drugs.

     

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