走向In Situ DNA结合的全长p53四聚合物的动力学
Özlem Demir1,2, Emilia P Barros1,3, Rommie E Amaro4
1Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA.
bioRxiv : the preprint server for biology
|November 24, 2025
概括
恢复瘤抑制剂p53的活性是一种有前途的癌症治疗方法. 这项研究模拟了全长的p53四分体,揭示了其DNA相互作用和动态,包括癌症突变.
科学领域:
- 分子生物学分子生物学
- 生物物理学的生物物理.
- 计算生物学 计算生物学
背景情况:
- 蛋白质p53是一种关键的人类瘤抑制剂,在约50%的癌症中经常因突变而失活.
- 恢复p53活性是一种备受追捧的癌症治疗策略,在临床前模型中显示出前景.
- 全长的p53 (fl-p53) 是一种多域蛋白质,其结构和动态在生理学上是复杂的.
研究的目的:
- 为了生成与DNA结合的野生类型全长p53四度体的第一个原子模型.
- 通过使用先进的计算模拟来研究野生类型和突变p53的构造景观和动态.
- 了解p53四重化和癌症突变如何影响其DNA结合和整体结构.
主要方法:
- 综合分子建模结合了晶体结构和无序域建模.
- 在显式溶剂中安东2超级计算机上微秒级的分子动力学模拟.
- 马尔科夫状态建模 (MSM) 来分析构造景观并确定关键动态特征.
- 分析DNA曲,蛋白质与蛋白质相互作用,以及可用药物的口袋动态.
主要成果:
- 产生了DNA结合的野生型fl-p53四聚体的详细模型,揭示了DNA曲和紧的复合体形成.
- 由于二次元-二次元接口,观察到内部和外部p53DNA结合域 (DBDs) 之间的不同动态.
- 野生类型的p53四重体采用了一个独特的四级DBD组织,这种组织在分析的癌症突变中没有发现 (Y220C,G245S).
- 在循环6 (L6) 中发现了一个未被探索的加密口袋,并捕获了四重化和突变对其动态的影响.
结论:
- 这项研究为与DNA结合的全长p53四分体的结构动态提供了前所未有的见解.
- 癌症突变和四重化显著改变了p53的结构格局和动态,特别是影响了DBD组织和神秘口袋的可访问性.
- 这些发现为开发针对癌症p53重新激活的新型治疗策略奠定了基础.
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