p53四聚体显示出其C末端结构域与DNA结合结构域之间的诱导契合相互作用。

The p53 tetramer shows an induced-fit interaction of the C-terminal domain with the DNA-binding domain.

作者信息

D'Abramo M, Bešker N, Desideri A, Levine A J, Melino G, Chillemi G

机构信息

Dipartimento di Chimica, Sapienza University of Rome, Rome, Italy.

CINECA, SCAI-SuperComputing Applications and Innovation Department, Rome, Italy.

出版信息

Oncogene. 2016 Jun 23;35(25):3272-81. doi: 10.1038/onc.2015.388. Epub 2015 Oct 19.

Abstract

The Trp53 gene is the most frequently mutated gene in all human cancers. Its protein product p53 is a very powerful transcription factor that can activate different biochemical pathways and affect the regulation of metabolism, senescence, DNA damage response, cell cycle and cell death. The understanding of its function at the molecular level could be of pivotal relevance for therapy. Investigation of long-range intra- and interdomain communications in the p53 tetramer-DNA complex was performed by means of an atomistic model that included the tetramerization helices in the C-terminal domain, the DNA-binding domains and a consensus DNA-binding site of 18 base pairs. Nonsymmetric dynamics are illustrated in the four DNA-binding domains, with loop L1 switching from inward to outward conformations with respect to the DNA major groove. Direct intra- and intermonomeric long-range communications between the tetramerization and DNA-binding domains are noted. These long-distance conformational changes link the C terminus with the DNA-binding domain and provide a biophysical rationale for the reported functional regulation of the p53 C-terminal region. A fine characterization of the DNA deformation caused by p53 binding is obtained, with 'static' deformations always present and measured by the slide parameter in the central thymine-adenine base pairs; we also detect 'dynamic' deformations switched on and off by particular p53 tetrameric conformations and measured by the roll and twist parameters in the same base pairs. These different conformations can indeed modulate the electrostatic potential isosurfaces of the whole p53-DNA complex. These results provide a molecular/biophysical understanding of the evident role of the C terminus in post-translational modification that regulates the transcriptional function of p53. Furthermore, the unstructured C terminus is able to facilitate contacts between the core DNA-binding domains of the tetramer.

摘要

Trp53基因是所有人类癌症中最常发生突变的基因。其蛋白质产物p53是一种非常强大的转录因子,可激活不同的生化途径,并影响代谢、衰老、DNA损伤反应、细胞周期和细胞死亡的调控。在分子水平上对其功能的理解可能对治疗具有关键意义。通过一个原子模型对p53四聚体-DNA复合物中的长程域内和域间通讯进行了研究,该模型包括C端结构域中的四聚化螺旋、DNA结合结构域和一个18个碱基对的共有DNA结合位点。四个DNA结合结构域呈现出非对称动力学,环L1相对于DNA大沟从内向构象转变为外向构象。注意到四聚化结构域和DNA结合结构域之间存在直接的单体内部和单体间长程通讯。这些长距离构象变化将C末端与DNA结合结构域连接起来,并为报道的p53 C末端区域的功能调控提供了生物物理依据。获得了由p53结合引起的DNA变形的精细特征,“静态”变形始终存在,并通过中央胸腺嘧啶-腺嘌呤碱基对中的滑动参数进行测量;我们还检测到由特定p53四聚体构象开启和关闭的“动态”变形,并通过相同碱基对中的滚动和扭曲参数进行测量。这些不同的构象确实可以调节整个p53-DNA复合物的静电势等值面。这些结果为C末端在调节p53转录功能的翻译后修饰中的明显作用提供了分子/生物物理层面的理解。此外,无结构的C末端能够促进四聚体核心DNA结合结构域之间的接触。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6cd6/4929483/8c9fc4ddf4d0/onc2015388f1.jpg

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