Lambrughi Matteo, De Gioia Luca, Gervasio Francesco Luigi, Lindorff-Larsen Kresten, Nussinov Ruth, Urani Chiara, Bruschi Maurizio, Papaleo Elena
Computational Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Strandboulevarden 49, 2100, Copenhagen, Denmark.
Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
Nucleic Acids Res. 2016 Nov 2;44(19):9096-9109. doi: 10.1093/nar/gkw770. Epub 2016 Sep 6.
Binding-induced conformational changes of a protein at regions distant from the binding site may play crucial roles in protein function and regulation. The p53 tumour suppressor is an example of such an allosterically regulated protein. Little is known, however, about how DNA binding can affect distal sites for transcription factors. Furthermore, the molecular details of how a local perturbation is transmitted through a protein structure are generally elusive and occur on timescales hard to explore by simulations. Thus, we employed state-of-the-art enhanced sampling atomistic simulations to unveil DNA-induced effects on p53 structure and dynamics that modulate the recruitment of cofactors and the impact of phosphorylation at Ser215. We show that DNA interaction promotes a conformational change in a region 3 nm away from the DNA binding site. Specifically, binding to DNA increases the population of an occluded minor state at this distal site by more than 4-fold, whereas phosphorylation traps the protein in its major state. In the minor conformation, the interface of p53 that binds biological partners related to p53 transcription-independent functions is not accessible. Significantly, our study reveals a mechanism of DNA-mediated protection of p53 from interactions with partners involved in the p53 transcription-independent signalling. This also suggests that conformational dynamics is tightly related to p53 signalling.
蛋白质在远离结合位点的区域发生的结合诱导构象变化可能在蛋白质功能和调控中发挥关键作用。p53肿瘤抑制蛋白就是这样一种变构调节蛋白的例子。然而，关于DNA结合如何影响转录因子的远端位点，人们知之甚少。此外，局部扰动如何通过蛋白质结构进行传递的分子细节通常难以捉摸，且发生在模拟难以探索的时间尺度上。因此，我们采用了最先进的增强采样原子模拟，以揭示DNA对p53结构和动力学的影响，这些影响调节了辅因子的募集以及Ser215位点磷酸化的影响。我们表明，DNA相互作用促进了距DNA结合位点3纳米处区域的构象变化。具体而言，与DNA结合使该远端位点处一种被封闭的次要状态的丰度增加了4倍以上，而磷酸化则使蛋白质被困在其主要状态。在次要构象中，p53与参与p53非转录依赖性功能的生物伴侣结合的界面无法接近。重要的是，我们的研究揭示了一种DNA介导的保护p53免受与参与p53非转录依赖信号传导的伴侣相互作用的机制。这也表明构象动力学与p53信号传导密切相关。
