p53极端C末端结构域的瞬态流形结构:通过分子动力学模拟洞察无序、识别和结合多特异性
The transient manifold structure of the p53 extreme C-terminal domain: insight into disorder, recognition, and binding promiscuity by molecular dynamics simulations.
作者信息
Fadda E, Nixon M G
机构信息
Department of Chemistry, Maynooth University, and Hamilton Institute, Maynooth University, Maynooth, Kildare, Ireland.
出版信息
Phys Chem Chem Phys. 2017 Aug 16;19(32):21287-21296. doi: 10.1039/c7cp02485a.
The p53 tumour suppressor is a transcription activator that signals for cell cycle arrest and apoptosis. In its active form p53 is a tetramer, with each monomer organised in domains with different degrees of structural stability, ranging from the well folded DNA-binding domain (DBD) and tetramerization domain (TET), to the intrinsically disordered transactivation domain (TAD), and extreme C-terminal domain (CTD). Compared to all other domains, the structure/function relationship of the p53-CTD within the full-length p53 tetramer is still poorly understood due to its high degree of conformational disorder. Meanwhile, the structure of p53-CTD-like peptides has been well characterized when in complex with a variety of receptors, where, as other intrinsically disordered regions (IDR), it adopts specific, while diverse, conformations. Receptor-specific folding is likely to occur upon binding, either from a random coil, or as a result of an initial recognition of a pre-formed structural motif, known as molecular recognition feature (MoRF), selected by the receptor within the conformational ensemble of the IDP in solution. In this latter case, MoRFs act as nucleation sites, favouring the initiation of the folding process within the binding site. In this work we show the results of over 20 μs of cumulative molecular dynamics (MD) simulations of a 22 residue peptide unbound in solution with sequence corresponding to the p53-CTD 367-388 section. Such extensive sampling allowed us to identify and characterize the structure of specific sets of minimal structural MoRFs within the p53-CTD peptide conformational ensemble at equilibrium. These motifs are short, involving only 3 to 4 residues, and specifically localized within the peptide sequence. Corresponding patterns of secondary structure propensity along the p53-CTD sequence are also predicted by disorder prediction calculations. Based on these findings we discuss how the structural complementarity of specific minimal structural MoRFs to the binding site of different receptors could regulate the p53-CTD binding promiscuity.
p53肿瘤抑制因子是一种转录激活因子,可发出细胞周期停滞和凋亡信号。处于活性形式的p53是一种四聚体,每个单体由具有不同结构稳定性程度的结构域组成,从折叠良好的DNA结合结构域(DBD)和四聚化结构域(TET),到内在无序的反式激活结构域(TAD)和极端C末端结构域(CTD)。与所有其他结构域相比,全长p53四聚体内p53-CTD的结构/功能关系由于其高度的构象无序性而仍未得到很好的理解。同时,当与多种受体结合时,p53-CTD样肽的结构已得到很好的表征,在这种情况下,它与其他内在无序区域(IDR)一样,会采用特定但多样的构象。受体特异性折叠可能在结合时发生,要么从无规卷曲开始,要么是由于受体在溶液中IDP的构象集合中选择的预先形成的结构基序(称为分子识别特征,MoRF)的初始识别结果。在后一种情况下,MoRF充当成核位点,有利于在结合位点内启动折叠过程。在这项工作中,我们展示了对一个22个残基的肽进行超过20微秒的累积分子动力学(MD)模拟的结果,该肽在溶液中未结合,其序列对应于p53-CTD 367-388片段。如此广泛的采样使我们能够识别和表征处于平衡状态的p53-CTD肽构象集合内特定最小结构MoRF的特定集合的结构。这些基序很短,仅涉及3至4个残基,并且特定地定位在肽序列内。沿着p53-CTD序列的二级结构倾向的相应模式也通过无序预测计算进行了预测。基于这些发现我们讨论了特定最小结构MoRF与不同受体结合位点的结构互补性如何调节p53-CTD的结合多特异性。