Sobeh Mohamed Marzouk, Kitao Akio
School of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
Physics Department, Faculty of Science, Ain Shams University, Cairo 11566, Egypt.
J Chem Inf Model. 2022 Mar 14;62(5):1294-1307. doi: 10.1021/acs.jcim.1c01508. Epub 2022 Mar 2.
p53 is a transcriptional factor that regulates cell response to a variety of stresses. About a half of all human tumors contain p53 mutations, and the accumulation of mutations in the DNA binding domain of p53 (p53-DBD) can cause destabilization of p53 and its complex with DNA. To identify the key residues of the p53-DBD/DNA binding and to understand the dissociation mechanisms of the p53-DBD/DNA complex, the dissociation process of p53-DBD from a DNA duplex that contains the consensus sequence (the specific target of p53-DBD) was investigated by a combination of dissociation parallel cascade selection molecular dynamics (dPaCS-MD) and the Markov state model (MSM). This combination (dPaCS-MD/MSM) enabled us to simulate dissociation of the two large molecules based on an all-atom model with a short simulation time (11.2 ± 2.2 ns per trial) and to analyze dissociation pathways, free energy landscape (FEL), and binding free energy. Among 75 trials of dPaCS-MD, p53-DBD dissociated first from the major groove and then detached from the minor groove in 93% of the cases, while 7% of the cases unbinding from the minor groove occurred first. Minor groove binding is mainly stabilized by R248, identified as the most important residue that tightly binds deep inside the minor groove. The standard binding free energy calculated from the FEL was -10.9 ± 0.4 kcal/mol, which agrees with an experimental value of -11.1 kcal/mol. These results indicate that the dPaCS-MD/MSM combination can be a powerful tool to investigate dissociation mechanisms of two large molecules. Analysis of the p53 key residues for DNA binding indicates high correlations with cancer-related mutations, confirming that impairment of the interactions between p53-DBD and DNA can be frequently related to cancer.
p53是一种转录因子，可调节细胞对多种应激的反应。大约一半的人类肿瘤含有p53突变，p53 DNA结合结构域（p53-DBD）中的突变积累可导致p53及其与DNA复合物的不稳定。为了确定p53-DBD/DNA结合的关键残基并了解p53-DBD/DNA复合物的解离机制，结合解离平行级联选择分子动力学（dPaCS-MD）和马尔可夫状态模型（MSM），研究了p53-DBD从包含共有序列（p53-DBD的特异性靶标）的DNA双链体上的解离过程。这种组合（dPaCS-MD/MSM）使我们能够基于全原子模型在短模拟时间内（每次试验11.2±2.2纳秒）模拟两个大分子的解离，并分析解离途径、自由能景观（FEL）和结合自由能。在75次dPaCS-MD试验中，93%的情况下p53-DBD首先从大沟解离，然后从小沟脱离，而7%的情况是首先从小沟解离。小沟结合主要由R248稳定，R248被确定为紧密结合在小沟深处的最重要残基。根据FEL计算的标准结合自由能为-10.9±0.4千卡/摩尔，与实验值-11.1千卡/摩尔一致。这些结果表明，dPaCS-MD/MSM组合可以成为研究两个大分子解离机制的有力工具。对p53 DNA结合关键残基的分析表明与癌症相关突变高度相关，证实p53-DBD与DNA之间相互作用的受损可能经常与癌症有关。
