Computational Investigation on the p53-MDM2 Interaction Using the Potential of Mean Force Study
Computational Investigation on the p53-MDM2 Interaction Using the Potential of Mean Force Study
复制标题
DOI：
10.1021/acsomega.9b03372
复制
发表时间：
2020-04-21
期刊：
影响因子：
4.1
通讯作者：
Mattaparthi, Venkata Satish Kumar
中科院分区：
文献类型：
--
作者：
Das, Pundarikaksha;Mattaparthi, Venkata Satish Kumar
小鼠双分钟2(MDM2)蛋白被发现在许多人类肿瘤中过度产生，以抑制肿瘤抑制蛋白P53分子的功能。因此，通过破坏P53-MDM2的相互作用来重新激活癌细胞中的P53功能，可能为癌症治疗提供一种重要的途径。然而，P53-MDM2复合体在原子水平上的结构特征以及P53-MDM2复合体的结合/解离机制仍不清楚。因此，我们在这里用两个不同的力场：ff99SB和ff99SB-ILDN，根据自由能作为反应坐标的函数，证明了在p53-MDM2复合体的形成(解离)过程中，p53的反式激活结构域1可能的结合(解离)途径。从PMF图中，我们注意到PMF在P53-MDM2分离12埃时有一个最小值，解离能为30千卡摩尔(-1)。我们还分析了P53的构象动力学和稳定性与其与MDM2的分离距离的关系。P53的二级结构含量(螺旋和转角)随其与MDM2的分离距离而变化。在与最小PMF值对应的反应坐标上，从系综中分离出势能最低的P53-MDM2复合体结构，并进行分子动力学模拟，以确定界面表面积、界面上的相互作用残基以及复合体的稳定性。模拟结果强调了MDM2的Lys94和P53的Glu17之间的氢键和盐桥对P53-MDM2复合体稳定性的重要性。我们还对P53-MDM2复合体的界面残基进行了结合自由能计算和每残基能量分解分析。我们发现MDM2与P53之间的结合亲和力确实很高[从分子力学/泊松-玻尔兹曼表面积(MM/PBSA)计算的增量G(绑定)=-7.29kcal摩尔(-1)，从分子力学/广义承载表面积计算的增量G(绑定)=-53.29kcal摩尔(-1)]。用MM/PBSA方法得到的总结合能更接近实验值(-6.4~-9.0kcal摩尔~(-1))。甚至在重复的模拟运行中以及在不同力场进行的模拟中，也观察到P53-MDM2复合体结合谱遵循相同的趋势。我们发现来自MDM2的Lys51、Leu54、Tyr100和Tyr104以及来自p53的残基Phe19、Trp23和Leu26为p53-MDM2的相互作用提供了最高的能量贡献。我们的发现突出了p53-MDM2复合体的显著结构和结合特征，这可能有助于设计潜在的抑制剂来破坏p53-MDM2的相互作用。
Murine double minute 2 (MDM2) proteins are found to be overproduced by many human tumors in order to inhibit the functioning of p53 molecules, a tumor suppressor protein. Thus, reactivating p53 functioning in cancer cells by disrupting p53-MDM2 interactions may offer a significant approach in cancer treatment. However, the structural characterization of the p53-MDM2 complex at the atomistic level and the mechanism of binding/unbinding of the p53-MDM2 complex still remain unclear. Therefore, we demonstrate here the probable binding (unbinding) pathway of transactivation domain 1 of p53 during the formation (dissociation) of the p53-MDM2 complex in terms of free energy as a function of reaction coordinate from the potential of mean force (PMF) study using two different force fields: ff99SB and ff99SB-ILDN. From the PMF plot, we noticed the PMF to have a minimum value at a p53-MDM2 separation of 12 angstrom, with a dissociation energy of 30 kcal mol(-1). We also analyzed the conformational dynamics and stability of p53 as a function of its distance of separation from MDM2. The secondary structure content (helix and turns) in p53 was found to vary with its distance of separation from MDM2. The p53-MDM2 complex structure with lowest potential energy was isolated from the ensemble at the reaction coordinate corresponding to the minimum PMF value and subjected to molecular dynamics simulation to identify the interface surface area, interacting residues at the interface, and the stability of the complex. The simulation results highlight the importance of hydrogen bonds and the salt bridge between Lys94 of MDM2 and Glu17 of p53 in the stability of the p53-MDM2 complex. We also carried out the binding free energy calculations and the per residue energy decomposition analyses of the interface residues of the p53-MDM2 complex. We found that the binding affinity between MDM2 and p53 is indeed high [Delta G(bind) = -7.29 kcal mol(-1) from molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) and Delta G(bind) = -53.29 kcal mol(-1) from molecular mechanics/generalized borne surface area]. The total binding energy obtained using the MM/PBSA method was noticed to be closer to the experimental values (-6.4 to -9.0 kcal mol(-1)). The p53-MDM2 complex binding profile was observed to follow the same trend even in the duplicate simulation run and also in the simulation carried out with different force fields. We found that Lys51, Leu54, Tyr100, and Tyr104 from MDM2 and the residues Phe19, Trp23, and Leu26 from p53 provide the highest energy contributions for the p53-MDM2 interaction. Our findings highlight the prominent structural and binding characteristics of the p53-MDM2 complex that may be useful in designing potential inhibitors to disrupt the p53-MDM2 interactions.