a International Joint Research Laboratory of Nano-Micro Architecture Chemistry, Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry , Jilin University , Changchun 130023 , People's Republic of China.
b Key Laboratory for Molecular Enzymology & Engineering, The Ministry of Education, School of Life Sciences , Jilin University , Changchun 130023 , People's Republic of China.
J Biomol Struct Dyn. 2019 Feb;37(3):562-575. doi: 10.1080/07391102.2018.1433066. Epub 2018 Feb 12.
The Wilms' tumour suppressor protein (WT1) plays a multifaceted role in human cancer processes. Mutations on its DNA recognition domain could lead to Denys-Drash syndrome, and alternate splicing results in insertion of the tripeptide Lys-Thr-Ser (KTS) between the third and fourth zinc fingers (ZFs), leading to changes in the DNA-binding function. However, detailed recognition mechanisms of the WT1-DNA complex have not been explored. To clarify the mutational effects upon WT1 towards DNA binding at the atomic level, molecular dynamics simulations and the molecular mechanics/Poisson Boltzmann surface area (MM/PBSA) method were employed. The simulation results indicate that mutations in ZF domains (E427Q and Q369H) may weaken the binding affinity, and the statistical analyses of the hydrogen bonds and hydrophobic interactions show that eight residues (Lys351, Arg366, Arg375, Arg376, Lys399, Arg403, Arg424 and Arg430) have a significant influence on recognition and binding to DNA. Insertion of the tripeptide KTS could form an immobilized hydrogen-bonding network with Arg403, affecting the flexibility and angle of the linker between ZF3 and ZF4, thus influencing the recognition between the protein and the DNA triplet at its 5' terminus. These results represent the first step towards a thorough characterization of the WT1 recognition mechanisms, providing a better understanding of the structure-function relationship of WT1 and its mutants.
Wilms 瘤抑制蛋白（WT1）在人类癌症过程中发挥着多方面的作用。其 DNA 识别域的突变可导致 Denys-Drash 综合征，而交替剪接导致三肽 Lys-Thr-Ser（KTS）插入第三和第四个锌指（ZF）之间，导致 DNA 结合功能发生变化。然而，WT1-DNA 复合物的详细识别机制尚未得到探索。为了在原子水平上阐明 WT1 突变对 DNA 结合的影响，采用分子动力学模拟和分子力学/泊松-玻尔兹曼表面积（MM/PBSA）方法。模拟结果表明，ZF 结构域（E427Q 和 Q369H）的突变可能会削弱结合亲和力，氢键和疏水相互作用的统计分析表明，有八个残基（Lys351、Arg366、Arg375、Arg376、Lys399、Arg403、Arg424 和 Arg430）对识别和与 DNA 结合有重大影响。插入三肽 KTS 可以与 Arg403 形成固定的氢键网络，影响 ZF3 和 ZF4 之间连接区的灵活性和角度，从而影响蛋白与 DNA 三核苷酸 5'末端的识别。这些结果代表了对 WT1 识别机制进行全面表征的第一步，为更好地理解 WT1 及其突变体的结构-功能关系提供了依据。
