Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization.
Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization.
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YhdE 二聚介导的 dTTP 结合和催化的分子动力学模拟研究
DOI：
10.1371/journal.pone.0134879
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Jia Z
中科院分区：
文献类型：
--
作者：
Wang N;Jiang J;Li X;Tan H;Zheng J;Chen G;Jia Z
YhdE 是一种 Maf 样（多拷贝相关丝化）蛋白，在细胞代谢途径中主要充当 dTTP 酶，将 dTTP 水解为 dTMP 和两个磷酸分子。先前已经确定了 YhdE 的两种晶体结构，分别代表开放和封闭的活性位点构象。基于这些结构，我们进行了分子动力学模拟和自由能计算，以研究 dTTP 与 YhdE 的结合和水解。我们的结果表明，YhdE 在室温下的闭合状态在结构上比其开放状态更紧凑。 YhdE开放态是有利于dTTP结合的构象，而闭合态是有利于催化反应的结构构象。这一观察结果得到了 YhdE 同源物与核苷酸类似物复合物结构的支持。自由能计算表明，YhdE二聚化优先发生在dTTP结合中，有利于连续的协同反应。研究发现关键残基 R11、R12 和 K80 有助于底物稳定。此外，YhdE二聚化和dTTP的结合通过YhdE中从催化中心的dTTP结合位点到YhdE二聚体的分子间β链的直接变构通讯网络诱导协同效应。
YhdE is a Maf-like (multicopy associated filamentation) protein that primarily acts as dTTPase to hydrolyze dTTP into dTMP and two phosphate molecules in cell metabolism pathway. Two crystal structures of YhdE have been previously determined, representing the open and closed active site conformations, respectively. Based on the structures, we have carried out molecular dynamics simulations and free energy calculations to investigate dTTP binding to and hydrolysis by YhdE. Our results suggest that YhdE closed state is structurally more compact than its open state at room temperature. YhdE open state is a favorable conformation for dTTP binding and closed state is a structurally favorable conformation for catalytic reaction. This observation is supported by the structure of YhdE homolog in complex with a nucleotide analog. Free energy calculations reveal that YhdE dimerization occurs preferentially in dTTP binding and is favorable for successive cooperative reaction. The key residues R11, R12 and K80, are found to contribute to the substrate stabilization. Further, YhdE dimerization and binding of dTTP induce the cooperative effect through a direct allosteric communication network in YhdE from the dTTP binding sites in the catalytic center to the intermolecular β-strand in YhdE dimer.