CAS-MPG Partner Institute for Computational Biology, Key laboratory of Computational Biology, Chinese Academy of Sciences, Shanghai, China.
PLoS Comput Biol. 2009 Nov;5(11):e1000574. doi: 10.1371/journal.pcbi.1000574. Epub 2009 Nov 20.
Many fundamental cellular processes such as gene expression are tightly regulated by protein allostery. Allosteric signal propagation from the regulatory to the active site requires long-range communication, the molecular mechanism of which remains a matter of debate. A classical example for long-range allostery is the activation of the methionine repressor MetJ, a transcription factor. Binding of its co-repressor SAM increases its affinity for DNA several-fold, but has no visible conformational effect on its DNA binding interface. Our molecular dynamics simulations indicate correlated domain motions within MetJ, and quenching of these dynamics upon SAM binding entropically favors DNA binding. From monitoring conformational fluctuations alone, it is not obvious how the presence of SAM is communicated through the largely rigid core of MetJ and how SAM thereby is able to regulate MetJ dynamics. We here directly monitored the propagation of internal forces through the MetJ structure, instead of relying on conformational changes as conventionally done. Our force distribution analysis successfully revealed the molecular network for strain propagation, which connects collective domain motions through the protein core. Parts of the network are directly affected by SAM binding, giving rise to the observed quenching of fluctuations. Our results are in good agreement with experimental data. The force distribution analysis suggests itself as a valuable tool to gain insight into the molecular function of a whole class of allosteric proteins.
许多基本的细胞过程，如基因表达，都受到蛋白质变构的严格调控。变构信号从调节部位到活性部位的传递需要长程通讯，其分子机制仍存在争议。长程变构的一个经典例子是甲硫氨酸阻遏物 MetJ 的激活，这是一种转录因子。其共抑制剂 SAM 的结合使其对 DNA 的亲和力增加几倍，但对其 DNA 结合界面没有明显的构象效应。我们的分子动力学模拟表明 MetJ 内的相关结构域运动，并且 SAM 结合时这些动力学的猝灭使 DNA 结合具有优势。仅从监测构象波动来看，尚不清楚 SAM 如何通过 MetJ 的刚性核心传递，以及 SAM 如何能够调节 MetJ 的动力学。我们在这里直接监测内部力通过 MetJ 结构的传播，而不是像传统方法那样依赖构象变化。我们的力分布分析成功地揭示了应变传播的分子网络，该网络通过蛋白质核心连接集体结构域运动。网络的一部分直接受到 SAM 结合的影响，导致观察到的波动猝灭。我们的结果与实验数据吻合良好。力分布分析本身可以作为一种有价值的工具，深入了解整个变构蛋白类别的分子功能。
