Free Energy Landscape for the Entire Transport Cycle of Triose-Phosphate/Phosphate Translocator
Free Energy Landscape for the Entire Transport Cycle of Triose-Phosphate/Phosphate Translocator
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磷酸丙糖/磷酸转运蛋白整个运输循环的自由能景观
DOI：
10.1016/j.str.2018.05.012
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发表时间：
2018
期刊：
影响因子：
5.7
通讯作者：
Nureki O
中科院分区：
文献类型：
--
作者：
Takemoto M;Lee Y;Ishitani R;Nureki O
次级活性转运体利用其他化学物质的电化学势转移其底物，并经历大规模的构象变化。尽管进行了广泛的结构研究，但运输机制的原子细节仍然难以捉摸。我们对磷酸三糖/磷酸转运体(TPT)进行了一系列全原子分子动力学模拟，TPT在叶绿体基质中严格与无机磷(PI)进行反交换，输出有机磷。有偏采样方法，包括弦方法和伞形采样，成功地再现了向内和向外的状态之间的构象变化，以及底物结合。整个TPT过渡途径的自由能图谱显示了交替的通道和底物转运机制，这表明PII是通过带正电荷的残基沿着过渡途径传递的。此外，保守的Glu207还起到了“分子开关”的作用，连接了局部底物结合和整体构象转变。我们的结果为反转运蛋白的底物传输机制提供了原子细节的见解。
Secondary active transporters translocate their substrates using the electrochemical potentials of other chemicals and undergo large-scale conformational changes. Despite extensive structural studies, the atomic details of the transport mechanism still remain elusive. We performed a series of all-atom molecular dynamics simulations of the triose-phosphate/phosphate translocator (TPT), which exports organic phosphates in the chloroplast stroma in strict counter exchange with inorganic phosphate (Pi). Biased sampling methods, including the string method and umbrella sampling, successfully reproduced the conformational changes between the inward- and outward-facing states, along with the substrate binding. The free energy landscape of this entire TPT transition pathway demonstrated the alternating access and substrate translocation mechanisms, which revealed that Piis relayed by positively charged residues along the transition pathway. Furthermore, the conserved Glu207 functions as a "molecular switch", linking the local substrate binding and the global conformational transition. Our results provide atomic-detailed insights into the substrate transport mechanism of the antiporter.