Department of Computational and Systems Biology, School of Medicine , University of Pittsburgh , Pittsburgh , Pennsylvania 15260 , United States.
J Phys Chem B. 2018 May 31;122(21):5336-5346. doi: 10.1021/acs.jpcb.7b10340. Epub 2017 Dec 26.
Computational evaluation of the energetics of substrate binding, transport, and release events of neurotransmitter transporters at the molecular level is a challenge, as the structural transitions of these membrane proteins involve coupled global and local changes that span time scales of several orders of magnitude, from nanoseconds to seconds. Here, we provide a quantitative assessment of the energetics of dopamine (DA) translocation through the human DA transporter (hDAT), using a combination of molecular modeling, simulation, and analysis tools. DA-binding and -unbinding events, which generally involve local configurational changes, are evaluated using free-energy perturbation or adaptive biasing force methods. The global transitions between the outward-facing state and the inward-facing state, on the other hand, require a dual-boost accelerated molecular dynamics simulation. We present results on DA-binding/unbinding energetics under different conditions, as well as the conformational energy landscape of hDAT in both DA-bound and -unbound states. The study provides a tractable method of approach for quantitative evaluation of substrate-binding energetics and efficient estimation of conformational energy landscape, in general.
在分子水平上计算神经递质转运体的底物结合、转运和释放事件的能量学是一项挑战，因为这些膜蛋白的结构转变涉及耦合的全局和局部变化，跨越几个数量级的时间尺度，从纳秒到秒。在这里，我们使用分子建模、模拟和分析工具，对多巴胺（DA）通过人源多巴胺转运体（hDAT）的转运的能量学进行了定量评估。DA 结合和释放事件通常涉及局部构象变化，使用自由能微扰或自适应偏置力方法进行评估。另一方面，外向状态和内向状态之间的全局转变需要双重加速分子动力学模拟。我们给出了不同条件下 DA 结合/释放能学的结果，以及 DA 结合和未结合状态下 hDAT 的构象能量景观。该研究为定量评估底物结合能学和有效估计构象能量景观提供了一种可行的方法。
