A kinetic mechanism for enhanced selectivity of membrane transport
A kinetic mechanism for enhanced selectivity of membrane transport
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DOI：
10.1371/journal.pcbi.1007789
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发表时间：
2020-07-01
影响因子：
4.3
通讯作者：
Rosenberg, John M.
中科院分区：
文献类型：
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作者：
Bisignano, Paola;Lee, Michael A.;Rosenberg, John M.
通常认为膜转运是通过交替进入机制发生的，其中转运蛋白采用至少两种状态，可从膜的两侧进入，以交换来自细胞外环境和细胞质或来自细胞质和细胞器的细胞内基质的底物（仅在真核生物中）。近年来，许多高分辨率结构支持了多种运输分子的通用框架，尽管运输路径上的其他状态正在变得至关重要。鉴于为了提高整体转运速率，底物结合通常较弱，因此转运蛋白很可能转运错误的底物。对于许多被肠道吸收或通过内源性转运蛋白穿过血脑屏障的药物化合物来说，情况确实如此。对细菌糖转运蛋白 vSGLT 的对接研究表明，许多剧毒化合物与正位点的结合相容，进一步激发了其他选择性模式的选择压力。受最近的研究的启发，我们在分子动力学模拟中观察到底物输送失败，其中通电的离子仍然下降其浓度梯度，我们假设一些转运蛋白进化到利用这种“滑动”机制来增加底物选择性并减少有毒分子的摄取。在这里，我们通过构建和探索包含滑移路径的动力学传输模型来测试这个想法。虽然滑移降低了总体生产通量，但当与更容易滑移的第二种有毒分子结合时，总体底物选择性显着增加，抑制了错误化合物的积累。我们表明，在我们的模型中增加底物选择性的数学框架类似于最初为 tRNA 合酶提出的经典校对机制；然而，由于运输循环是可逆的，我们确定了选择性基本上是无限的并且以“解毒”模式从细胞中输出不正确的底物的条件。讨论了校对和膜滑移的细胞后果以及对未来药物开发的影响。
Membrane transport is generally thought to occur via an alternating access mechanism in which the transporter adopts at least two states, accessible from two different sides of the membrane to exchange substrates from the extracellular environment and the cytoplasm or from the cytoplasm and the intracellular matrix of the organelles (only in eukaryotes). In recent years, a number of high resolution structures have supported this general framework for a wide class of transport molecules, although additional states along the transport pathway are emerging as critically important. Given that substrate binding is often weak in order to enhance overall transport rates, there exists the distinct possibility that transporters may transport the incorrect substrate. This is certainly the case for many pharmaceutical compounds that are absorbed in the gut or cross the blood brain barrier through endogenous transporters. Docking studies on the bacterial sugar transporter vSGLT reveal that many highly toxic compounds are compatible with binding to the orthosteric site, further motivating the selective pressure for additional modes of selectivity. Motivated by recent work in which we observed failed substrate delivery in a molecular dynamics simulation where the energized ion still goes down its concentration gradient, we hypothesize that some transporters evolved to harness this 'slip' mechanism to increase substrate selectivity and reduce the uptake of toxic molecules. Here, we test this idea by constructing and exploring a kinetic transport model that includes a slip pathway. While slip reduces the overall productive flux, when coupled with a second toxic molecule that is more prone to slippage, the overall substrate selectivity dramatically increases, suppressing the accumulation of the incorrect compound. We show that the mathematical framework for increased substrate selectivity in our model is analogous to the classic proofreading mechanism originally proposed for tRNA synthase; however, because the transport cycle is reversible we identified conditions in which the selectivity is essentially infinite and incorrect substrates are exported from the cell in a 'detoxification' mode. The cellular consequences of proofreading and membrane slippage are discussed as well as the impact on future drug development.