Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE.
Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE.
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单向转运蛋白 GLUT1 和质子同向转运蛋白 XylE 的热力学和功能差异的分子决定因素
DOI：
10.1371/journal.pcbi.1005603
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发表时间：
2017-06
影响因子：
4.3
通讯作者：
Gong H
中科院分区：
文献类型：
--
作者：
Ke M;Yuan Y;Jiang X;Yan N;Gong H
在哺乳动物中，Glut1促进了D-葡萄糖跨细胞膜的下行转运。XylE是一种与GLUT1同源的大肠杆菌，它利用质子梯度作为能源来驱动D-木糖的上行运输。以往对XylE和GLUT1的研究表明，酸性残基(XylE中的Asp27)和中性残基(GLUT1中的Asn29)之间的差异是它们机制差异的关键因素。在这项工作中，我们结合计算和生化方法来研究XylE的质子耦合机制以及GLUT1和XylE之间的功能差异。利用分子动力学模拟，我们评估了载脂蛋白内向和向外构象转变的自由能分布。我们的结果揭示了质子化状态与XylE的构象择优之间的关系，这是由晶体结构支持的。此外，我们的模拟表明，XylE和GLUT1之间的热力学差异不能用质子化位置上的单个残基变化来解释。为了了解分子基础，我们应用贝叶斯网络模型分析了构象转变过程中氢键网络结构的变化。这些模型和随后的实验验证表明，需要多次残基取代才能产生XylE和GLUT1之间的热力学和功能差异。尽管缺乏对底物的模拟研究，但这些计算和生化表征提供了前所未有的对质子转运体和单转运体之间的机制差异的洞察。
GLUT1 facilitates the down-gradient translocation of D-glucose across cell membrane in mammals. XylE, an Escherichia coli homolog of GLUT1, utilizes proton gradient as an energy source to drive uphill D-xylose transport. Previous studies of XylE and GLUT1 suggest that the variation between an acidic residue (Asp27 in XylE) and a neutral one (Asn29 in GLUT1) is a key element for their mechanistic divergence. In this work, we combined computational and biochemical approaches to investigate the mechanism of proton coupling by XylE and the functional divergence between GLUT1 and XylE. Using molecular dynamics simulations, we evaluated the free energy profiles of the transition between inward- and outward-facing conformations for the apo proteins. Our results revealed the correlation between the protonation state and conformational preference in XylE, which is supported by the crystal structures. In addition, our simulations suggested a thermodynamic difference between XylE and GLUT1 that cannot be explained by the single residue variation at the protonation site. To understand the molecular basis, we applied Bayesian network models to analyze the alteration in the architecture of the hydrogen bond networks during conformational transition. The models and subsequent experimental validation suggest that multiple residue substitutions are required to produce the thermodynamic and functional distinction between XylE and GLUT1. Despite the lack of simulation studies with substrates, these computational and biochemical characterizations provide unprecedented insight into the mechanistic difference between proton symporters and uniporters.
影响因子：
2.9
作者：
Thomas, James R.;Gedeon, Patrick C.;Madura, Jeffry D.
通讯作者：
Madura, Jeffry D.