Conformational dynamics and putative substrate extrusion pathways of the N -glycosylated outer membrane factor CmeC from Campylobacter jejuni
Conformational dynamics and putative substrate extrusion pathways of the N -glycosylated outer membrane factor CmeC from Campylobacter jejuni
复制标题
空肠弯曲杆菌 N-糖基化外膜因子 CmeC 的构象动力学和假定底物挤出途径
DOI：
10.1101/2022.08.31.506067
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发表时间：
2022
期刊：
影响因子：
--
通讯作者：
Newman K
中科院分区：
文献类型：
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作者：
Newman K
外排机制CmeABC的外膜因子CmeC在赋予空肠弯曲菌抗生素和胆汁抗性中起重要作用。奇怪的是，这种机制中的蛋白质是N-糖基化的，聚糖在外排系统的有效功能中起着关键作用。在这里，我们采用原子平衡分子动力学模拟的CmeC在一个代表性的模型的C。空肠外膜的蛋白质及其相关聚糖的动力学。我们表明，N-聚糖是更构象不稳定比以前认为的。CmeC的细胞外环自由地访问开放和闭合状态，表明在这一侧不存在门控机制，而狭窄的周质入口保持紧密闭合，通过与溶剂化阳离子的配位来调节。我们确定了几个阳离子结合位点的蛋白质的内表面上。此外，我们已经使用转向分子动力学模拟来阐明胆汁酸，鹅去氧胆酸，和大环内酯类抗生素，红霉素的易位途径。这些和额外的平衡模拟表明，阴离子胆汁酸利用多价阳离子爬上酸性残基的梯子，该梯子排列在蛋白质的内表面。结合起来，这些结果进一步了解外膜因子的动力学，并允许深入了解抗生素和其他已知底物在该区域的外排机制的易位途径。
The outer membrane factor CmeC of the efflux machinery CmeABC plays an important role in conferring antibiotic and bile resistance to Campylobacter jejuni. Curiously, the proteins in this machinery are N-glycosylated, with the glycans playing a key role in the effective function of the efflux system. Here we have employed atomistic equilibrium molecular dynamics simulations of CmeC in a representative model of the C. jejuni outer membrane to characterise the dynamics of the protein and its associated glycans. We show that the N-glycans are more conformationally labile than had previously been thought. The extracellular loops of CmeC visit the open and closed states freely suggesting the absence of a gating mechanism on this side, while the narrow periplasmic entrance remains tightly closed, regulated via coordination to solvated cations. We identify several cation binding sites on the interior surface of the protein. Additionally, we have used steered molecular dynamics simulations to elucidate translocation pathways for a bile acid, chenodeoxycholic acid, and a macrolide antibiotic, erythromycin. These, and additional equilibrium simulations suggest that the anionic bile acid utilizes multivalent cations to climb a ladder of acidic residues that line the interior surface of the protein. In combination, these results further our understanding of the dynamics of outer membrane factors and allow insight into the translocation pathways of antibiotics and other known substrates in this region of the efflux machinery.