Porter domain opening and closing motions in the multi-drug efflux transporter AcrB
Porter domain opening and closing motions in the multi-drug efflux transporter AcrB
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DOI：
10.1016/j.bbamem.2012.10.016
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发表时间：
2013-02-01
影响因子：
3.4
通讯作者：
Kandt, Christian
中科院分区：
文献类型：
--
作者：
Fischer, Nadine;Kandt, Christian
在大肠杆菌多药外排泵中，核黄素抗性蛋白B作为主动转运蛋白。核黄素抗性蛋白A / B -大肠杆菌素耐受蛋白。在相同的反应循环中间体所有的吖啶黄抗性蛋白B的X-射线结构显示高度相似的构象的底物招募和运输的转运蛋白结构域。为了评估这种结构同质性是吖啶黄素抗性蛋白B的内在特征还是源于其他原因，我们在150 mM NaCl溶液中对膜包埋的、不对称的、无底物的野生型吖啶黄素抗性蛋白B进行了一系列六个独立的、无偏的100 ns分子动力学模拟。我们发现的搬运工域更灵活，比以前假设显示清晰的开放和关闭运动的近端结合口袋（土地T-状态）和出口的药物运输通道（O-中间体）。同时，疏水结合口袋有利于在所有三个原聚体中的闭合构象。我们的研究结果表明，在晶体结构中看到的构象均匀性可能是绑定的，但结构上未解决的基板的影响。我们的模拟进一步暗示，已知的三个反应循环中间体中的每一个都至少发生在两个变体中，Thr 676环独立地调节转运蛋白结构域的访问，并可能在底物转运中起关键作用。在100 ns的时间尺度上，我们发现没有证据支持建议的LLL静息状态下的基板。如果近端结合口袋的动力学有抑制作用，对吖啶黄抗性蛋白B泵活性降低的生命时间的基板可访问的构象，所观察到的动力学可以提供一个结构上的解释，为吖啶黄抗性蛋白B活性增强作用的衔接蛋白吖啶黄抗性蛋白A稳定PC 1和PC 2亚结构域的方向。(C)2012 Elsevier B. V.保留所有权利。
Acriflavine resistance protein B acts as the active transporter in the multi-drug efflux pump Acriflavine resistance proteins A / B - Tolerance to colicins protein in Escherichia coli. Within the same reaction cycle intermediate all Acriflavine resistance protein B X-ray structures display highly similar conformations of the substrate-recruiting and transporting porter domain. To assess if this structural homogeneity is an intrinsic feature of Acriflavine resistance protein B or stems from other causes we performed a series of six independent, unbiased 100 ns molecular dynamics simulations of membrane-embedded, asymmetric, substrate-free wild type Acriflavine resistance protein B in a 150 mM NaCl solution. We find the porter domain more flexible than previously assumed displaying clear opening and closing motions of the proximal binding pocket (Land T-state) and the exit of the drug transport channels (O-intermediate). Concurrently the hydrophobic binding pocket favors a closed conformation in all three protomers. Our findings suggest that the conformational homogeneity seen in the crystal structures is likely an effect of bound but structurally unresolved substrate. Our simulations further imply that each of the known three reaction cycle intermediates occurs in at least two variants, the Thr676 loop independently regulates porter domain access and likely plays a key role in substrate transport. On a 100 ns time scale we find no evidence supporting the proposed LLL resting state in the absence of substrate. If the proximal binding pocket dynamics have an inhibiting effect on Acriflavine resistance protein B pump activity lowering the life time of substrate-accessible conformations, the observed dynamics could provide a structural explanation for the Acriflavine resistance protein B activity-enhancing effect of the adaptor protein Acriflavine resistance protein A stabilizing PC1 and PC2 subdomain orientations. (C) 2012 Elsevier B.V. All rights reserved.