School of Engineering and Science, Jacobs University Bremen, Bremen, Germany.
PLoS Comput Biol. 2010 Jun 10;6(6):e1000806. doi: 10.1371/journal.pcbi.1000806.
The tripartite complex AcrAB-TolC is the major efflux system in Escherichia coli. It extrudes a wide spectrum of noxious compounds out of the bacterium, including many antibiotics. Its active part, the homotrimeric transporter AcrB, is responsible for the selective binding of substrates and energy transduction. Based on available crystal structures and biochemical data, the transport of substrates by AcrB has been proposed to take place via a functional rotation, in which each monomer assumes a particular conformation. However, there is no molecular-level description of the conformational changes associated with the rotation and their connection to drug extrusion. To obtain insights thereon, we have performed extensive targeted molecular dynamics simulations mimicking the functional rotation of AcrB containing doxorubicin, one of the two substrates that were co-crystallized so far. The simulations, including almost half a million atoms, have been used to test several hypotheses concerning the structure-dynamics-function relationship of this transporter. Our results indicate that, upon induction of conformational changes, the substrate detaches from the binding pocket and approaches the gate to the central funnel. Furthermore, we provide strong evidence for the proposed peristaltic transport involving a zipper-like closure of the binding pocket, responsible for the displacement of the drug. A concerted opening of the channel between the binding pocket and the gate further favors the displacement of the drug. This microscopically well-funded information allows one to identify the role of specific amino acids during the transitions and to shed light on the functioning of AcrB.
三组分复合物 AcrAB-TolC 是大肠杆菌中的主要外排系统。它将多种有害物质，包括许多抗生素，从细菌中排出。其活性部分，同源三聚体转运蛋白 AcrB，负责底物的选择性结合和能量转导。基于现有晶体结构和生化数据，AcrB 转运底物的过程被提出是通过功能旋转发生的，其中每个单体都采用特定的构象。然而，目前还没有关于与旋转相关的构象变化及其与药物外排的联系的分子水平描述。为了深入了解这一点，我们进行了广泛的靶向分子动力学模拟，模拟了包含阿霉素（迄今为止共结晶的两种底物之一）的 AcrB 的功能旋转。这些模拟包含近 50 万个原子，用于测试与该转运蛋白结构-动力学-功能关系相关的几个假设。我们的结果表明，在诱导构象变化后，底物从结合口袋中脱离，并接近中央漏斗的入口。此外，我们还提供了有力的证据，证明了所提出的蠕动式运输涉及结合口袋的拉链式关闭，这是药物位移的原因。结合口袋和入口之间通道的协同打开进一步有利于药物的位移。这些微观上有充分依据的信息使人们能够识别在转变过程中特定氨基酸的作用，并阐明 AcrB 的功能。
