Resistance‐nodulation‐cell division family proteins are transmembrane proteins identified as large spectrum drug transporters involved in multidrug resistance. A prototypical case in this superfamily, responsible for antibiotic resistance in selected gram‐negative bacteria, is AcrB. AcrB forms a trimer using the proton motive force to efflux drugs, implementing a functional rotation mechanism. Unfortunately, the size of the system (1049 amino acid per monomer and membrane) has prevented a systematic dynamical exploration, so that the mild understanding of this coupled transport jeopardizes our ability to counter it. The large number of crystal structures of AcrB prompts studies to further our understanding of the mechanism. To this end, we present a novel strategy based on two key ingredients, which are to study dynamics by exploiting information embodied in the numerous crystal structures obtained to date, and to systematically consider subdomains, their dynamics, and their interactions. Along the way, we identify the subdomains responsible for dynamic events, refine the states (A, B, E) of the functional rotation mechanism, and analyze the evolution of intramonomer and intermonomer interfaces along the functional cycle. Our analysis shows the relevance of AcrB's efflux mechanism as a template within the HAE1 family but not beyond. It also paves the way to targeted simulations exploiting the most relevant degrees of freedom at certain steps, and to a targeting of specific interfaces to block the drug efflux. Our work shows that complex dynamics can be unveiled from static snapshots, a strategy that may be used on a variety of molecular machines of large size.

中文翻译：

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在没有显式动力学的情况下研究动力学：AcrB基于结构的出口机制研究

耐药性结节细胞分裂家族蛋白是跨膜蛋白，被认为是涉及多药耐药性的广谱药物转运蛋白。在这个超家族中，一个典型的案例是AcrB，它负责所选革兰氏阴性细菌的抗生素耐药性。AcrB利用质子原动力形成三聚体，使药物外流，从而实现功能性旋转机制。不幸的是，系统的大小（每个单体和膜1049个氨基酸）阻止了系统的动态探索，因此，对这种耦合运输的温和理解损害了我们抵抗它的能力。AcrB的大量晶体结构促使人们进一步研究其机理。为此，我们提出了一种基于两个关键要素的新颖策略，它们是通过利用迄今获得的众多晶体结构中包含的信息来研究动力学，并系统地考虑子域，其动力学及其相互作用。一路上，我们确定负责动态事件的子域，完善功能旋转机制的状态（A，B，E），并分析功能周期内单体和单体间界面的演变。我们的分析表明，AcrB外排机制作为HAE1家族内模板的相关性，但没有超出范围。它还为在某些步骤中利用最相关的自由度进行有针对性的模拟铺平了道路，并为特定接口的靶向铺平了道路，以阻止药物外流。我们的工作表明，可以从静态快照中揭示复杂的动态，