Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.
Center for Nonlinear Sciences, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.
Sci Rep. 2017 Nov 28;7(1):16521. doi: 10.1038/s41598-017-16497-w.
Antibiotic efflux is one of the most critical mechanisms leading to bacterial multidrug resistance. Antibiotics are effluxed out of the bacterial cell by a tripartite efflux pump, a complex machinery comprised of outer membrane, periplasmic adaptor, and inner membrane protein components. Understanding the mechanism of efflux pump assembly and its dynamics could facilitate discovery of novel approaches to counteract antibiotic resistance in bacteria. We built here an intact atomistic model of the Pseudomonas aeruginosa MexAB-OprM pump in a Gram-negative membrane model that contained both inner and outer membranes separated by a periplasmic space. All-atom molecular dynamics (MD) simulations confirm that the fully assembled pump is stable in the microsecond timescale. Using a combination of all-atom and coarse-grained MD simulations and sequence covariation analysis, we characterized the interface between MexA and OprM in the context of the entire efflux pump. These analyses suggest a plausible mechanism by which OprM is activated via opening of its periplasmic aperture through a concerted interaction with MexA.
抗生素外排是导致细菌多重耐药性的最关键机制之一。抗生素通过三联外排泵从细菌细胞中排出，这是一种由外膜、周质腔适配器和内膜蛋白组成的复杂机制。了解外排泵组装及其动力学的机制可以促进发现对抗细菌耐药性的新方法。我们在这里构建了一个完整的、原子级的铜绿假单胞菌 MexAB-OprM 泵在革兰氏阴性膜模型中的模型，该模型包含由周质腔隔开的内、外膜。全原子分子动力学（MD）模拟证实，完全组装的泵在微秒时间尺度上是稳定的。通过全原子和粗粒 MD 模拟以及序列协变分析的结合，我们在整个外排泵的背景下表征了 MexA 和 OprM 之间的界面。这些分析表明了一种合理的机制，即通过 MexA 的协同作用打开其周质腔孔，从而激活 OprM。
