The rise in multi-drug resistant Gram-negative bacterial infections has led to an increased need for “last-resort” antibiotics such as polymyxins. However, the emergence of polymyxin-resistant strains threatens to bring about a post-antibiotic era. Thus, there is a need to develop new polymyxin-based antibiotics, but a lack of knowledge of the mechanism of action of polymyxins hinders such efforts. It has recently been suggested that polymyxins induce cell lysis of the Gram-negative bacterial inner membrane (IM) by targeting trace amounts of lipopolysaccharide (LPS) localized there. We use multiscale molecular dynamics (MD), including long-timescale coarse-grained (CG) and all-atom (AA) simulations, to investigate the interactions of polymyxin B1 (PMB1) with bacterial IM models containing phospholipids (PLs), small quantities of LPS, and IM proteins. LPS was observed to (transiently) phase separate from PLs at multiple LPS concentrations, and associate with proteins in the IM. PMB1 spontaneously inserted into the IM and localized at the LPS-PL interface, where it cross-linked lipid headgroups via hydrogen bonds, sampling a wide range of interfacial environments. In the presence of membrane proteins, a small number of PMB1 molecules formed interactions with them, in a manner that was modulated by local LPS molecules. Electroporation-driven translocation of PMB1 via water-filled pores was favored at the protein-PL interface, supporting the 'destabilizing' role proteins may have within the IM. Overall, this in-depth characterization of PMB1 modes of interaction reveals how small amounts of mislocalized LPS may play a role in pre-lytic targeting and provides insights that may facilitate rational improvement of polymyxin-based antibiotics.

中文翻译：

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大肠杆菌内膜中的多粘菌素 B1：蛋白质和脂多糖介导的插入的复杂故事


多重耐药革兰氏阴性菌感染的增加导致对多粘菌素等“最后手段”抗生素的需求增加。然而，多粘菌素耐药菌株的出现有可能带来后抗生素时代。因此，需要开发新的基于多粘菌素的抗生素，但缺乏对多粘菌素作用机制的了解阻碍了这种努力。最近有人提出，多粘菌素通过靶向位于革兰氏阴性细菌内膜 （IM） 的痕量脂多糖 （LPS） 来诱导细胞裂解。我们使用多尺度分子动力学 （MD），包括长时间尺度粗粒 （CG） 和全原子 （AA） 模拟，来研究多粘菌素 B1 （PMB1） 与含有磷脂 （PL）、少量 LPS 和 IM 蛋白的细菌 IM 模型的相互作用。观察到 LPS 在多个 LPS 浓度下与 PL （瞬时）相分离，并与 IM 中的蛋白质结合。PMB1 自发插入 IM 并定位在 LPS-PL 界面，在那里它通过氢键交联脂质头基，对各种界面环境进行采样。在膜蛋白存在下，少量 PMB1 分子以受局部 LPS 分子调节的方式与它们形成相互作用。在蛋白质-PL 界面上，电穿孔驱动的 PMB1 通过充满水的孔转位受到青睐，支持蛋白质在 IM 中可能具有的“不稳定”作用。总体而言，对 PMB1 相互作用模式的深入表征揭示了少量错位 LPS 如何在溶出前靶向中发挥作用，并提供了可能促进基于多粘菌素的抗生素的合理改进的见解。