Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Enterobacterial Common Antigen.,The Journal of Physical Chemistry B

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Modeling and Simulation of Bacterial Outer Membranes with Lipopolysaccharides and Enterobacterial Common Antigen.
The Journal of Physical Chemistry B ( IF 2.8 ) Pub Date : 2020-06-01 , DOI: 10.1021/acs.jpcb.0c03353
Ya Gao _{1,

2} , Jumin Lee ₂ , Göran Widmalm ₃ , Wonpil Im _{2,

4}

Affiliation

Enterobacterial common antigen (ECA) is a surface glycolipid shared by all members of the Enterobacteriaceae family. In addition to lipopolysaccharides (LPS), ECA is an important component in the outer membrane (OM) of Gram-negative bacteria, making the OM an effective, selective barrier against the permeation of toxic molecules. Previous modeling and simulation studies represented OMs exclusively with LPS in the outer leaflet. In this work, various ECA molecules were first modeled and incorporated into symmetric bilayers with LPS in different ratios, and all-atom molecular dynamics simulations were conducted to investigate the properties of the mixed bilayers mimicking OM outer leaflets. Dynamic and flexible conformational ensembles are sampled for each ECA/LPS system. Incorporation of ECA_LPS (an LPS core-linked form) and ECA_PG (a phosphatidylglycerol-linked form) affects lipid packing and ECA/LPS distributions on the bilayer surface. Hydrophobic thickness and chain order parameter analyses indicate that incorporation of ECA_PG makes the acyl chains of LPS more flexible and disordered and thus increases the area per lipid of LPS. The calculated area per lipid of each ECA/LPS provides a good estimate for building more realistic OMs with different ratios of ECA/LPS, which will be useful in order to characterize their interactions with outer membrane proteins in more realistic OMs.

中文翻译：

具有脂多糖和肠细菌共同抗原的细菌外膜的建模和模拟。

肠杆菌共同抗原 (ECA) 是一种由肠杆菌科所有成员共享的表面糖脂。除脂多糖 (LPS) 外，ECA 还是革兰氏阴性菌外膜 (OM) 的重要成分，使 OM 成为防止有毒分子渗透的有效选择性屏障。以前的建模和模拟研究仅在外传单中代表了带有 LPS 的 OM。在这项工作中，首先对各种 ECA 分子进行建模，并以不同比例将 LPS 结合到对称双层中，并进行了全原子分子动力学模拟，以研究模拟 OM 外小叶的混合双层的特性。为每个 ECA/LPS 系统采样动态和灵活的构象集合。加入 ECA _LPS（LPS 核心连接形式）和 ECA _PG（磷脂酰甘油连接形式）影响双层表面上的脂质堆积和 ECA/LPS 分布。疏水厚度和链序参数分析表明，ECA _{PG 的}掺入使 LPS 的酰基链更加灵活和无序，从而增加了 LPS 的单位脂质面积。每个 ECA/LPS 的每个脂质的计算面积为构建具有不同 ECA/LPS 比率的更真实的 OM 提供了一个很好的估计，这将有助于在更真实的 OM 中表征它们与外膜蛋白的相互作用。

更新日期：2020-07-16

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