Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.
Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.
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OmpF 和 LPS 的动力学和相互作用：对孔隙可达性和离子渗透性的影响。
DOI：
10.1016/j.bpj.2016.01.002
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发表时间：
2016
影响因子：
3.4
通讯作者：
Im,Wonpil
中科院分区：
文献类型：
--
作者：
Patel,DhilonS;Re,Suyong;Wu,EmiliaL;Qi,Yifei;Klebba,PhillipE;Widmalm,Göran;Yeom,MinSun;Sugita,Yuji;Im,Wonpil
革兰氏阴性菌不对称外膜由内叶磷脂和外叶脂多糖组成。外膜蛋白F(OmpF)是一种三聚体孔蛋白，负责小分子在大肠杆菌外膜上的被动转运。在这里，我们用全原子分子动力学模拟方法研究了脂多糖环境中不同程度的异质性对OmpF结构和动力学的影响。这些模拟提供了对脂多糖成分的灵活性和动态的洞察，这些成分高度依赖于局部环境，其中脂类A是最刚性的，O-抗原是最灵活的。在非均相的脂多糖体系中，观察到O-抗原多糖的灵活性增加，其中相邻的O-抗原重复单元相互作用较弱，因此更具动态性，而在均相的脂多糖体系中，由于紧密堆积，相互作用强烈，但总体灵活性有限。通过比较OmpF表面残基与内毒素核心糖之间相互作用的分子水平细节与实验数据，证实了内毒素核心寡糖在屏蔽单抗识别的OmpF表面表位方面的重要性。内毒素环境对体离子(K+和ClOPMF)的迁移有影响，但−的离子选择性主要受体离子浓度的影响。
The asymmetric outer membrane of Gram-negative bacteria is formed of the inner leaflet with phospholipids and the outer leaflet with lipopolysaccharides (LPS). Outer membrane protein F (OmpF) is a trimeric porin responsible for the passive transport of small molecules across the outer membrane ofEscherichia coli. Here, we report the impact of different levels of heterogeneity in LPS environments on the structure and dynamics of OmpF using all-atom molecular dynamics simulations. The simulations provide insight into the flexibility and dynamics of LPS components that are highly dependent on local environments, with lipid A being the most rigid and O-antigen being the most flexible. Increased flexibility of O-antigen polysaccharides is observed in heterogeneous LPS systems, where the adjacent O-antigen repeating units are weakly interacting and thus more dynamic, compared to homogeneous LPS systems in which LPS interacts strongly with each other with limited overall flexibility due to dense packing. The model systems were validated by comparing molecular-level details of interactions between OmpF surface residues and LPS core sugars with experimental data, establishing the importance of LPS core oligosaccharides in shielding OmpF surface epitopes recognized by monoclonal antibodies. There are LPS environmental influences on the movement of bulk ions (K+and Cl−), but the ion selectivity of OmpF is mainly affected by bulk ion concentration.
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影响因子：
3.3
作者：
Klauda, Jeffery B.;Venable, Richard M.;Freites, J. Alfredo;O'Connor, Joseph W.;Tobias, Douglas J.;Mondragon-Ramirez, Carlos;Vorobyov, Igor;MacKerell, Alexander D., Jr.;Pastor, Richard W.
通讯作者：
Pastor, Richard W.
DOI：
10.1016/j.bbapap.2008.11.005
发表时间：
2009-05
期刊：
Biochimica et biophysica acta
影响因子：
--
作者：
Delcour AH
通讯作者：
Delcour AH
影响因子：
3.4
作者：
E. Wu;O. Engström;Sunhwan Jo;Danielle Stuhlsatz;M. S. Yeom;Jeffery B. Klauda;G. Widmalm;W. Im
通讯作者：
E. Wu;O. Engström;Sunhwan Jo;Danielle Stuhlsatz;M. S. Yeom;Jeffery B. Klauda;G. Widmalm;W. Im
影响因子：
5.5
作者：
Guvench, Olgun;Hatcher, Elizabeth;Venable, Richard M.;Pastor, Richard W.;MacKerell, Alexander D., Jr.
通讯作者：
MacKerell, Alexander D., Jr.
影响因子：
3.4
作者：
E. Wu;P. Fleming;M. S. Yeom;G. Widmalm;Jeffery B. Klauda;K. Fleming;W. Im
通讯作者：
E. Wu;P. Fleming;M. S. Yeom;G. Widmalm;Jeffery B. Klauda;K. Fleming;W. Im