Membrane thinning and lateral gating are consistent features of BamA across multiple species.
Membrane thinning and lateral gating are consistent features of BamA across multiple species.
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DOI：
10.1371/journal.pcbi.1008355
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发表时间：
2020-10
影响因子：
4.3
通讯作者：
Gumbart JC
中科院分区：
文献类型：
--
作者：
Liu J;Gumbart JC
在革兰氏阴性菌中，β-桶状外膜蛋白（OMPs）的折叠和插入是由β-桶状组装机械（BAM）复合物介导的。这一过程的两种主要模型被提出：混合桶模型，该模型认为BamA β-桶中的侧门可以作为进入的OMP的模板；被动模型，该模型认为BamA侧门附近的薄膜加速了OMP的自发插入。为了检验这两种模型的关键要素，我们在大肠杆菌、肠炎沙门氏菌、杜氏嗜血杆菌和淋病奈瑟菌的原生、物种特异性外膜上对含有和不含POTRA结构域的BamA及其同源物大肠杆菌的TamA进行了45.5 μs的平衡分子动力学模拟。在这些平衡模拟中，我们一致地观察到所有蛋白质的侧门附近的膜变薄。我们还观察到淋病奈瑟菌偶有自发的侧向门打开和门界面β-链的滑动，表明门是动态的。另外14 μs的自由能计算表明，打开BamA/TamA的侧门所需的能量因物种而异，但始终低于Omp85同源物FhaC。我们的综合结果表明，OMP插入利用了混合枪管和被动模型的各个方面。革兰氏阴性菌，如大肠杆菌，在其周围有第二层外膜。这种外膜提供了一层额外的保护，但也提出了一个额外的挑战，在它的结构，加剧了缺乏化学能在细菌细胞的这一区域。例如，外膜中的蛋白质通过BamA插入，BamA本身是一个完整的膜蛋白。BamA协助插入过程的确切机制尚不清楚。在这里，我们使用广泛的模拟在其原生外膜环境中来自多个物种的BamA的原子细节来阐明这一过程。我们发现BamA的侧门，一个被提出的进入膜的途径，是动态的，尽管在一定程度上因物种而异。另一方面，在BamA侧门附近的外膜变薄在所有模拟中都得到了一致的观察。我们得出结论，BamA的多种特征有助于蛋白质插入外膜。
In Gram-negative bacteria, the folding and insertion of β-barrel outer membrane proteins (OMPs) to the outer membrane are mediated by the β-barrel assembly machinery (BAM) complex. Two leading models of this process have been put forth: the hybrid barrel model, which claims that a lateral gate in BamA’s β-barrel can serve as a template for incoming OMPs, and the passive model, which claims that a thinned membrane near the lateral gate of BamA accelerates spontaneous OMP insertion. To examine the key elements of these two models, we have carried out 45.5 μs of equilibrium molecular dynamics simulations of BamA with and without POTRA domains from Escherichia coli, Salmonella enterica, Haemophilus ducreyi and Neisseria gonorrhoeae, together with BamA’s homolog, TamA from E. coli, in their native, species-specific outer membranes. In these equilibrium simulations, we consistently observe membrane thinning near the lateral gate for all proteins. We also see occasional spontaneous lateral gate opening and sliding of the β-strands at the gate interface for N. gonorrhoeae, indicating that the gate is dynamic. An additional 14 μs of free-energy calculations shows that the energy necessary to open the lateral gate in BamA/TamA varies by species, but is always lower than the Omp85 homolog, FhaC. Our combined results suggest OMP insertion utilizes aspects of both the hybrid barrel and passive models. Gram-negative bacteria such as Escherichia coli have a second, outer membrane surrounding them. This outer membrane provides an additional layer of protection, but also presents an additional challenge in its construction, exacerbated by the lack of chemical energy in this region of the bacterial cell. For example, proteins in the outer membrane are inserted via BamA, itself an integral membrane protein. The precise mechanisms by which BamA assists in the insertion process are still unclear. Here, we use extensive simulations in atomistic detail of BamA from multiple species in its native outer membrane environment to shed light on this process. We find that the lateral gate of BamA, a proposed pathway into the membrane, is dynamic, although to a degree varying by species. On the other hand, thinning of the outer membrane near BamA’s lateral gate is observed consistently across all simulations. We conclude that multiple features of BamA contribute to protein insertion into the outer membrane.
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DOI：
10.1126/science.aad3460
发表时间：
2016-01-08
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Bakelar J;Buchanan SK;Noinaj N
通讯作者：
Noinaj N
影响因子：
3.4
作者：
Fleming, Patrick J.;Patel, Dhilon S.;Im, Wonpil
通讯作者：
Im, Wonpil
影响因子：
3.1
作者：
AlBitar-Nehme, Sami;Basheer, Soorej M.;Caroff, Martine
通讯作者：
Caroff, Martine
影响因子：
16.8
作者：
Gruss, Fabian;Zaehringer, Franziska;Maier, Timm
通讯作者：
Maier, Timm
影响因子：
5.5
作者：
Balusek, Curtis;Hwang, Hyea;Gumbart, James C.
通讯作者：
Gumbart, James C.