General features of transmembrane beta barrels from a large database.
General features of transmembrane beta barrels from a large database.
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DOI：
10.1073/pnas.2220762120
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发表时间：
2023-07-18
影响因子：
11.1
通讯作者：
Slusky, Joanna S. G.
中科院分区：
文献类型：
--
作者：
Montezano, Daniel;Bernstein, Rebecca;Copeland, Matthew M.;Slusky, Joanna S. G.
外膜蛋白（OMP）是革兰氏阴性菌外膜的主要成分，也是疫苗的常用靶点。我们创建了一个算法，从序列中识别细菌外膜蛋白。我们算法的质量使我们能够从原核基因组中识别出大多数OMP（> 190万），包括> 270，000个与先前结构解析的OMP无关的OMP。我们确定了11种类型的外膜蛋白在我们的数据库。最大类型的信号序列-用于靶向膜插入机器-根据系统发育类别而变化。所有其他类型的外膜蛋白都有不相关的信号序列，这就提出了这些蛋白如何折叠的问题。我们的网络访问数据库将允许进一步探索各种外膜蛋白，以发现疫苗开发的目标。大型数据集为以前由范例研究的主题提供了新的见解。我们使用协同进化数据创建了一个大型、高质量的跨膜β桶（TMBB）数据库。通过对生成的进化接触图进行简单的特征检测，我们的方法（IsItABarrel）在区分蛋白质类时达到了95.88%的平衡准确率。此外，与IsItABarrel的比较揭示了在以前的TMBB算法中的高误报率。除了比以前的数据集更准确外，我们的数据库（在线提供）还包含来自38个门的1，938，936种细菌TMBB蛋白，分别是以前的TMBB-DB和OMPdb的17倍和2.2倍。我们预计，由于其质量和大小，该数据库将作为一个有用的资源，需要高质量的TMBB序列数据。我们发现TMBB可以分为11种类型，其中3种以前没有报道过。我们发现含TMBB的生物体之间蛋白质组百分比存在巨大差异，一些生物体使用其蛋白质组的6.79%用于TMBB，而另一些生物体仅使用其蛋白质组的0.27%。TMBB长度的分布提示先前假设的重复事件。此外，我们还发现不同种类细菌的C-末端β-信号虽然有LGLGLGYRF的保守序列，但也存在差异。然而，这种β信号仅是原型TMBB的特征。这10种非原型桶型具有其他C-末端基序，并且这些替代基序是否促进TMBB插入或执行任何其他信号传导功能仍有待确定。
Outer membrane proteins (OMPs) are the main component of Gram-negative bacterial outer membranes and are frequently vaccine targets. We created an algorithm that identifies bacterial OMPs from sequence. The quality of our algorithm allows us to identify most OMPs (>1.9 million) from prokaryotic genomes including >270,000 unrelated to previously structurally resolved OMPs. We identify eleven types of OMPs in our database. The largest type’s signal sequence—used for targeting the membrane-insertion machinery—varies by phylogenetic class. All other types of OMPs have unrelated signal sequences, raising questions of how these proteins fold. Our web-accessible database will allow for further exploration of the varieties of outer membrane proteins to uncover targets for vaccine development. Large datasets contribute new insights to subjects formerly investigated by exemplars. We used coevolution data to create a large, high-quality database of transmembrane β-barrels (TMBB). By applying simple feature detection on generated evolutionary contact maps, our method (IsItABarrel) achieves 95.88% balanced accuracy when discriminating among protein classes. Moreover, comparison with IsItABarrel revealed a high rate of false positives in previous TMBB algorithms. In addition to being more accurate than previous datasets, our database (available online) contains 1,938,936 bacterial TMBB proteins from 38 phyla, respectively, 17 and 2.2 times larger than the previous sets TMBB-DB and OMPdb. We anticipate that due to its quality and size, the database will serve as a useful resource where high-quality TMBB sequence data are required. We found that TMBBs can be divided into 11 types, three of which have not been previously reported. We find tremendous variance in proteome percentage among TMBB-containing organisms with some using 6.79% of their proteome for TMBBs and others using as little as 0.27% of their proteome. The distribution of the lengths of the TMBBs is suggestive of previously hypothesized duplication events. In addition, we find that the C-terminal β-signal varies among different classes of bacteria though its consensus sequence is LGLGYRF. However, this β-signal is only characteristic of prototypical TMBBs. The ten non-prototypical barrel types have other C-terminal motifs, and it remains to be determined if these alternative motifs facilitate TMBB insertion or perform any other signaling function.
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影响因子：
8
作者：
Hsieh, Daniel;Davis, Alexander;Nanda, Vikas
通讯作者：
Nanda, Vikas
影响因子：
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Hassabis D
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通讯作者：
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通讯作者：
Li, YX
影响因子：
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通讯作者：
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