Landscape of Eukaryotic Transmembrane Beta Barrel Proteins.,Journal of Proteome Research

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Landscape of Eukaryotic Transmembrane Beta Barrel Proteins.
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2020-02-01 , DOI: 10.1021/acs.jproteome.9b00740
Ahmed F Roumia ₁ , Margarita C Theodoropoulou ₁ , Konstantinos D Tsirigos _{2,

3} , Henrik Nielsen ₃ , Pantelis G Bagos ₁

Affiliation

Even though in the last few years several families of eukaryotic β-barrel outer membrane proteins have been discovered, their computational characterization and their annotation in public databases are far from complete. The PFAM database includes only very few characteristic profiles for these families, and in most cases, the profile hidden Markov models (pHMMs) have been trained using prokaryotic and eukaryotic proteins together. Here, we present for the first time a comprehensive computational analysis of eukaryotic transmembrane β-barrels. Twelve characteristic pHMMs were built, based on an extensive literature search, which can discriminate eukaryotic β-barrels from other classes of proteins (globular and bacterial β-barrel ones), as well as between mitochondrial and chloroplastic ones. We built eight novel profiles for the chloroplastic β-barrel families that are not present in the PFAM database and also updated the profile for the MDM10 family (PF12519) in the PFAM database and divide the porin family (PF01459) into two separate families, namely, VDAC and TOM40.

中文翻译：

真核跨膜β桶蛋白的景观。

即使在最近几年中发现了几个真核β-桶外膜蛋白家族，但它们的计算特性和在公共数据库中的注释还远远不够。PFAM数据库仅包含这些家族的极少数特征谱，并且在大多数情况下，已经使用原核和真核蛋白一起训练了谱隐马尔可夫模型（pHMM）。在这里，我们首次提出了真核跨膜β-桶的综合计算分析。在广泛的文献检索基础上，构建了十二种特征性pHMM，可以将真核β-桶与其他类型的蛋白质（球状和细菌性β-桶蛋白）以及线粒体和叶绿体蛋白区分开。

更新日期：2020-02-12

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