Landscape of Eukaryotic Transmembrane Beta Barrel Proteins
| Autor: | Konstantinos D. Tsirigos, Henrik Nielsen, Margarita C. Theodoropoulou, Ahmed F. Roumia, Pantelis G. Bagos |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Hidden Markov model
0303 health sciences Voltage-dependent anion channel Eukaryota Porins Proteins General Chemistry Computational biology Biology Chloroplast Biochemistry Transmembrane Transmembrane protein Mitochondria 03 medical and health sciences 0302 clinical medicine Beta barrel Eukaryotic Cells Porin Computational analysis Bacterial outer membrane 030217 neurology & neurosurgery 030304 developmental biology Beta barrels |
| Zdroj: | Online Research Database In Technology UnpayWall ORCID Microsoft Academic Graph Roumia, A F, Theodoropoulou, M C, Tsirigos, K D, Nielsen, H & Bagos, P G 2020, ' Landscape of Eukaryotic Transmembrane Beta Barrel Proteins ', Journal of Proteome Research, vol. 19, no. 3, pp. 1209-1221 . https://doi.org/10.1021/acs.jproteome.9b00740 |
| ISSN: | 1535-3907 |
| DOI: | 10.1021/acs.jproteome.9b00740 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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