Landscape of Eukaryotic Transmembrane Beta Barrel Proteins

Ahmed F. Roumia, Margarita C. Theodoropoulou, Konstantinos D. Tsirigos, Henrik Nielsen, Pantelis G. Bagos*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

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.
Original languageEnglish
JournalJournal of Proteome Research
Volume19
Issue number3
Pages (from-to)1209-1221
ISSN1535-3893
DOIs
Publication statusPublished - 2020

Keywords

  • Eukaryota
  • Mitochondria
  • Chloroplast
  • Transmembrane
  • Beta barrels
  • Hidden Markov model

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