Landscape of Eukaryotic Transmembrane Beta Barrel Proteins
Data
2020Language
en
Soggetto
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. Copyright © 2020 American Chemical Society.
Collections
Related items
Showing items related by title, author, creator and subject.
-
Investigating Molecular Determinants of Cancer Cell Resistance to Ionizing Radiation Through an Integrative Bioinformatics Approach
Toy H.I., Karakülah G., Kontou P.I., Alotaibi H., Georgakilas A.G., Pavlopoulou A. (2021)Eradication of cancer cells through exposure to high doses of ionizing radiation (IR) is a widely used therapeutic strategy in the clinical setting. However, in many cases, cancer cells can develop remarkable resistance ... -
Enhancer of rudimentary homologue interacts with scaffold attachment factor B at the nuclear matrix to regulate SR protein phosphorylation
Drakouli S., Lyberopoulou A., Papathanassiou M., Mylonis I., Georgatsou E. (2017)Scaffold attachment factor B1 (SAFB1) is an integral component of the nuclear matrix of vertebrate cells. It binds to DNA on scaffold/matrix attachment region elements, as well as to RNA and a multitude of different proteins, ... -
Proteomic analysis of the mitochondrial glucocorticoid receptor interacting proteins reveals pyruvate dehydrogenase and mitochondrial 60 kDa heat shock protein as potent binding partners
Karra A.G., Sioutopoulou A., Gorgogietas V., Samiotaki M., Panayotou G., Psarra A.-M.G. (2022)Glucocorticoids are steroid hormones that regulate plethora biological actions such as growth and metabolism, immune response, and apoptosis. Glucocorticoids actions are mediated via glucocorticoid receptors which act ...