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Functional and genomic analyses of α-solenoid proteins

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Item Type:Article
Title:Functional and genomic analyses of α-solenoid proteins
Creators Name:Fournier, D. and Palidwor, G.A. and Shcherbinin, S. and Szengel, A. and Schaefer, M.H. and Perez-Iratxeta, C. and Andrade-Navarro, M.A.
Abstract:{alpha}-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some {alpha}-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of {alpha}-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of {alpha}-solenoids. Unexpectedly, we identified occurrences of {alpha}-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known {alpha}-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that {alpha}-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of {alpha}-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that {alpha}-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of {alpha}-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/.
Keywords:Genomics, Protein Conformation, Proteins
Source:PLoS ONE
Publisher:Public Library of Science
Page Range:e79894
Date:21 November 2013
Official Publication:https://doi.org/10.1371/journal.pone.0079894
PubMed:View item in PubMed

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