Functional and genomic analyses of alpha-solenoid proteins

PLoS One. 2013 Nov 21;8(11):e79894. doi: 10.1371/journal.pone.0079894. eCollection 2013.

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/.

MeSH terms

  • Genomics*
  • Protein Conformation
  • Proteins / chemistry
  • Proteins / genetics
  • Proteins / physiology*

Substances

  • Proteins

Grants and funding

This work is funded by the Collaborative Research Center for Theoretical Biology: Robustness, Modularity and Evolutionary Design of Living Systems [Sonderforschungsbereich 618 (SFB 618)], Humboldt-University of Berlin, Germany. Website: http://www.biologie.hu-berlin.de/forschung/SFB_618. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.