title: Functional and genomic analyses of alpha-solenoid proteins.
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/.
authors.affiliation: Max-Delbrück Center for Molecular Medicine, Berlin, Germany.
authors.forename: David
authors.initials: D
authors.lastname: Fournier
authors.forename: Gareth A
authors.initials: GA
authors.lastname: Palidwor
authors.forename: Sergey
authors.initials: S
authors.lastname: Shcherbinin
authors.forename: Angelika
authors.initials: A
authors.lastname: Szengel
authors.forename: Martin H
authors.initials: MH
authors.lastname: Schaefer
authors.forename: Carol
authors.initials: C
authors.lastname: Perez-Iratxeta
authors.forename: Miguel A
authors.initials: MA
authors.lastname: Andrade-Navarro
mesh_terms: D023281:Genomics; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000502:physiology*
chemical_list: D011506:Proteins