Functional and genomic analyses of alpha-solenoid proteins.

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 ex...

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Autores principales:	David Fournier, Gareth A Palidwor, Sergey Shcherbinin, Angelika Szengel, Martin H Schaefer, Carol Perez-Iratxeta, Miguel A Andrade-Navarro
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/88a72ad9995a458a8a90390d1b8e954e
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spelling	oai:doaj.org-article:88a72ad9995a458a8a90390d1b8e954e2021-11-18T08:45:17ZFunctional and genomic analyses of alpha-solenoid proteins.1932-620310.1371/journal.pone.0079894https://doaj.org/article/88a72ad9995a458a8a90390d1b8e954e2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24278209/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Alpha-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/.David FournierGareth A PalidworSergey ShcherbininAngelika SzengelMartin H SchaeferCarol Perez-IratxetaMiguel A Andrade-NavarroPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 11, p e79894 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q David Fournier Gareth A Palidwor Sergey Shcherbinin Angelika Szengel Martin H Schaefer Carol Perez-Iratxeta Miguel A Andrade-Navarro Functional and genomic analyses of alpha-solenoid proteins.
description	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/.
format	article
author	David Fournier Gareth A Palidwor Sergey Shcherbinin Angelika Szengel Martin H Schaefer Carol Perez-Iratxeta Miguel A Andrade-Navarro
author_facet	David Fournier Gareth A Palidwor Sergey Shcherbinin Angelika Szengel Martin H Schaefer Carol Perez-Iratxeta Miguel A Andrade-Navarro
author_sort	David Fournier
title	Functional and genomic analyses of alpha-solenoid proteins.
title_short	Functional and genomic analyses of alpha-solenoid proteins.
title_full	Functional and genomic analyses of alpha-solenoid proteins.
title_fullStr	Functional and genomic analyses of alpha-solenoid proteins.
title_full_unstemmed	Functional and genomic analyses of alpha-solenoid proteins.
title_sort	functional and genomic analyses of alpha-solenoid proteins.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/88a72ad9995a458a8a90390d1b8e954e
work_keys_str_mv	AT davidfournier functionalandgenomicanalysesofalphasolenoidproteins AT garethapalidwor functionalandgenomicanalysesofalphasolenoidproteins AT sergeyshcherbinin functionalandgenomicanalysesofalphasolenoidproteins AT angelikaszengel functionalandgenomicanalysesofalphasolenoidproteins AT martinhschaefer functionalandgenomicanalysesofalphasolenoidproteins AT carolpereziratxeta functionalandgenomicanalysesofalphasolenoidproteins AT miguelaandradenavarro functionalandgenomicanalysesofalphasolenoidproteins
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Functional and genomic analyses of alpha-solenoid proteins.

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