Can bioinformatics help in the identification of moonlighting proteins?

Protein multitasking or moonlighting is the capability of certain proteins to execute two or more unique biological functions. This ability to perform moonlighting functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Usually...

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Autores: Hernández, Sergi, Franco, Luís, Calvo Vidal, Verónica Alejandra, Ferragut, Gabriela, Hermoso Pulido, Antonio, Amela, Isaac, Gómez, Antonio, Querol, Enrique, Cedano, Juan
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2014
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/58785
Acceso en línea:http://hdl.handle.net/10230/58785
http://dx.doi.org/10.1042/BST20140241
Access Level:acceso abierto
Palabra clave:Bioinformatics
Moonlighting protein
Multitasking protein
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spelling Can bioinformatics help in the identification of moonlighting proteins?Hernández, SergiFranco, LuísCalvo Vidal, Verónica AlejandraFerragut, GabrielaHermoso Pulido, AntonioAmela, IsaacGómez, AntonioQuerol, EnriqueCedano, JuanBioinformaticsMoonlighting proteinMultitasking proteinProtein multitasking or moonlighting is the capability of certain proteins to execute two or more unique biological functions. This ability to perform moonlighting functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Usually, moonlighting proteins are revealed experimentally by serendipity, and the proteins described probably represent just the tip of the iceberg. It would be helpful if bioinformatics could predict protein multifunctionality, especially because of the large amounts of sequences coming from genome projects. In the present article, we describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. The sequence analysis has been performed: (i) by remote homology searches using PSI-BLAST, (ii) by the detection of functional motifs, and (iii) by the co-evolutionary relationship between amino acids. Programs designed to identify functional motifs/domains are basically oriented to detect the main function, but usually fail in the detection of secondary ones. Remote homology searches such as PSI-BLAST seem to be more versatile in this task, and it is a good complement for the information obtained from protein–protein interaction (PPI) databases. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can be used only in very restricted situations, but can suggest how the evolutionary process of the acquisition of the second function took place.This research was supported by Ministerio de Ciencia e Innovación of Spain [grant numbers BFU2010-22209-C02-01 and BIO2013-48704-R], the Centre de Referència de R+D de Biotecnologia de la Generalitat de Catalunya, La Marató de TV3 [grant number 101930/31/32/33] and the Comisión Coordinadora del Interior de Uruguay.Portland Press202420242014info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/58785http://dx.doi.org/10.1042/BST20140241reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésBiochemical Society Transactions. 2014 Dec;42(6):1692-7info:eu-repo/grantAgreement/ES/3PN/BFU2010-22209-C02-01info:eu-repo/grantAgreement/ES/1PE/BIO2013-48704-RThis is an Open Access article distributed under the terms of the Creative Commons Attribution Licence (CC-BY) (http://creativecommons.org/licenses/by/3.0/) which permits unrestricted use, distribution and reproduction in any medium, provided the original work is properly cited.http://creativecommons.org/licenses/by/3.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/587852026-05-29T05:05:01Z
dc.title.none.fl_str_mv Can bioinformatics help in the identification of moonlighting proteins?
title Can bioinformatics help in the identification of moonlighting proteins?
spellingShingle Can bioinformatics help in the identification of moonlighting proteins?
Hernández, Sergi
Bioinformatics
Moonlighting protein
Multitasking protein
title_short Can bioinformatics help in the identification of moonlighting proteins?
title_full Can bioinformatics help in the identification of moonlighting proteins?
title_fullStr Can bioinformatics help in the identification of moonlighting proteins?
title_full_unstemmed Can bioinformatics help in the identification of moonlighting proteins?
title_sort Can bioinformatics help in the identification of moonlighting proteins?
dc.creator.none.fl_str_mv Hernández, Sergi
Franco, Luís
Calvo Vidal, Verónica Alejandra
Ferragut, Gabriela
Hermoso Pulido, Antonio
Amela, Isaac
Gómez, Antonio
Querol, Enrique
Cedano, Juan
author Hernández, Sergi
author_facet Hernández, Sergi
Franco, Luís
Calvo Vidal, Verónica Alejandra
Ferragut, Gabriela
Hermoso Pulido, Antonio
Amela, Isaac
Gómez, Antonio
Querol, Enrique
Cedano, Juan
author_role author
author2 Franco, Luís
Calvo Vidal, Verónica Alejandra
Ferragut, Gabriela
Hermoso Pulido, Antonio
Amela, Isaac
Gómez, Antonio
Querol, Enrique
Cedano, Juan
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Bioinformatics
Moonlighting protein
Multitasking protein
topic Bioinformatics
Moonlighting protein
Multitasking protein
description Protein multitasking or moonlighting is the capability of certain proteins to execute two or more unique biological functions. This ability to perform moonlighting functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Usually, moonlighting proteins are revealed experimentally by serendipity, and the proteins described probably represent just the tip of the iceberg. It would be helpful if bioinformatics could predict protein multifunctionality, especially because of the large amounts of sequences coming from genome projects. In the present article, we describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. The sequence analysis has been performed: (i) by remote homology searches using PSI-BLAST, (ii) by the detection of functional motifs, and (iii) by the co-evolutionary relationship between amino acids. Programs designed to identify functional motifs/domains are basically oriented to detect the main function, but usually fail in the detection of secondary ones. Remote homology searches such as PSI-BLAST seem to be more versatile in this task, and it is a good complement for the information obtained from protein–protein interaction (PPI) databases. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can be used only in very restricted situations, but can suggest how the evolutionary process of the acquisition of the second function took place.
publishDate 2014
dc.date.none.fl_str_mv 2014
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/58785
http://dx.doi.org/10.1042/BST20140241
url http://hdl.handle.net/10230/58785
http://dx.doi.org/10.1042/BST20140241
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Biochemical Society Transactions. 2014 Dec;42(6):1692-7
info:eu-repo/grantAgreement/ES/3PN/BFU2010-22209-C02-01
info:eu-repo/grantAgreement/ES/1PE/BIO2013-48704-R
dc.rights.none.fl_str_mv http://creativecommons.org/licenses/by/3.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/3.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Portland Press
publisher.none.fl_str_mv Portland Press
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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