Bioinformatics and moonlighting proteins

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• dc.contributor.author Hernández, Sergi
• dc.contributor.author Franco, Luís
• dc.contributor.author Calvo Vidal, Verónica Alejandra
• dc.contributor.author Ferragut, Gabriela
• dc.contributor.author Hermoso Pulido, Antonio
• dc.contributor.author Amela, Isaac
• dc.contributor.author Gómez, Antonio
• dc.contributor.author Querol, Enrique
• dc.contributor.author Cedano, Juan
• dc.date.accessioned 2024-01-23T07:14:55Z
• dc.date.available 2024-01-23T07:14:55Z
• dc.date.issued 2015
• dc.description.abstract Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyze and describe several approaches that use sequences, structures, interactomics, and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are (a) remote homology searches using Psi-Blast, (b) detection of functional motifs and domains, (c) analysis of data from protein–protein interaction databases (PPIs), (d) match the query protein sequence to 3D databases (i.e., algorithms as PISITE), and (e) mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs) has the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations – it requires the existence of multialigned family protein sequences – but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/), previously published by our group, has been used as a benchmark for the all of the analyses.
• dc.description.sponsorship This research was supported by Ministerio de Economía y Competitividad of Spain [BIO2013-48704-R and BFU2013-50176-EXP], by the Centre de Referència de R+D de Biotecnologia de la Generalitat de Catalunya, and from the Comisión Coordinadora del Interior de Uruguay.
• dc.format.mimetype application/pdf
• dc.identifier.citation Hernández S, Franco L, Calvo A, Ferragut G, Hermoso A, Amela I, et al. Bioinformatics and moonlighting proteins. Front Bioeng Biotechnol. 2015 Jun 24;3:90. DOI: 10.3389/fbioe.2015.00090
• dc.identifier.doi http://dx.doi.org/10.3389/fbioe.2015.00090
• dc.identifier.issn 2296-4185
• dc.identifier.uri http://hdl.handle.net/10230/58784
• dc.language.iso eng
• dc.publisher Frontiers
• dc.relation.ispartof Frontiers in Bioengineering and Biotechnology. 2015 Jun 24;3:90
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PN/BIO2013-48704-R
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2013-50176-EXP
• dc.rights © 2015 Hernández, Franco, Calvo, Ferragut, Hermoso, Amela, Gómez, Querol and Cedano. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Multitasking
• dc.subject.keyword Multifunctional
• dc.subject.keyword Moonlighting protein
• dc.subject.keyword Bioinformatics
• dc.subject.keyword Protein function
• dc.subject.keyword Protein evolution
• dc.title Bioinformatics and moonlighting proteins
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion