Interface similarity improves comparison of DNA-binding proteins: the homeobox example

10th Spanish Symposium, JBI 2010, Torremolinos, Spain, October 27-29, 2010. Revised Selected Papers

Detalles Bibliográficos
Autores: Sebastián Yagüe, Álvaro, Pérez Cantalapiedra, Carlos, Contreras-Moreira, Bruno
Tipo de recurso: otro
Fecha de publicación:2012
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/51825
Acceso en línea:http://hdl.handle.net/10261/51825
Access Level:acceso abierto
Palabra clave:protein-DNA
transcription factor
recognition
specificity
homeodomains
homeobox
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network_acronym_str ES
network_name_str España
repository_id_str
spelling Interface similarity improves comparison of DNA-binding proteins: the homeobox exampleSebastián Yagüe, ÁlvaroPérez Cantalapiedra, CarlosContreras-Moreira, Brunoprotein-DNAtranscription factorrecognitionspecificityhomeodomainshomeobox10th Spanish Symposium, JBI 2010, Torremolinos, Spain, October 27-29, 2010. Revised Selected PapersThe recently published 3D-footprint database contains an up-to-date repository of protein-DNA complexes of known structure that belong to different superfamilies and bind to DNA with distinct specificities. This repository can be scanned by means of sequence alignments in order to look for similar DNA-binding proteins, which might in turn recognize similar DNA motifs. Here we take the complete set of Homeobox proteins from Drosophila melanogaster and their preferred DNA motifs, which would fall in the largest 3D-footprint superfamily and were recently characterized by Noyes and collaborators, and annotate their interface residues. We then analyze the observed amino acid substitutions at equivalent interface positions and their effect on recognition. Finally we estimate to what extent interface similarity, computed over the set of residues which mediate DNA recognition, outperforms BLAST expectation values when deciding whether two aligned Homeobox proteins might bind to the same DNA motif.This work was funded by Programa Euroinvestigación 2008 [EUI2008-03612].Peer reviewedSpringer Nature2012info:eu-repo/semantics/otherhttp://purl.org/coar/resource_type/c_3248info:eu-repo/semantics/bookParthttp://hdl.handle.net/10261/51825reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1007/978-3-642-28062-7_8info:eu-repo/semantics/openAccessoai:digital.csic.es:10261/518252026-05-22T06:33:51Z
dc.title.none.fl_str_mv Interface similarity improves comparison of DNA-binding proteins: the homeobox example
title Interface similarity improves comparison of DNA-binding proteins: the homeobox example
spellingShingle Interface similarity improves comparison of DNA-binding proteins: the homeobox example
Sebastián Yagüe, Álvaro
protein-DNA
transcription factor
recognition
specificity
homeodomains
homeobox
title_short Interface similarity improves comparison of DNA-binding proteins: the homeobox example
title_full Interface similarity improves comparison of DNA-binding proteins: the homeobox example
title_fullStr Interface similarity improves comparison of DNA-binding proteins: the homeobox example
title_full_unstemmed Interface similarity improves comparison of DNA-binding proteins: the homeobox example
title_sort Interface similarity improves comparison of DNA-binding proteins: the homeobox example
dc.creator.none.fl_str_mv Sebastián Yagüe, Álvaro
Pérez Cantalapiedra, Carlos
Contreras-Moreira, Bruno
author Sebastián Yagüe, Álvaro
author_facet Sebastián Yagüe, Álvaro
Pérez Cantalapiedra, Carlos
Contreras-Moreira, Bruno
author_role author
author2 Pérez Cantalapiedra, Carlos
Contreras-Moreira, Bruno
author2_role author
author
dc.subject.none.fl_str_mv protein-DNA
transcription factor
recognition
specificity
homeodomains
homeobox
topic protein-DNA
transcription factor
recognition
specificity
homeodomains
homeobox
description 10th Spanish Symposium, JBI 2010, Torremolinos, Spain, October 27-29, 2010. Revised Selected Papers
publishDate 2012
dc.date.none.fl_str_mv 2012
dc.type.none.fl_str_mv info:eu-repo/semantics/other
http://purl.org/coar/resource_type/c_3248
dc.type.openaire.fl_str_mv info:eu-repo/semantics/bookPart
format other
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/51825
url http://hdl.handle.net/10261/51825
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1007/978-3-642-28062-7_8
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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