Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.

We consider the problem of how to detect cognate pairs of proteins that bind when each belongs to a large family of paralogs. To illustrate the problem, we have undertaken a genomewide analysis of interactions of members of the PE and PPE protein families of Mycobacterium tuberculosis. Our computati...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Robert Riley, Matteo Pellegrini, David Eisenberg
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/bdfa560007144321b68048f6ed7fcb54
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:bdfa560007144321b68048f6ed7fcb54
record_format	dspace
spelling	oai:doaj.org-article:bdfa560007144321b68048f6ed7fcb542021-11-25T05:41:59ZIdentifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.1553-734X1553-735810.1371/journal.pcbi.1000174https://doaj.org/article/bdfa560007144321b68048f6ed7fcb542008-09-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/18787688/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358We consider the problem of how to detect cognate pairs of proteins that bind when each belongs to a large family of paralogs. To illustrate the problem, we have undertaken a genomewide analysis of interactions of members of the PE and PPE protein families of Mycobacterium tuberculosis. Our computational method uses structural information, operon organization, and protein coevolution to infer the interaction of PE and PPE proteins. Some 289 PE/PPE complexes were predicted out of a possible 5,590 PE/PPE pairs genomewide. Thirty-five of these predicted complexes were also found to have correlated mRNA expression, providing additional evidence for these interactions. We show that our method is applicable to other protein families, by analyzing interactions of the Esx family of proteins. Our resulting set of predictions is a starting point for genomewide experimental interaction screens of the PE and PPE families, and our method may be generally useful for detecting interactions of proteins within families having many paralogs.Robert RileyMatteo PellegriniDavid EisenbergPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 4, Iss 9, p e1000174 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Robert Riley Matteo Pellegrini David Eisenberg Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.
description	We consider the problem of how to detect cognate pairs of proteins that bind when each belongs to a large family of paralogs. To illustrate the problem, we have undertaken a genomewide analysis of interactions of members of the PE and PPE protein families of Mycobacterium tuberculosis. Our computational method uses structural information, operon organization, and protein coevolution to infer the interaction of PE and PPE proteins. Some 289 PE/PPE complexes were predicted out of a possible 5,590 PE/PPE pairs genomewide. Thirty-five of these predicted complexes were also found to have correlated mRNA expression, providing additional evidence for these interactions. We show that our method is applicable to other protein families, by analyzing interactions of the Esx family of proteins. Our resulting set of predictions is a starting point for genomewide experimental interaction screens of the PE and PPE families, and our method may be generally useful for detecting interactions of proteins within families having many paralogs.
format	article
author	Robert Riley Matteo Pellegrini David Eisenberg
author_facet	Robert Riley Matteo Pellegrini David Eisenberg
author_sort	Robert Riley
title	Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.
title_short	Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.
title_full	Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.
title_fullStr	Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.
title_full_unstemmed	Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.
title_sort	identifying cognate binding pairs among a large set of paralogs: the case of pe/ppe proteins of mycobacterium tuberculosis.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/bdfa560007144321b68048f6ed7fcb54
work_keys_str_mv	AT robertriley identifyingcognatebindingpairsamongalargesetofparalogsthecaseofpeppeproteinsofmycobacteriumtuberculosis AT matteopellegrini identifyingcognatebindingpairsamongalargesetofparalogsthecaseofpeppeproteinsofmycobacteriumtuberculosis AT davideisenberg identifyingcognatebindingpairsamongalargesetofparalogsthecaseofpeppeproteinsofmycobacteriumtuberculosis
_version_	1718414541205798912

Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis.

Ejemplares similares