Titre
A multi-scale coevolutionary approach to predict interactions between protein domains.
Type
article
Institution
Externe
Périodique
Auteur(s)
Croce, G.
Auteure/Auteur
Gueudré, T.
Auteure/Auteur
Ruiz Cuevas, M.V.
Auteure/Auteur
Keidel, V.
Auteure/Auteur
Figliuzzi, M.
Auteure/Auteur
Szurmant, H.
Auteure/Auteur
Weigt, M.
Auteure/Auteur
Liens vers les personnes
ISSN
1553-7358
Statut éditorial
Publié
Date de publication
2019-10
Volume
15
Numéro
10
Première page
e1006891
Peer-reviewed
Oui
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Publication Status: epublish
Résumé
Interacting proteins and protein domains coevolve on multiple scales, from their correlated presence across species, to correlations in amino-acid usage. Genomic databases provide rapidly growing data for variability in genomic protein content and in protein sequences, calling for computational predictions of unknown interactions. We first introduce the concept of direct phyletic couplings, based on global statistical models of phylogenetic profiles. They strongly increase the accuracy of predicting pairs of related protein domains beyond simpler correlation-based approaches like phylogenetic profiling (80% vs. 30-50% positives out of the 1000 highest-scoring pairs). Combined with the direct coupling analysis of inter-protein residue-residue coevolution, we provide multi-scale evidence for direct but unknown interaction between protein families. An in-depth discussion shows these to be biologically sensible and directly experimentally testable. Negative phyletic couplings highlight alternative solutions for the same functionality, including documented cases of convergent evolution. Thereby our work proves the strong potential of global statistical modeling approaches to genome-wide coevolutionary analysis, far beyond the established use for individual protein complexes and domain-domain interactions.
PID Serval
serval:BIB_9F0D5311B690
PMID
Open Access
Oui
Date de création
2023-09-21T12:32:20.440Z
Date de création dans IRIS
2025-05-21T01:14:43Z