Accéder directement au contenu Accéder directement à la navigation
Article dans une revue

Centrality Measures in Residue Interaction Networks to Highlight Amino Acids in Protein–Protein Binding

Abstract : Residue interaction networks (RINs) describe a protein structure as a network of interacting residues. Central nodes in these networks, identified by centrality analyses, highlight those residues that play a role in the structure and function of the protein. However, little is known about the capability of such analyses to identify residues involved in the formation of macromolecular complexes. Here, we performed six different centrality measures on the RINs generated from the complexes of the SKEMPI 2 database of changes in protein–protein binding upon mutation in order to evaluate the capability of each of these measures to identify major binding residues. The analyses were performed with and without the crystallographic water molecules, in addition to the protein residues. We also investigated the use of a weight factor based on the inter-residue distances to improve the detection of these residues. We show that for the identification of major binding residues, closeness, degree, and PageRank result in good precision, whereas betweenness, eigenvector, and residue centrality analyses give a higher sensitivity. Including water in the analysis improves the sensitivity of all measures without losing precision. Applying weights only slightly raises the sensitivity of eigenvector centrality analysis. We finally show that a combination of multiple centrality analyses is the optimal approach to identify residues that play a role in protein–protein interaction.
Type de document :
Article dans une revue
Liste complète des métadonnées

https://hal.univ-lille.fr/hal-03373325
Contributeur : Lilloa Université de Lille Connectez-vous pour contacter le contributeur
Soumis le : lundi 11 octobre 2021 - 14:26:59
Dernière modification le : mardi 19 octobre 2021 - 11:33:30

Fichier

fbinf-01-684970.pdf
Fichiers produits par l'(les) auteur(s)

Licence


Distributed under a Creative Commons Paternité 4.0 International License

Identifiants

Collections

`

Citation

Guillaume Brysbaert, Marc Lensink. Centrality Measures in Residue Interaction Networks to Highlight Amino Acids in Protein–Protein Binding. Frontiers in Bioinformatics, 2021, Frontiers in Bioinformatics, 1, ⟨10.3389/fbinf.2021.684970⟩. ⟨hal-03373325⟩

Partager

Métriques

Consultations de la notice

12

Téléchargements de fichiers

12