Persistent homology reveals strong phylogenetic signal in 3D protein structures - Archive ouverte HAL Access content directly
Journal Articles PNAS Nexus Year : 2024

Persistent homology reveals strong phylogenetic signal in 3D protein structures

Abstract

Changes that occur in proteins over time provide a phylogenetic signal that can be used to decipher their evolutionary history and the relationships between organisms. Sequence comparison is the most common way to access this phylogenetic signal, while those based on 3D structure comparisons are still in their infancy. In this study, we propose an effective approach based on Persistent Homology Theory (PH) to extract the phylogenetic information contained in protein structures. PH provides efficient and robust algorithms for extracting and comparing geometric features from noisy datasets at different spatial resolutions. PH has a growing number of applications in the life sciences, including the study of proteins (e.g. classification, folding). However, it has never been used to study the phylogenetic signal they may contain. Here, using 518 protein families, representing 22,940 protein sequences and structures, from 10 major taxonomic groups, we show that distances calculated with PH from protein structures correlate strongly with phylogenetic distances calculated from protein sequences, at both small and large evolutionary scales. We test several methods for calculating PH distances and propose some refinements to improve their relevance for addressing evolutionary questions. This work opens up new perspectives in evolutionary biology by proposing an efficient way to access the phylogenetic signal contained in protein structures, as well as future developments of topological analysis in the life sciences.
Fichier principal
Vignette du fichier
bouDagher_PNASnexus_2024.pdf (1.34 Mo) Télécharger le fichier
Origin Files produced by the author(s)
Licence

Dates and versions

hal-04599673 , version 1 (03-06-2024)

Licence

Identifiers

Cite

Léa Bou Dagher, Dominique Madern, Philippe Malbos, Céline Brochier-Armanet. Persistent homology reveals strong phylogenetic signal in 3D protein structures. PNAS Nexus, 2024, 3 (4), pp.158. ⟨10.1093/pnasnexus/pgae158⟩. ⟨hal-04599673⟩
18 View
1 Download

Altmetric

Share

Gmail Mastodon Facebook X LinkedIn More