ArticlePLoS computational biology2013
Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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37 citing papers in PubMed, 57 citations in OpenAlex.
- Universal and Lineage-Specific Patterns in the Distribution of ECOD Domain Homology Groups Across Superkingdoms.Proteins · 2026Article
- Domain classification of archaeal proteomes reveals conserved fold repertoire.PLoS computational biology · 2026Article
- Phylogeny Building for Structural Phylogenomic Research.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases.Molecular biology and evolution · 2025Article
- Evolution of intrinsic disorder in the structural domains of viral and cellular proteomes.Scientific reports · 2025Article
- Tracing the birth and intrinsic disorder of loops and domains in protein evolution.Biophysical reviews · 2024Review
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Protein Fold Usages in Ribosomes: Another Glance to the Past.International journal of molecular sciences · 2024Article
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- Origins and Functional Significance of Eukaryotic Protein Folds.Journal of molecular evolution · 2023Article
- Biological Catalysis and Information Storage Have Relied onBiomolecules · 2023Review
- Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich.PLoS computational biology · 2022Article
- Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase.Protein science : a publication of the Protein Society · 2021Article
- The Role of Gene Duplication in the Divergence of Enzyme Function: A Comparative Approach.Frontiers in genetics · 2021Article
- Review
- On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment.eLife · 2020Article
- The origin and evolution of viruses inferred from fold family structure.Archives of virology · 2020Review
- Exploring the sequence fitness landscape of a bridge between protein folds.PLoS computational biology · 2020Article
- Short and simple sequences favored the emergence of N-helix phospho-ligand binding sites in the first enzymes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Bacterial Origin and Reductive Evolution of the CPR Group.Genome biology and evolution · 2020Article
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The spatial arrangements of secondary structures in proteins, irrespective of their connectivity, depict the overall shape and organization of protein domains. These features have been used in the CATH and SCOP classifications to hierarchically partition fold space and define the architectural make up of proteins. Here we use phylogenomic methods and a census of CATH structures in hundreds of genomes to study the origin and diversification of protein architectures (A) and their associated topologies (T) and superfamilies (H). Phylogenies that describe the evolution of domain structures and proteomes were reconstructed from the structural census and used to generate timelines of domain discovery. Phylogenies of CATH domains at T and H levels of structural abstraction and associated chronologies revealed patterns of reductive evolution, the early rise of Archaea, three epochs in the evolution of the protein world, and patterns of structural sharing between superkingdoms. Phylogenies of proteomes confirmed the early appearance of Archaea. While these findings are in agreement with previous phylogenomic studies based on the SCOP classification, phylogenies unveiled sharing patterns between Archaea and Eukarya that are recent and can explain the canonical bacterial rooting typically recovered from sequence analysis. Phylogenies of CATH domains at A level uncovered general patterns of architectural origin and diversification. The tree of A structures showed that ancient structural designs such as the 3-layer (αβα) sandwich (3.40) or the orthogonal bundle (1.10) are comparatively simpler in their makeup and are involved in basic cellular functions. In contrast, modern structural designs such as prisms, propellers, 2-solenoid, super-roll, clam, trefoil and box are not widely distributed and were probably adopted to perform specialized functions. Our timelines therefore uncover a universal tendency towards protein structural complexity that is remarkable.
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