ArticleScientific reports2023
Tracing the birth of structural domains from loops during protein evolution.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Revisiting Eck and Dayhoff's Building Block Model of Ferredoxin Evolution on Dayhoff's 100th Birthday.Journal of molecular evolution · 2026Article
- Tracing the Origin and Evolution of the Secondary Structure of RNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Tracing Molecular Chronologies Onto Growing Biological Networks.Methods in molecular biology (Clifton, N.J.) · 2026Article
- 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
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- Back in time to the Gly-rich prototype of the phosphate binding elementary function.Current research in structural biology · 2024Review
- Evolution of Intrinsic Disorder in Protein Loops.Life (Basel, Switzerland) · 2023Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The structures and functions of proteins are embedded into the loop scaffolds of structural domains. Their origin and evolution remain mysterious. Here, we use a novel graph-theoretical approach to describe how modular and non-modular loop prototypes combine to form folded structures in protein domain evolution. Phylogenomic data-driven chronologies reoriented a bipartite network of loops and domains (and its projections) into 'waterfalls' depicting an evolving 'elementary functionome' (EF). Two primordial waves of functional innovation involving founder 'p-loop' and 'winged-helix' domains were accompanied by an ongoing emergence and reuse of structural and functional novelty. Metabolic pathways expanded before translation functionalities. A dual hourglass recruitment pattern transferred scale-free properties from loop to domain components of the EF network in generative cycles of hierarchical modularity. Modeling the evolutionary emergence of the oldest P-loop and winged-helix domains with AlphFold2 uncovered rapid convergence towards folded structure, suggesting that a folding vocabulary exists in loops for protein fold repurposing and design.
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