ArticleeLife2015
A vocabulary of ancient peptides at the origin of folded proteins.
Article in eLife, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers.
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Who cites it
134 citing papers in PubMed.
- The history of enzyme evolution embedded in metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Contrastive learning unites sequence and structure in a global representation of protein space.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- TEDLH: domain HMMs for sensitive detection of remote homologues.Bioinformatics (Oxford, England) · 2026Article
- Review
- Exploring the structural lexicon of the Proteome via Metric Geometry.PLoS computational biology · 2026Article
- From atoms to fragments: a coarse representation for efficient and functional protein design.Bioinformatics (Oxford, England) · 2026Article
- Fold-Switching Proteins.Annual review of biophysics · 2026Review
- Descent from a common ancestor restricts exploration of protein sequence space.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Automatically Defining Protein Words for Diverse Functional Predictions Based on Attention Analysis of a Protein Language Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Evolution of intrinsically disordered regions in vertebrate galectins for phase separation.EMBO reports · 2026Article
- Structural basis for transcriptional regulation by the cell division regulator MraZ in Mycoplasma genitalium.Nature communications · 2026Article
- A universal polyphosphate kinase powers in vitro transcription.Nature communications · 2026Article
- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Structure and Disorder Predictions of Microproteins: Usage, Applications, and Pitfalls.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Coenzyme-protein interactions since early life.eLife · 2025Article
- Science of the gaps.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models.bioRxiv : the preprint server for biology · 2025Article
- RNA binding and coacervation promote preservation of peptide form and function across the heterochiral-homochiral divide.Protein science : a publication of the Protein Society · 2025Article
- On the emergence of metabolism: the evolution of proteins that powered life.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record.Genome biology and evolution · 2025Article
74 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The seemingly limitless diversity of proteins in nature arose from only a few thousand domain prototypes, but the origin of these themselves has remained unclear. We are pursuing the hypothesis that they arose by fusion and accretion from an ancestral set of peptides active as co-factors in RNA-dependent replication and catalysis. Should this be true, contemporary domains may still contain vestiges of such peptides, which could be reconstructed by a comparative approach in the same way in which ancient vocabularies have been reconstructed by the comparative study of modern languages. To test this, we compared domains representative of known folds and identified 40 fragments whose similarity is indicative of common descent, yet which occur in domains currently not thought to be homologous. These fragments are widespread in the most ancient folds and enriched for iron-sulfur- and nucleic acid-binding. We propose that they represent the observable remnants of a primordial RNA-peptide world.
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