ArticleProtein science : a publication of the Protein Society2010
A galaxy of folds.
Article in Protein science : a publication of the Protein Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 84 citations in OpenAlex.
- 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
- The Ascent of Miniproteins.Biochemistry · 2026Review
- TEDLH: domain HMMs for sensitive detection of remote homologues.Bioinformatics (Oxford, England) · 2026Article
- Structure and Disorder Predictions of Microproteins: Usage, Applications, and Pitfalls.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Exploiting peptide chirality and transport to dissect the complex mechanism of action of host peptides on bacteria.PLoS genetics · 2025Article
- Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record.Genome biology and evolution · 2025Article
- Protein Fold Usages in Ribosomes: Another Glance to the Past.International journal of molecular sciences · 2024Article
- Sequence, Structure, and Functional Space of Drosophila De Novo Proteins.Genome biology and evolution · 2024Article
- Article
- Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra.Genome biology · 2023Article
- Structural screens identify candidate human homologs of insect chemoreceptors and crypticeLife · 2023Article
- A review of visualisations of protein fold networks and their relationship with sequence and function.Biological reviews of the Cambridge Philosophical Society · 2023Review
- Similar protein segments shared between domains of different evolutionary lineages.Protein science : a publication of the Protein Society · 2022Article
- ProtGPT2 is a deep unsupervised language model for protein design.Nature communications · 2022Article
- Mechanisms of protein evolution.Protein science : a publication of the Protein Society · 2022Review
- Evidence for the emergence of β-trefoils by 'Peptide Budding' from an IgG-like β-sandwich.PLoS computational biology · 2022Article
- Evolution of networks of protein domain organization.Scientific reports · 2021Article
- Evolution, folding, and design of TIM barrels and related proteins.Current opinion in structural biology · 2021Review
- Bridging Themes: Short Protein Segments Found in Different Architectures.Molecular biology and evolution · 2021Article
- Master Blaster: an approach to sensitive identification of remotely related proteins.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many protein classification systems capture homologous relationships by grouping domains into families and superfamilies on the basis of sequence similarity. Superfamilies with similar 3D structures are further grouped into folds. In the absence of discernable sequence similarity, these structural similarities were long thought to have originated independently, by convergent evolution. However, the growth of databases and advances in sequence comparison methods have led to the discovery of many distant evolutionary relationships that transcend the boundaries of superfamilies and folds. To investigate the contributions of convergent versus divergent evolution in the origin of protein folds, we clustered representative domains of known structure by their sequence similarity, treating them as point masses in a virtual 2D space which attract or repel each other depending on their pairwise sequence similarities. As expected, families in the same superfamily form tight clusters. But often, superfamilies of the same fold are linked with each other, suggesting that the entire fold evolved from an ancient prototype. Strikingly, some links connect superfamilies with different folds. They arise from modular peptide fragments of between 20 and 40 residues that co-occur in the connected folds in disparate structural contexts. These may be descendants of an ancestral pool of peptide modules that evolved as cofactors in the RNA world and from which the first folded proteins arose by amplification and recombination. Our galaxy of folds summarizes, in a single image, most known and many yet undescribed homologous relationships between protein superfamilies, providing new insights into the evolution of protein domains.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.