ArticleProceedings of the National Academy of Sciences of the United States of America2017
Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 47 papers.
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47 citing papers in PubMed.
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- Coenzyme-protein interactions since early life.eLife · 2025Article
- Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes.Proteins · 2025Article
- Science of the gaps.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record.Genome biology and evolution · 2025Article
- In silico evolution of globular protein folds from random sequences.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- NeuroScale: evolutional scale-based protein language models enable prediction of neuropeptides.BMC biology · 2025Article
- Tracing the birth and intrinsic disorder of loops and domains in protein evolution.Biophysical reviews · 2024Review
- Protein language models learn evolutionary statistics of interacting sequence motifs.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Deep generative models of protein structure uncover distant relationships across a continuous fold space.Nature communications · 2024Article
- Reused Protein Segments Linked to Functional Dynamics.Molecular biology and evolution · 2024Article
- 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
- Retracing the evolution of a modern periplasmic binding protein.Protein science : a publication of the Protein Society · 2023Article
- Tracing the birth of structural domains from loops during protein evolution.Scientific reports · 2023Article
- Fluid protein fold space and its implications.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- Identification of a covert evolutionary pathway between two protein folds.Nature communications · 2023Article
- Creative destruction: New protein folds from old.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins share similar segments with one another. Such "reused parts"-which have been successfully incorporated into other proteins-are likely to offer an evolutionary advantage over de novo evolved segments, as most of the latter will not even have the capacity to fold. To systematically explore the evolutionary traces of segment "reuse" across proteins, we developed an automated methodology that identifies reused segments from protein alignments. We search for "themes"-segments of at least 35 residues of similar sequence and structure-reused within representative sets of 15,016 domains [Evolutionary Classification of Protein Domains (ECOD) database] or 20,398 chains [Protein Data Bank (PDB)]. We observe that theme reuse is highly prevalent and that reuse is more extensive when the length threshold for identifying a theme is lower. Structural domains, the best characterized form of reuse in proteins, are just one of many complex and intertwined evolutionary traces. Others include long themes shared among a few proteins, which encompass and overlap with shorter themes that recur in numerous proteins. The observed complexity is consistent with evolution by duplication and divergence, and some of the themes might include descendants of ancestral segments. The observed recursive footprints, where the same amino acid can simultaneously participate in several intertwined themes, could be a useful concept for protein design. Data are available at http://trachel-srv.cs.haifa.ac.il/rachel/ppi/themes/.
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