ArticlePLoS computational biology2013
Exploring fold space preferences of new-born and ancient protein superfamilies.
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 25 papers.
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Who cites it
25 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
- Avoiding Catastrophic Mutations Accurately Predicts Amino Acid to Codon Pairing.Journal of molecular evolution · 2026Article
- Coenzyme-protein interactions since early life.eLife · 2025Article
- A novel mobile genetic element with virus-like characteristics is widespread in the world's oceans.bioRxiv : the preprint server for biology · 2025Article
- IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes.PLoS computational biology · 2025Review
- Ig or Not Ig? That Is the Question: The Nucleating Supersecondary Structure of the Ig-Fold and the Extended Ig Universe.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Biological Catalysis and Information Storage Have Relied onBiomolecules · 2023Review
- Similar protein segments shared between domains of different evolutionary lineages.Protein science : a publication of the Protein Society · 2022Article
- 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
- Bridging Themes: Short Protein Segments Found in Different Architectures.Molecular biology and evolution · 2021Article
- A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit.Journal of molecular biology · 2021Article
- The Role of Gene Duplication in the Divergence of Enzyme Function: A Comparative Approach.Frontiers in genetics · 2021Article
- A Conserved Structural Role for the Walker-A Lysine in P-Loop Containing Kinases.Frontiers in molecular biosciences · 2021Article
- Review
- On the emergence of P-Loop NTPase and Rossmann enzymes from a Beta-Alpha-Beta ancestral fragment.eLife · 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
- Differences Between the Raw Material and the Products ofGenetics · 2019Article
- Exploring the dark foldable proteome by considering hydrophobic amino acids topology.Scientific reports · 2017Article
- The early history and emergence of molecular functions and modular scale-free network behavior.Scientific reports · 2016Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The evolution of proteins is one of the fundamental processes that has delivered the diversity and complexity of life we see around ourselves today. While we tend to define protein evolution in terms of sequence level mutations, insertions and deletions, it is hard to translate these processes to a more complete picture incorporating a polypeptide's structure and function. By considering how protein structures change over time we can gain an entirely new appreciation of their long-term evolutionary dynamics. In this work we seek to identify how populations of proteins at different stages of evolution explore their possible structure space. We use an annotation of superfamily age to this space and explore the relationship between these ages and a diverse set of properties pertaining to a superfamily's sequence, structure and function. We note several marked differences between the populations of newly evolved and ancient structures, such as in their length distributions, secondary structure content and tertiary packing arrangements. In particular, many of these differences suggest a less elaborate structure for newly evolved superfamilies when compared with their ancient counterparts. We show that the structural preferences we report are not a residual effect of a more fundamental relationship with function. Furthermore, we demonstrate the robustness of our results, using significant variation in the algorithm used to estimate the ages. We present these age estimates as a useful tool to analyse protein populations. In particularly, we apply this in a comparison of domains containing greek key or jelly roll motifs.
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