ArticleScientific reports2021
Evolution of networks of protein domain organization.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed, 50 citations in OpenAlex.
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- 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 the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model.Journal of molecular evolution · 2025Article
- ARIES domains: functional signaling units of type I interferon responses.The FEBS journal · 2025Review
- Genome-Wide Analysis and Expression Profiling of the JAZ Gene Family in Response to Abiotic Stress in Alfalfa.International journal of molecular sciences · 2025Article
- Lessons from Deep Learning Structural Prediction of Multistate Multidomain Proteins-The Case Study of Coiled-Coil NOD-like Receptors.International journal of molecular sciences · 2025Article
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- The Evolutionary Potential of Chromoanagenesis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Tracing the birth and intrinsic disorder of loops and domains in protein evolution.Biophysical reviews · 2024Review
- Molecular Functional and Transcriptome Analysis ofPlants (Basel, Switzerland) · 2024Article
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Deciphering domain structures of Aspergillus and Streptomyces GH3-β-Glucosidases: a screening system for enzyme engineering and biotechnological applications.BMC research notes · 2024Article
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- Detecting genetic gain and loss events in terms of protein domain: Method and implementation.Heliyon · 2024Article
- Living in trinity of extremes: Genomic and proteomic signatures of halophilic, thermophilic, and pH adaptation.Current research in structural biology · 2024Article
- Back in time to the Gly-rich prototype of the phosphate binding elementary function.Current research in structural biology · 2024Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evolution. A time series of networks revealed two ancient waves of structural novelty arising from ancient 'p-loop' and 'winged helix' domains and a massive 'big bang' of domain organization. The evolutionary recruitment of domains was highly modular, hierarchical and ongoing. Domain rearrangements elicited non-random and scale-free network structure. Comparative analyses of preferential attachment, randomness and modularity showed yin-and-yang complementary transition and biphasic patterns along the structural chronology. Remarkably, the evolving networks highlighted a central evolutionary role of cofactor-supporting structures of non-ribosomal peptide synthesis pathways, likely crucial to the early development of the genetic code. Some highly modular domains featured dual response regulation in two-component signal transduction systems with DNA-binding activity linked to transcriptional regulation of responses to environmental change. Interestingly, hub domains across the evolving networks shared the historical role of DNA binding and editing, an ancient protein function in molecular evolution. Our investigation unfolds historical source-sink patterns of evolutionary recruitment that further our understanding of protein architectures and functions.
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