ArticleScientific reports2016
The early history and emergence of molecular functions and modular scale-free network behavior.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- 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
- Tracing the birth and intrinsic disorder of loops and domains in protein evolution.Biophysical reviews · 2024Review
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.Viruses · 2024Review
- Primitive purine biosynthesis connects ancient geochemistry to modern metabolism.Nature ecology & evolution · 2024Article
- Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction.Life (Basel, Switzerland) · 2024Review
- 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
- Evolution of Intrinsic Disorder in Protein Loops.Life (Basel, Switzerland) · 2023Article
- Tracing the birth of structural domains from loops during protein evolution.Scientific reports · 2023Article
- Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-Modular Coupling.International journal of molecular sciences · 2022Article
- Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer.Science advances · 2022Article
- The rise of hierarchy and modularity in biological networks explained by empedocles' double tale ∼2,400 years before darwin and systems biology.Frontiers in genetics · 2022Article
- Evolution of networks of protein domain organization.Scientific reports · 2021Article
- Deriving and Using Descriptors of Elementary Functions in Rational Protein Design.Frontiers in bioinformatics · 2021Article
- The Compressed Vocabulary of Microbial Life.Frontiers in microbiology · 2021Article
- On the evolution of protein-adenine binding.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism.Nature ecology & evolution · 2019Article
- More Pieces of Ancient than Recent Theoretical Minimal Proto-tRNA-Like RNA Rings in Genes Coding for tRNA Synthetases.Journal of molecular evolution · 2019Article
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3 authors.
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Abstract
The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold. Here we trace domain history onto a bipartite network of elementary functional loop sequences and domain structures defined at the fold superfamily level of SCOP classification. The resulting 'elementary functionome' network and its loop motif and structural domain graph projections create evolutionary 'waterfalls' describing the emergence of primordial functions. Waterfalls reveal how ancient loops are shared by domain structures in two initial waves of functional innovation that involve founder 'p-loop' and 'winged helix' domain structures. They also uncover a dynamics of modular motif embedding in domain structures that is ongoing, which transfers 'preferential' cooption properties of ancient loops to emerging domains. Remarkably, we find that the emergence of molecular functions induces hierarchical modularity and power law behavior in network evolution as the network of motifs and structures expand metabolic pathways and translation.
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