ArticleProceedings of the National Academy of Sciences of the United States of America2021
Helicase-like functions in phosphate loop containing beta-alpha polypeptides.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 28 citations in OpenAlex.
- The history of enzyme evolution embedded in metabolism.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The Borderlands of Foldability: Lessons from Simplified Proteins.Trends in chemistry · 2026Article
- A universal polyphosphate kinase powers in vitro transcription.Nature communications · 2026Article
- Rapid discovery of new-to-nature protein domains by novelty-first forcing of language models.bioRxiv : the preprint server for biology · 2025Article
- Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models.bioRxiv : the preprint server for biology · 2025Article
- Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History.Proteins · 2025Article
- Role of Electron Spin, Chirality, and Charge Dynamics in Promoting the Persistence of Nascent Nucleic Acid-Peptide Complexes.The journal of physical chemistry. B · 2025Article
- Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases.Molecular biology and evolution · 2025Article
- On Protein Loops, Prior Molecular States and Common Ancestors of Life.Journal of molecular evolution · 2024Review
- Sequence, Structure, and Functional Space of Drosophila De Novo Proteins.Genome biology and evolution · 2024Article
- Back in time to the Gly-rich prototype of the phosphate binding elementary function.Current research in structural biology · 2024Review
- Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts.Nature communications · 2023Article
- Tracing the birth of structural domains from loops during protein evolution.Scientific reports · 2023Article
- Mixed anhydrides at the intersection between peptide and RNA autocatalytic sets: evolution of biological coding.Interface focus · 2023Article
- On the Origins of Enzymes: Phosphate-Binding Polypeptides Mediate Phosphoryl Transfer to Synthesize Adenosine Triphosphate.Journal of the American Chemical Society · 2023Article
- Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life.Biophysics and physicobiology · 2023Article
- An evolutionary history of the CoA-binding protein Nat/Ivy.Protein science : a publication of the Protein Society · 2022Review
- A Short Tale of the Origin of Proteins and Ribosome Evolution.Microorganisms · 2022Review
- Uniform binding and negative catalysis at the origin of enzymes.Protein science : a publication of the Protein Society · 2022Article
- Folding and Evolution of a Repeat Protein on the Ribosome.Frontiers in molecular biosciences · 2022Article
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Authors and funding
6 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The P-loop Walker A motif underlies hundreds of essential enzyme families that bind nucleotide triphosphates (NTPs) and mediate phosphoryl transfer (P-loop NTPases), including the earliest DNA/RNA helicases, translocases, and recombinases. What were the primordial precursors of these enzymes? Could these large and complex proteins emerge from simple polypeptides? Previously, we showed that P-loops embedded in simple βα repeat proteins bind NTPs but also, unexpectedly so, ssDNA and RNA. Here, we extend beyond the purely biophysical function of ligand binding to demonstrate rudimentary helicase-like activities. We further constructed simple 40-residue polypeptides comprising just one β-(P-loop)-α element. Despite their simplicity, these P-loop prototypes confer functions such as strand separation and exchange. Foremost, these polypeptides unwind dsDNA, and upon addition of NTPs, or inorganic polyphosphates, release the bound ssDNA strands to allow reformation of dsDNA. Binding kinetics and low-resolution structural analyses indicate that activity is mediated by oligomeric forms spanning from dimers to high-order assemblies. The latter are reminiscent of extant P-loop recombinases such as RecA. Overall, these P-loop prototypes compose a plausible description of the sequence, structure, and function of the earliest P-loop NTPases. They also indicate that multifunctionality and dynamic assembly were key in endowing short polypeptides with elaborate, evolutionarily relevant functions.
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