ArticleProceedings of the National Academy of Sciences of the United States of America2020
On the evolution of protein-adenine binding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 41 citations in OpenAlex.
- Compositionally Biased Regions Within Structured Protein Domains.Biomolecules · 2026Article
- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Coenzyme-protein interactions since early life.eLife · 2025Article
- Comparative Dynamics Enables Discovery of Embedded Bacterial Ferredoxin Domains in Large Redox Enzymes.Proteins · 2025Article
- ATP allosterically regulates an acyl-CoA oxidase.Nature communications · 2025Article
- Metabolomic profiling of adenine-induced CKD: pathway interconnections and kidney injury.Toxicology research · 2025Article
- From Catalysis of Evolution to Evolution of Catalysis.Accounts of chemical research · 2024Article
- Reused Protein Segments Linked to Functional Dynamics.Molecular biology and evolution · 2024Article
- Back in time to the Gly-rich prototype of the phosphate binding elementary function.Current research in structural biology · 2024Review
- A transient vesicular glue for amplification and temporal regulation of biocatalytic reaction networks.Chemical science · 2023Article
- Mechanistic Insights into Harmine-Mediated Inhibition of Human DNA Methyltransferases and Prostate Cancer Cell Growth.ACS chemical biology · 2023Article
- Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase.Current research in structural biology · 2023Article
- Defining A Global Map of Functional Group-based 3D Ligand-binding Motifs.Genomics, proteomics & bioinformatics · 2022Article
- Human Virus Genomes Are Enriched in Conserved Adenine/Thymine/Uracil Multiple Tracts That Pause Polymerase Progression.Frontiers in microbiology · 2022Article
- De novo proteins from random sequences through in vitro evolution.Current opinion in structural biology · 2021Review
- Bridging Themes: Short Protein Segments Found in Different Architectures.Molecular biology and evolution · 2021Article
- Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.Science advances · 2021Article
- Driving forces in the origins of life.Open biology · 2021Article
- Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages.Frontiers in cellular and infection microbiology · 2021Article
- Fuzzle 2.0: Ligand Binding in Natural Protein Building Blocks.Frontiers in molecular biosciences · 2021Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins' interactions with ancient ligands may reveal how molecular recognition emerged and evolved. We explore how proteins recognize adenine: a planar rigid fragment found in the most common and ancient ligands. We have developed a computational pipeline that extracts protein-adenine complexes from the Protein Data Bank, structurally superimposes their adenine fragments, and detects the hydrogen bonds mediating the interaction. Our analysis extends the known motifs of protein-adenine interactions in the Watson-Crick edge of adenine and shows that all of adenine's edges may contribute to molecular recognition. We further show that, on the proteins' side, binding is often mediated by specific amino acid segments ("themes") that recur across different proteins, such that different proteins use the same themes when binding the same adenine-containing ligands. We identify numerous proteins that feature these themes and are thus likely to bind adenine-containing ligands. Our analysis suggests that adenine binding has emerged multiple times in evolution.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.