ArticlePloS one2016
Sequence-Specific Recognition of DNA by Proteins: Binding Motifs Discovered Using a Novel Statistical/Computational Analysis.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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Who cites it
9 citing papers in PubMed, 16 citations in OpenAlex.
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- The harmonized activities of HER2-HER3 heterodimer and deacetylated FOXA1 evade hormone response by regulating FOXA1 chromatin binding.Nucleic acids research · 2025Article
- A quest for cytosolic sequons and their functions.Scientific reports · 2024Article
- Ned Seeman and the prediction of amino acid-basepair motifs mediating protein-nucleic acid recognition.Biophysical journal · 2022Review
- Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182.ACS omega · 2022Article
- ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants.Nucleic acids research · 2022Article
- Amino Acid Interaction (INTAA) web server.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Decades of intensive experimental studies of the recognition of DNA sequences by proteins have provided us with a view of a diverse and complicated world in which few to no features are shared between individual DNA-binding protein families. The originally conceived direct readout of DNA residue sequences by amino acid side chains offers very limited capacity for sequence recognition, while the effects of the dynamic properties of the interacting partners remain difficult to quantify and almost impossible to generalise. In this work we investigated the energetic characteristics of all DNA residue-amino acid side chain combinations in the conformations found at the interaction interface in a very large set of protein-DNA complexes by the means of empirical potential-based calculations. General specificity-defining criteria were derived and utilised to look beyond the binding motifs considered in previous studies. Linking energetic favourability to the observed geometrical preferences, our approach reveals several additional amino acid motifs which can distinguish between individual DNA bases. Our results remained valid in environments with various dielectric properties.
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