ArticleProteins2016
Statistical analysis of structural determinants for protein-DNA-binding specificity.
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 38 citations in OpenAlex.
- A meta-analysis of genome-wide association studies to identify candidate genes associated with feed efficiency traits in pigs.Journal of animal science · 2025Pooled it
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- Molecular Mechanisms of Gain-of-Function Mutations in λ Cro Revealed by Molecular Dynamics Simulations.ACS physical chemistry Au · 2025Article
- DNA binding and transposition activity of the Sleeping Beauty transposase: role of structural stability of the primary DNA-binding domain.Nucleic acids research · 2025Article
- Accurate prediction of nucleic acid binding proteins using protein language model.Bioinformatics advances · 2025Article
- Deciphering the Intracellular Action of the Antimicrobial Peptide A11 via an In-Depth Analysis of Its Effect on the Global Proteome ofACS infectious diseases · 2024Article
- EGPDI: identifying protein-DNA binding sites based on multi-view graph embedding fusion.Briefings in bioinformatics · 2024Article
- Improved prediction of DNA and RNA binding proteins with deep learning models.Briefings in bioinformatics · 2024Article
- Conformational Change of Transcription Factors from Search to Specific Binding: AThe journal of physical chemistry. B · 2022Article
- Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1.Nature communications · 2022Article
- Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches.Biomolecules · 2022Review
- Insights into protein-DNA interactions from hydrogen bond energy-based comparative protein-ligand analyses.Proteins · 2022Article
- The molecular basis of FimT-mediated DNA uptake during bacterial natural transformation.Nature communications · 2022Article
- ProDFace: A web-tool for the dissection of protein-DNA interfaces.Frontiers in molecular biosciences · 2022Article
- A comparative study of protein-ssDNA interactions.NAR genomics and bioinformatics · 2021Article
- New insights into protein-DNA binding specificity from hydrogen bond based comparative study.Nucleic acids research · 2019Article
- An SVM-based method for assessment of transcription factor-DNA complex models.BMC bioinformatics · 2018Article
- Structural changes in DNA-binding proteins on complexation.Nucleic acids research · 2018Article
- Article
- DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
DNA-binding proteins play critical roles in biological processes including gene expression, DNA packaging and DNA repair. They bind to DNA target sequences with different degrees of binding specificity, ranging from highly specific (HS) to nonspecific (NS). Alterations of DNA-binding specificity, due to either genetic variation or somatic mutations, can lead to various diseases. In this study, a comparative analysis of protein-DNA complex structures was carried out to investigate the structural features that contribute to binding specificity. Protein-DNA complexes were grouped into three general classes based on degrees of binding specificity: HS, multispecific (MS), and NS. Our results show a clear trend of structural features among the three classes, including amino acid binding propensities, simple and complex hydrogen bonds, major/minor groove and base contacts, and DNA shape. We found that aspartate is enriched in HS DNA binding proteins and predominately binds to a cytosine through a single hydrogen bond or two consecutive cytosines through bidentate hydrogen bonds. Aromatic residues, histidine and tyrosine, are highly enriched in the HS and MS groups and may contribute to specific binding through different mechanisms. To further investigate the role of protein flexibility in specific protein-DNA recognition, we analyzed the conformational changes between the bound and unbound states of DNA-binding proteins and structural variations. The results indicate that HS and MS DNA-binding domains have larger conformational changes upon DNA-binding and larger degree of flexibility in both bound and unbound states. Proteins 2016; 84:1147-1161. © 2016 Wiley Periodicals, Inc.
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Registered trials
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