ArticleNucleic acids research2008
Protein-DNA interactions: structural, thermodynamic and clustering patterns of conserved residues in DNA-binding proteins.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Several multiple sequence alignment-perturbing methods enhance AlphaFold3 sampling of alternative protein states.Communications chemistry · 2026Article
- RGTBind: RBF-gate graph transformer with spatially biased attention for protein-DNA binding-site prediction.Journal of molecular modeling · 2026Article
- Article
- Mutations found in cancer patients compromise DNA binding of the winged helix protein STK19.Scientific reports · 2024Article
- How acidic amino acid residues facilitate DNA target site selection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Host-pathogen protein-nucleic acid interactions: A comprehensive review.Computational and structural biotechnology journal · 2022Review
- ProDFace: A web-tool for the dissection of protein-DNA interfaces.Frontiers in molecular biosciences · 2022Article
- Proximity labeling: an emerging tool for probingPlant communications · 2021Review
- Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification.BMC bioinformatics · 2020Article
- Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties.PLoS computational biology · 2020Article
- The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis.Bioinformatics (Oxford, England) · 2019Article
- Molecular Modeling Applied to Nucleic Acid-Based Molecule Development.Biomolecules · 2018Review
- Functional insights into the Streptococcus pneumoniae HicBA toxin-antitoxin system based on a structural study.Nucleic acids research · 2018Article
- Structural changes in DNA-binding proteins on complexation.Nucleic acids research · 2018Article
- Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism.Nucleic acids research · 2018Article
- Functional details of the Mycobacterium tuberculosis VapBC26 toxin-antitoxin system based on a structural study: insights into unique binding and antibiotic peptides.Nucleic acids research · 2017Article
- An overview of the prediction of protein DNA-binding sites.International journal of molecular sciences · 2015Review
- Bioinformatic analysis of the protein/DNA interface.Nucleic acids research · 2014Article
- mCSM: predicting the effects of mutations in proteins using graph-based signatures.Bioinformatics (Oxford, England) · 2014Article
- DNA motif elucidation using belief propagation.Nucleic acids research · 2013Article
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4 authors.
Funding
Abstract
Amino acid residues, which play important roles in protein function, are often conserved. Here, we analyze thermodynamic and structural data of protein-DNA interactions to explore a relationship between free energy, sequence conservation and structural cooperativity. We observe that the most stabilizing residues or putative hotspots are those which occur as clusters of conserved residues. The higher packing density of the clusters and available experimental thermodynamic data of mutations suggest cooperativity between conserved residues in the clusters. Conserved singlets contribute to the stability of protein-DNA complexes to a lesser extent. We also analyze structural features of conserved residues and their clusters and examine their role in identifying DNA-binding sites. We show that about half of the observed conserved residue clusters are in the interface with the DNA, which could be identified from their amino acid composition; whereas the remaining clusters are at the protein-protein or protein-ligand interface, or embedded in the structural scaffolds. In protein-protein interfaces, conserved residues are highly correlated with experimental residue hotspots, contributing dominantly and often cooperatively to the stability of protein-protein complexes. Overall, the conservation patterns of the stabilizing residues in DNA-binding proteins also highlight the significance of clustering as compared to single residue conservation.
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