ArticleNucleic acids research2014
Bioinformatic analysis of the protein/DNA interface.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Adaptation of DNA to Protein Binding Revealed by Spectroscopy and Molecular Simulation.The journal of physical chemistry. B · 2025Article
- Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide Repeats.Journal of chemical information and modeling · 2025Article
- Insights into DNA solvation found in protein-DNA structures.Biophysical journal · 2022Review
- Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks.Acta crystallographica. Section D, Structural biology · 2022Article
- A deterministic code for transcription factor-DNA recognition through computation of binding interfaces.NAR genomics and bioinformatics · 2022Article
- Kinetics of the Conformational Transformation between B- and A-Forms in the Drew-Dickerson Dodecamer.ACS omega · 2020Article
- Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org.Acta crystallographica. Section D, Structural biology · 2020Article
- Accurate Representation of Protein-Ligand Structural Diversity in the Protein Data Bank (PDB).International journal of molecular sciences · 2020Article
- The Involvement of the McsB Arginine Kinase in Clp-Dependent Degradation of the MgsR Regulator inFrontiers in microbiology · 2020Article
- Natural Products Containing 'Rare' Organophosphorus Functional Groups.Molecules (Basel, Switzerland) · 2019Review
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- DNAproDB: an interactive tool for structural analysis of DNA-protein complexes.Nucleic acids research · 2017Article
- Knowledge-based prediction of protein backbone conformation using a structural alphabet.PloS one · 2017Article
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- RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information.Nucleic acids research · 2015Article
- Local dynamics of proteins and DNA evaluated from crystallographic B factors.Acta crystallographica. Section D, Biological crystallography · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Prots. Struct. Funct. Genet., 41:271-287)] and dinucleotide conformers [Svozil, Kalina, Omelka and Schneider (2008) (DNA conformations and their sequence preferences. Nucleic Acids Res., 36:3690-3706)], respectively. Assembling the mutually interacting protein blocks and dinucleotide conformers into 'interaction matrices' revealed their correlations and conformer preferences at the interface relative to their occurrence outside the interface. The analyzed data demonstrated important differences between complexes of various types of proteins such as transcription factors and nucleases, distinct interaction patterns for the DNA minor groove relative to the major groove and phosphate and importance of water-mediated contacts. Water molecules mediate proportionally the largest number of contacts in the minor groove and form the largest proportion of contacts in complexes of transcription factors. The generally known induction of A-DNA forms by complexation was more accurately attributed to A-like and intermediate A/B conformers rare in naked DNA molecules.
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