ArticleInternational journal of molecular sciences2020
Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 13 citations in OpenAlex.
- Cancer-associated TRF1 mutations alter PARP1 interaction dynamics: an in silico study.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- Protein Representation in Metric Spaces for Protein Druggability Prediction: A Case Study on Aspirin.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting.Nucleic acids research · 2025Article
- Chia Derived Peptides Affecting Bacterial Membrane and DNA: Insights from Staphylococcus aureus and Escherichia coli Studies.Plant foods for human nutrition (Dordrecht, Netherlands) · 2024Article
- Cryo-EM Structure of AAV2 Rep68 bound to integration site AAVS1: Insights into the mechanism of DNA melting.bioRxiv : the preprint server for biology · 2024Article
- Identification and Functional Analysis of a Novel Hydrophobic Protein VdHP1 from Verticillium dahliae.Microbiology spectrum · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Interaction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein-DNA complexes, we propose that distortion of the DNA minor groove resulting from interactions with hydrophobic amino acid residues is a universal element of protein-DNA recognition. We provide evidence to support this by associating each DNA minor groove-binding amino acid residue with the local dimensions of the DNA double helix using a novel algorithm. The widened DNA minor grooves are associated with high GC content. However, some AT-rich sequences contacted by hydrophobic amino acids (e.g., phenylalanine) display extreme values of minor groove width as well. For a number of hydrophobic amino acids, distinct secondary structure preferences could be identified for residues interacting with the widened DNA minor groove. These results hold even after discarding the most populous families of minor groove-binding proteins.
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Registered trials
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