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.

• Klíčová slova
• DNA shape, hydrophobic, indirect readout, minor groove, protein–DNA interaction, specific recognition,
• MeSH
• algoritmy MeSH
• aminokyselinové motivy MeSH
• aminokyseliny chemie   MeSH
• Arabidopsis metabolismus   MeSH
• DNA vazebné proteiny metabolismus   MeSH
• DNA chemie   MeSH
• fenylalanin chemie   MeSH
• hydrofobní a hydrofilní interakce * MeSH
• konformace nukleové kyseliny MeSH
• kyselina glutamová chemie   MeSH
• lidé MeSH
• proteiny chemie   MeSH
• Saccharomyces cerevisiae metabolismus   MeSH
• sekundární struktura proteinů MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• aminokyseliny MeSH
• DNA vazebné proteiny MeSH
• DNA MeSH
• fenylalanin MeSH
• kyselina glutamová MeSH
• proteiny MeSH