Hydrophobic Amino Acids as Universal Elements of Protein-Induced DNA Structure Deformation.

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 hydrophob

SUBMITTER: Faltejskova K 

PROVIDER: S-EPMC7312683 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature