Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors.

ABSTRACT: Activator proteins 1 (AP-1) comprise one of the largest families of eukaryotic basic leucine zipper transcription factors. Despite advances in the characterization of AP-1 DNA-binding sites, our ability to predict new binding sites and explain how the proteins achieve different gene expression levels remains limited. Here we address the role of sequence-specific DNA flexibility for stability and specific binding of AP-1 factors, using microsecond-long molecular dynamics simulations. As a model system, we employ yeast AP-1 factor Yap1 binding to three different response elements from two genetic environments. Our data show that Yap1 actively exploits the sequence-specific flexibility of DNA within the response element to form stable protein-DNA complexes. The stability also depends on the f

SUBMITTER: Horberg J 

PROVIDER: S-EPMC8450079 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature