Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA.

ABSTRACT: Transcription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here, we constructed a TF model system using the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on DNA by employing all-atom molecular-dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to one strand of DNA with significant energetic bias compared with the other, or nonpreferred strand. The preferential DNA-strand binding becomes most prominent in the static process, from nonspecific to specific DNA binding, but less distinct during diffusive movements of the domain protein on the DNA. Remarkably, w

SUBMITTER: Dai L 

PROVIDER: S-EPMC8201915 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature