Open AccessRevealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA
Author(s) -
Liqiang Dai,
Yongping Xu,
Zhenwei Du,
XiaoDong Su,
Yu Jin
Publication year - 2021
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.2102621118
Subject(s) - hmg box , dna binding domain , dna , biology , protein–dna interaction , transcription factor , genetics , dna binding site , biophysics , dna clamp , computational biology , dna binding protein , gene , promoter , reverse transcriptase , gene expression , polymerase chain reaction
Significance In transcription factors’ search for target genes, one-dimensional diffusion of the protein along DNA is essential. Experimentally, it remains challenging to resolve the individual diffusional steps of protein on DNA. Here, we report mainly all-atom equilibrium simulations of a WRKY domain protein in association with and diffusion along DNA. We demonstrate a complete stepping cycle of the protein for one base pair on DNA within microseconds, along with stochastic motions. Processive protein diffusions on DNA have been further sampled in a coarse-grained model. We have also found preferential DNA-strand association of the domain protein, which becomes most prominent at specific DNA binding, and it can be common for small-domain proteins to balance movements on the DNA with the sequence recognition.