1 Main Manuscript for Revealing Atomic-scale Molecular Diffusion of a Plant Transcription Factor WRKY domain protein along DNA Liqiang Dai 1† , Yongping Xu 2† , Zhenwei Du 2 , Xiao-dong Su 2 *, and Jin Yu 3 * 1 Beijing Computational Science Research Center, Beijing, 100193, China 2 State Key Laboratory of Protein and Plant Gene Research, and Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China 3 Department of Physics and Astronomy, University of California, Irvine, CA 92697, USA † These authors are of equal contributions * Corresponding authors: Jin Yu, Xiao-dong Su Email: jin.yu@uci.edu; xdsu@pku.edu.cn ORCID: 0000-0001-8224-1374 Classification Biophysics and Computational Biology Keywords facilitated diffusion, molecular dynamics, specific recognition, WRKY, transcription factor Author Contributions Jin Yu and Xiao-dong Su designed the study. Liqiang Dai conducted the MD simulations and coarse-grained simulations and analyzed the related data. Yongping Xu solved the crystal structure of WRKY-DNA complex and conducted ITC experiment. Zhenwei Du conducted the single-molecule fluorescence experiments of WRKY diffusing on DNA. This PDF file includes: Main Text Figures 1 to 5 Supplementary Information . CC-BY-ND 4.0 International license preprint (which was not certified by peer review) is the author/funder. It is made available under a The copyright holder for this this version posted February 15, 2020. . https://doi.org/10.1101/2020.02.14.950295 doi: bioRxiv preprint