ArticleProceedings of the National Academy of Sciences of the United States of America2021
Revealing atomic-scale molecular diffusion of a plant-transcription factor WRKY domain protein along DNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 41 citations in OpenAlex.
- Functional and regulatory complexity: challenges and prospects for understanding rice WRKY transcription factors.Journal of experimental botany · 2026Review
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.PNAS nexus · 2026Article
- WRKY transcription factors govern selenium metabolism in Broussonetia papyrifera: genome-wide identification, expression profiling, and regulatory network analysis.BMC plant biology · 2026Article
- Polyacylated Delphinidin Biosynthesis Catalysed by PhF3'5'H-PhBGLU12-PhSCPL2 Determines the Blue Pigmentation in Cineraria (Pericallis hybrida).Plant biotechnology journal · 2025Article
- Article
- Conformational plasticity of disordered regions enables sequence-diverse DNA recognition by transcription factor AflR.Nature communications · 2025Article
- Genome-Wide Expression Profile ofInternational journal of molecular sciences · 2025Article
- AlkD's Conformational Dynamics Regulated by Protein-DNA Interactions for Effective Target Recognition.The journal of physical chemistry letters · 2025Article
- Mechanisms of enhanced or impaired DNA target selectivity driven by protein dimerization.bioRxiv : the preprint server for biology · 2025Article
- Multisite λ-Dynamics for Protein-DNA Binding Affinity Prediction.Journal of chemical theory and computation · 2025Article
- Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences.Biophysical journal · 2025Article
- Identification of WRKY transcription factors in Ipomoea pes-caprae and functional role of IpWRKY16 in sweet potato salt stress response.BMC plant biology · 2024Article
- Transient interactions modulate the affinity of NF-κB transcription factors for DNA.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Nonspecific vs. specific DNA binding free energetics of a transcription factor domain protein.Biophysical journal · 2023Article
- Genome-Wide Characterization of the Maize (International journal of molecular sciences · 2023Article
- Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes.Functional & integrative genomics · 2023Article
- Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field.Nucleic acids research · 2022Article
- Insights into protein-DNA interactions from hydrogen bond energy-based comparative protein-ligand analyses.Proteins · 2022Article
- Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations.PLoS computational biology · 2022Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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, without employing acceleration forces or bias, we captured a complete one-base-pair stepping cycle of the protein tracking along major groove of DNA with a homogeneous poly-adenosine sequence, as individual hydrogen bonds break and reform at the protein-DNA binding interface. Further DNA-groove tracking motions of the protein forward or backward, with occasional sliding as well as strand crossing to minor groove of DNA, were also captured. The processive diffusion of WRKY along DNA has been further sampled via coarse-grained MD simulations. The study thus provides structural dynamics details on diffusion of a small TF domain protein, suggests how the protein approaches a specific recognition site on DNA, and supports further high-precision experimental detection. The stochastic movements revealed in the TF diffusion also provide general clues about how other protein walkers step and slide along DNA.
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