Dynamics of Dof domain-DNA interaction in wheat: Insights from atomistic simulations and free energy landscape.

DNA-binding one zinc finger protein (Dof) is a plant-specific transcription factor involved in numerous biological processes. In the current study, the plausible mechanism underlying Dof domain-DNA interaction in wheat was investigated using extensive molecular dynamics (MD) simulations analysis. We depicted that one key residue Lys29, possessing the ability to disturb the interaction between Dof domain-DNA upon substitution to Arg29. Frequent conformational changes were observed in Lys29Arg (K29R)-DNA complex during the entire MD simulation period, which significantly altered the interactions, thereby indicating the importance of Lys29 in complex stability. Principal component analysis and free energy landscape results also suggested strong affinity between wild-type Dof domain and DNA due to restricted atomic movement. Our study not only substantiates the structural and mechanistic insights of Dof transcription factor but also provides new avenues toward employment of these key amino acid residues in genetic engineering for development of abiotic stress tolerance crop plant.