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Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation

1
National Agri-Food Biotechnology Institute (NABI), Mohali 140306, Punjab, India
2
Dr. A.P.J. Abdul Kalam Technical University, Lucknow, Uttar Pradesh 226031, India
3
Meerut Institute of Engineering and Technology, Meerut, Uttar Pradesh 250005, India
4
National Institute for Plant Biotechnology (NIPB), New Delhi 110012, India
*
Author to whom correspondence should be addressed.
Biology 2019, 8(4), 83; https://doi.org/10.3390/biology8040083
Received: 30 June 2019 / Revised: 21 September 2019 / Accepted: 30 September 2019 / Published: 4 November 2019
(This article belongs to the Section Plant Science)
A precise understanding of the molecular mechanism involved in stress conditions has great importance for crop improvement. Biomolecules, such as WRKY proteins, which are the largest transcription factor family that is widely distributed in higher plants, plays a significant role in plant defense response against various biotic and abiotic stressors. In the present study, an extensive homology-based three-dimensional model construction and subsequent interaction study of WRKY DNA-binding domain (DBD) in CcWRKY1 (Type I), CcWRKY51 (Type II), and CcWRKY70 (Type III) belonging to pigeonpea, a highly tolerant crop species, was performed. Evaluation of the generated protein models was done to check their reliability and accuracy based on the quantitative and qualitative parameters. The final model was subjected to investigate the comparative binding analysis of different types of WRKY–DBD with DNA-W-box (a cis-acting element) by protein–DNA docking and molecular dynamics (MD) simulation. The DNA binding specificity with WRKY variants was scrutinized through protein–DNA interaction using the HADDOCK server. The stability, as well as conformational changes of protein–DNA complex, was investigated through molecular dynamics (MD) simulations for 100 ns using GROMACS. Additionally, the comparative stability and dynamic behavior of each residue of the WRKY–DBD type were analyzed in terms of root mean square deviation (RMSD), root mean square fluctuation (RMSF)values of the backbone atoms for each frame taking the minimized structure as a reference. The details of DNA binding activity of three different types of WRKY–DBD provided here will be helpful to better understand the regulation of WRKY gene family members in plants. View Full-Text
Keywords: pigeonpea; DNA binding; molecular modeling; WRKY transcription factor; DBD; molecular dynamics simulation; protein–DNA interaction pigeonpea; DNA binding; molecular modeling; WRKY transcription factor; DBD; molecular dynamics simulation; protein–DNA interaction
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Singh, A.; Sharma, A.K.; Singh, N.K.; Sonah, H.; Deshmukh, R.; Sharma, T.R. Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation. Biology 2019, 8, 83.

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