Structural modeling and molecular simulation analysis of HvAP2/EREBP from barley

Abstract

AP2/ERF transcription factors play a critical role in plant development and stress adaptation. This study reports the three-dimensional ab initio-based model of AP2/EREBP protein of barley and its interaction with DNA. Full-length coding sequence of HvAP2/EREBP gene isolated from two Indian barley cultivars, RD 2503 and RD 31, was used to model the protein. Of five protein models obtained, the one with lowest C-score was chosen for further analysis. The N- and C-terminal regions of HvAP2 protein were found to be highly disordered. The dynamic properties of AP2/EREBP and its interaction with DNA were investigated by molecular dynamics simulation. Analysis of trajectories from simulation yielded the equilibrated conformation between 2-10ns for protein and 7-15ns for protein-DNA complex. We established relationship between DNA having GCC box and DNA-binding domain of HvAP2/EREBP was established by modeling 11-base-pair-long nucleotide sequence and HvAP2/EREBP protein using ab initio method. Analysis of protein–DNA interaction showed that a β-sheet motif constituting amino acid residues THR105, ARG100, ARG93, and ARG83 seems to play important role in stabilizing the complex as they form strong hydrogen bond interactions with the DNA motif. Taken together, this study provides first-hand comprehensive information detailing structural conformation and interactions of HvAP2/EREBP proteins in barley. The study intensifies the role of computational approaches for preliminary examination of unknown proteins in the absence of experimental information. It also provides molecular insight into protein–DNA binding for understanding and enhancing abiotic stress resistance for improving the water use efficiency in crop plants.

Keywords:

• barley
• HvAP2/EREBP
• AP2 domain
• transcription factor
• docking
• molecular dynamics simulations

Acknowledgments

We thank the Director, ICAR-Indian Institute of Wheat and Barley Research, Karnal, for providing necessary facilities and barley seeds. The authors are thankful to Jawaharlal Nehru University for the use of all computational facilities for this work. We acknowledge the support of Balasubramani GL for protein–DNA simulation study. This paper is IIWBR Contribution N> 69.

Disclosure statement

No potential conflict of interests were disclosed.

Additional information

Funding

This work was supported by the Indian Council of Agricultural Research, New Delhi [grant number DWR/RP/10-5.3].