title: 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.
authors.affiliation: a Plant Biotechnology Laboratory , ICAR-Indian Institute of Wheat and Barley , Karnal 132001 , Haryana , India.
authors.forename: Bharati
authors.initials: B
authors.lastname: Pandey
authors.affiliation: a Plant Biotechnology Laboratory , ICAR-Indian Institute of Wheat and Barley , Karnal 132001 , Haryana , India.
authors.forename: Pradeep
authors.initials: P
authors.lastname: Sharma
authors.affiliation: b Agricultural Knowledge Management Unit , Indian Agricultural Research Institute , New Delhi 110032 , India.
authors.forename: Chetna
authors.initials: C
authors.lastname: Tyagi
authors.affiliation: c School of Biotechnology , Jawaharlal Nehru University , New Delhi 110067 , India.
authors.forename: Sukriti
authors.initials: S
authors.lastname: Goyal
authors.affiliation: c School of Biotechnology , Jawaharlal Nehru University , New Delhi 110067 , India.
authors.forename: Abhinav
authors.initials: A
authors.lastname: Grover
authors.affiliation: a Plant Biotechnology Laboratory , ICAR-Indian Institute of Wheat and Barley , Karnal 132001 , Haryana , India.
authors.forename: Indu
authors.initials: I
authors.lastname: Sharma
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D018744:DNA, Plant / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics; D005838:Genotype; D001467:Hordeum / Q000145:classification / Q000235:genetics; D006860:Hydrogen Bonding; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics; D011485:Protein Binding; D011487:Protein Conformation; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics
chemical_list: D018744:DNA, Plant; D004268:DNA-Binding Proteins; D010940:Plant Proteins; D014157:Transcription Factors; C093680:ethylene-responsive element binding protein
keywords: AP2 domain; HvAP2/EREBP; barley; docking; molecular dynamics simulations; transcription factor