title: Evidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement.
abstract: Biotic stress is a major cause of heavy loss in grape productivity. In order to develop biotic stress-resistant grape varieties, the key defense genes along with its pathway have to be deciphered. In angiosperm plants, lipase-like protein phytoalexin deficient 4 (PAD4) is well known to be essential for systemic resistance against biotic stress. PAD4 functions together with its interacting partner protein enhanced disease susceptibility 1 (EDS1) to promote salicylic acid (SA)-dependent and SA-independent defense pathway. Existence and structure of key protein of systemic resistance EDS1 and PAD4 are not known in grapes. Before SA pathway studies are taken in grape, molecular evidence of EDS1: PAD4 complex is to be established. To establish this, EDS1 protein sequence was retrieved from NCBI and homologous PAD4 protein was generated using Arabidopsis thaliana as template and conserved domains were confirmed. In this study, computational methods were used to model EDS1 and PAD4 and simulated the interactions of EDS1 and PAD4. Since no structural details of the proteins were available, homology modeling was employed to construct three-dimensional structures. Further, molecular dynamic simulations were performed to study the dynamic behavior of the EDS1 and PAD4. The modeled proteins were validated and subjected to molecular docking analysis. Molecular evidence of stable complex of EDS1:PAD4 in grape supporting SA defense pathway in response to biotic stress is reported in this study. If SA defense pathway genes are explored, then markers of genes involved can play pivotal role in grape variety development especially against biotic stress leading to higher productivity.
authors.affiliation: a Centre for Agricultural Bioinformatics , Indian Agricultural Statistics Research Institute , Library Avenue, Pusa, New Delhi 110012 , India.
authors.forename: Gitanjali
authors.initials: G
authors.lastname: Tandon
authors.forename: Sarika
authors.initials: S
authors.lastname: Jaiswal
authors.forename: M A
authors.initials: MA
authors.lastname: Iquebal
authors.forename: Sunil
authors.initials: S
authors.lastname: Kumar
authors.forename: Sukhdeep
authors.initials: S
authors.lastname: Kaur
authors.forename: Anil
authors.initials: A
authors.lastname: Rai
authors.forename: Dinesh
authors.initials: D
authors.lastname: Kumar
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000737:chemistry* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D020156:Salicylic Acid / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D015398:Signal Transduction; D055672:Static Electricity; D013312:Stress, Physiological; D040681:Structural Homology, Protein; D013816:Thermodynamics; D027843:Vitis / Q000737:chemistry* / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D004268:DNA-Binding Proteins; C118837:EDS1 protein, Arabidopsis; D002265:Carboxylic Ester Hydrolases; C400766:PAD4 protein, Arabidopsis; D020156:Salicylic Acid
keywords: EDS1; GROMACS; PAD4; biotic stress; grape; molecular dynamics simulation; salicylic acid pathway; systemic resistance