title: Protein modeling and molecular dynamics simulation of SlWRKY4 protein cloned from drought tolerant tomato (Solanum habrochaites) line EC520061.
abstract: WRKY genes are members of one of the largest families of plant transcription factors and play an important role in response to biotic and abiotic stresses, and overall growth and development. Understanding the interaction of WRKY proteins with other proteins/ligands in plant cells is of utmost importance to develop plants having tolerance to biotic and abiotic stresses. The SlWRKY4 gene was cloned from a drought tolerant wild species of tomato (Solanum habrochaites) and the secondary structure and 3D modeling of this protein were predicted using Schrödinger Suite-Prime. Predicted structures were also subjected to plot against Ramachandran's conformation, and the modeled structure was minimized using Macromodel. Finally, the minimized structure was simulated in the water environment to check the protein stability. The behavior of the modeled structure was well-simulated and analyzed through RMSD and RMSF of the protein. The present work provides the modeled 3D structure of SlWRKY4 that will help in understanding the mechanism of gene regulation by further in silico interaction studies.
authors.affiliation: Division of Crop Improvement, Indian Institute of Vegetable Research, Varanasi, 221305, UP, India. S.Karkute@icar.gov.in.
authors.forename: Suhas G
authors.initials: SG
authors.lastname: Karkute
authors.affiliation: Department of Bioinformatics, Bharathiar University, Coimbatore, 641 046, TN, India. drmurugesh@icloud.com.
authors.forename: Murugesh
authors.initials: M
authors.lastname: Easwaran
authors.affiliation: Division of Crop Improvement, Indian Institute of Vegetable Research, Varanasi, 221305, UP, India. ranjit.gujjar@gmail.com.
authors.forename: Ranjit Singh
authors.initials: RS
authors.lastname: Gujjar
authors.affiliation: Department of Bioinformatics, Bharathiar University, Coimbatore, 641 046, TN, India. shanmughavel@buc.edu.in.
authors.forename: Shanmughavel
authors.initials: S
authors.lastname: Piramanayagam
authors.affiliation: Division of Crop Improvement, Indian Institute of Vegetable Research, Varanasi, 221305, UP, India. singhvns@gmail.com.
authors.forename: Major
authors.initials: M
authors.lastname: Singh
mesh_terms: D000595:Amino Acid Sequence; D016000:Cluster Analysis; D017124:Conserved Sequence; D018551:Solanum lycopersicum / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics; D011487:Protein Conformation; D021281:Quantitative Structure-Activity Relationship; D016415:Sequence Alignment
chemical_list: D010940:Plant Proteins
keywords: 3D structure; Drought; Molecular dynamic simulation; Protein modeling; Tomato; WRKY