Homology Modeling, Structure and Active Site Prediction of Stem Rust Resistant Protein in Wheat

Homology modeling is very helpful tool which produces 3D models when the target and template are closely related. The stem rust resistance gene Rpg1 encodes RPG1 protein, which plays a complex role in stem rust resistance. Homology modeling of RPG1 is important to study its role and pathway. The homology modeling of this protein was done using MODELLER 9.11. Then models of same proteins were superimposed to check the validation. NIH server containing tools, ERRAT was used to evaluate the 3D structure of protein RPG1, ERRAT score for this model was 77%. This score was further improved by doing loop optimization of RPG1 using similar tool. It was improved upto 80%. 3D model of stem rust resistance was further used to analyze the activity of protein. Active sites of RPG1 were detected by using ADDS (Automated active sites detection, docking and scoring). Total of 15 active sites were identified and active sites with highest score were used in further studies. The information achieved may be useful to understand the biology of stem rust disease in wheat which may further help to manipulate the disease mechanism.