Primary, Secondary and Tertiary Structural Analysis of Disease Resistance Protein RGA4 of ZEA Maize Using Bioinformatics Tools

Abstract: Objective: Disease resistance protein RGA4 of Zea Maize is mitochondrial carrier-like protein having UniProtKB ID: B6STS5. B6STS5 has been identified as an important protein involved in ADP binding. Therefore B6STR5 is considered as a significant protein for various diseases. The experimental 3D structure of B6STS5 is not available. Therefore, present study aims for analysis of primary, secondary and tertiary structure of disease resistance protein RGA4 of Zea Maize using bioinformatics tools and proposing the best 3D model after evaluating various parameters. Methods: Primary structure analysis was done by ProtParam, Secondary structure analysis was done by SOPMA and Jpred4 and Tertiary structure analysis was done by using two different softwares namely SPDBV and I-Tasser. All the predicted 3-D models were analyzed and validated by PROCHECK, ProQ and SolvX. Results: Model2 predicted by I-Tasser showed top results with 67.10% of the residues in the most favorable region, 22.00% in the allowed region, 7.90% in the generously allowed region and 3.00% in the disallowed region. The RMSD between the modeled and the template structure was found to be 1.96 �. Quality of predicted Model2 developed by I-Tasser had checked by ProQ and found the best LGscore of 2.485 and MaxSub of 0.061 which indicates that the model is very good. PROCHECK and SolvX also confirmed the same. Conclusion: In this study, homology model was developed for B6STS5 using SPDBV and I-Tasser. The models developed were validated using PROCHECK, ProQ and SolvX. These analyses validated the homology model2 produced by I-Tasser is best, robust as well as reliable enough to be used for future study.

Keywords: B6STS5, Homology modeling, SPDBV, I-TASSER, PROCHECK, ProQ, SolvX, ProtParam, SOPMA.