In silico Structural and Functional Annotation of Tomato Chocolate spot Virus

Aims: The study aims to predict in-silico the structural and functional annotation of Tomato Chocolate Spot Virus (TCSV) retrieved from Uniprotkb with the accession number C7EXM3.

Study design: To use the In-silico approach for the structural and functional annotation of the Tomato Chocolate Spot Virus.

Place and Duration of Study: The research was conducted at the Bioinformatics Unit, Chevron Biotechnology Centre, Modibbo Adama University Yola, Nigeria. Between August 2021 to September 2021.

Methodology: The sequence of the Tomato Chocolate Spot Virus was retrieved from Uniprotkb with accession number C7EXM3, Physicochemical characteristics were computed using the ProtParam tool. The sever SOPMA was used for secondary structure analysis (Helix, Sheets and Coils). The tool CELLO v2.5 was used to predict the subcellular localization of the protein. Four different Homology Modelling tools (trRosetta, Lomet, RaptorX and IntFOLD5) were used to predict the 3D structure of the protein, the quality of the predicted proteins was assessed used PROCHECK. Three tools (InterProScan, NCBI conserved domains and Phobius) were used to get the possible function(s) of the protein.

Results: ProtParam tool computed various Physical and Chemical properties such as Molecular weight (MW) 20396.96 Daltons, isoelectric point (pI) of 6.92. Instability Index 41.94, and Grand Average Hydropathy (GRAVY) -0.503. SOPMA was used for calculating the secondary structure parameters of the protein as Helices (Hh) 43.48%, Extended strands (Ee) 18.48%, Random coils (Cc) 38.04%. CELLO v2.5 was used for subcellular localization of the protein, it predicted that the protein can be both Nuclear and Cytoplasmic with the reliability of 1.653 and 1.504 respectively. Different Homology modelling tools were used to obtain the best 3D structure of the protein. Furthermore, PROCHECK was used to assess the quality of the models obtained. Model from trRosetta was found to be the best because of the quality of the Ramachandran Plot obtained from PROCHECK which has more than 90% of amino acid in the most favourable regions. NCBI-CDD and interproScan predicted that protein is a DNA double-strand break repair Rad50 ATPase, which is involved in the early steps of DNA double-strand break (DSB) repair. Furthermore, the Phobius server predicted the protein to be non-cytoplasmic in its domain, which means they help target proteins to their final destinations.

Conclusion: The study has helped in obtaining the 3D structure of the protein Tomato Chocolate Spot Virus from different Modelling tools, as well as the possible function of the protein.