Department of Virology, S.V. University, Tirupati-517502.
Abstracts of Research Papers Presented during the National Symposium of Indian Virological Society at Unit of Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi-110 012, October 14–1.
Cucumber Mosaic Virus (CMV) causes infectious chlorosis, mosaic or heart rot of banana. The cucumber mosaic virus (CMV-Banana) was maintained on tobacco plants by sap transmission. The virus was purified and Molecular weight of coat protein determined by using SDS-PAGE. Then the amino acid sequence of the coat protein was obtained from SwissProt protein database (Q66135). The phylogenetic analysis is performed using coat protein sequences of various strains of cucumber mosaic virus. The 218 amino acid sequence was searched for the presence of templates by using PDB-BLAST. It had identity with few other aligned 3D structures. Later submitted to secondary structure prediction servers, followed by fold recognition servers, Template 1F 15 of 218 amino acid length was selected from the prediction of FUGUE server. The alignment of the template 1F 15 chain C with query was submitted in PIR format to the Modeller that produced 20 different models and out of these one having least energy was chosen for further refinement of the model. Loops were built SPDBV software version 3.7 satisfying the Ramachandran Plot and verified 3D structure. Protein energy was minimized using Sybyl 6.7 software to set the conformations. Finally, 3D structure of the coat protein of CMV-Banana was predicted. Then the sequence of structure alignment with the secondary structure precisions was done using JOY server. The best binding sites of the Protein at 5Ao resolution were predicted using SITE 1D Module of Sybyl 6.7 software. Here we described a largely automated procedure modeling protein structure from sequence alignments with homologues of known structures.
