In silico Modeling of Coat Protein of Cucumber Mosaic Virus Strain Banana and Building its Virion from the Modeled Polypeptide Chain

Protein homology modeling was applied in understanding the architecture of Cucumber mosaic virus strain banana. Cucumber mosaic virus is a causative for infectious chlorosis disease on banana. The 3-dimensional structure for the 218 amino acid residue coat protein of this virus strain was predicted by homology modeling approach. Structural templates for the 218 residue amino acid strain were searched using PDBBLAST tool. The template was confirmed by detecting the template with fold recognition tools like FUGUE. Sequence to structure alignment was achieved using JOY server. PDB structure 1F15 was used as template for modeling and the structure was modeled using Modeller v 6.0. Loops were built by using SPDBV software v. 4.0.1. Modeled structure was validated by using PROCHECK and Verify 3D. Energy minimization was done using Tripos Sybyl v 6.7. Structural polymer, a trimer similar to that of the template was modeled using magic fit algorithm SPDBV software. Further, a tricky step was performed for building the virion structure by applying the biomolecular rotational symmetries of the template (CMV strain_FNY). Here, we describe a largely automated procedure for modeling protein structure from sequence alignments with homologous structures. The advanced step in viral protein modeling, we have used is to build the complete virion. Structure was deposited into theoretical model archive of PDB with identification code 2IKA.