Plant viruses from the Potyviridae family have a significant impact on crop productivity worldwide. We conducted a bioinformatic analysis of the VPg sequences from several members of the Potyviridae family. All analyzed primary structures of VPg contain an invariant arginine, which, according to the model we proposed earlier, is located in the functionally important α1–α2 hairpin of the viral protein and forms a recognition contact during the formation of its complex with the eIF4E host cell. Among the amino acid mutations observed in the sequences of VPg PVY, we separately considered those associated with adaptation to the host plant. Several strain-specific mutations were identified, the functional roles of which are currently unclear. For each of the Potyviridae species considered, a consensus VPg sequence was determined. 3D-models of the corresponding proteins were constructed by de novo molecular modelling using the consensus amino acid sequences. Cross-comparative analysis of the theoretical models and the experimental VPg PVY structure obtained by NMR showed that all these proteins share a high degree of structural homology and contain the conserved arginine within the α1–α2 hairpin. However, the spatial position of this arginine may vary across models, which apparently reflects species-specific differences in the VPg recognition module.
Kolesnikova et al. (Sat,) studied this question.