Insight into virus movement mechanism using in silico approaches by employing SeMV as a model system

Viral infections in plants are a big threat to agriculture and the economy. Though the viral infection mechanism is well documented, the cell-to-cell trafficking of the virus is poorly understood. The plant virus is known to encode movement protein (MP) for trafficking the virus from an infected cell to a healthy cell. The movement protein is known to increase plant cells’ size exclusion limit (SEL) of plasmodesmata (PD). However, the exact mechanism of the viral trafficking remained unclear. In this study, we proposed a possible mechanism of viral trafficking by using Sesbania mosaic virus (SeMV) as a model system. The movement protein and RNA-dependent RNA polymerase (RdRp) of SeMV were modeled using the ab initio method. It is also known that MP binds with VPg in the movement process and RdRp requires P10 for replication. The models of VPg and P10 were extracted from the structure of polyprotein 2a. The complexes MP-VPg and RdRp-P10 were built with the help of molecular docking and were subjected to molecular dynamic simulation to get stable complexes. The trafficking complex (MP+VPg + RdRp + P10) was obtained by performing the molecular docking of these two complexes. Through MDS, the stability of the trafficking complex was confirmed. For the first time, a trafficking complex was proposed to understand its role in navigation of the viral complex through the host’s plasmodesmata. Modeling and MD simulations for MP, RdRp, VPg, and P10 of Sesbania Mosaic VirusProposed a mechanism of serine cleavage of polyprotein2a to release P10 and VPgStability of trafficking complex (RdRp-P10 and MP-VPg) was analysedA hypothesis was proposed on intercellular movement of SeMV—a plant virus Modeling and MD simulations for MP, RdRp, VPg, and P10 of Sesbania Mosaic Virus Proposed a mechanism of serine cleavage of polyprotein2a to release P10 and VPg Stability of trafficking complex (RdRp-P10 and MP-VPg) was analysed A hypothesis was proposed on intercellular movement of SeMV—a plant virus