Elucidating the role of genome in geminiviral capsid dynamics

Geminiviridae is the largest group of single-stranded (ss) DNA viruses, infecting a wide range of plant species and posing a significant threat to agriculture. Hence, we used molecular dynamics simulations to explore the structural impacts and the stability of Ageratum yellow vein virus (AYVV) capsids in the presence and absence of DNA. The findings show that dimers, trimers, pentamers, and higher multimers are remarkably stable when bound to DNA during the course of the 300 ns simulation. On the contrary, the oligomers demonstrate significant instability and disintegration in the absence of DNA. While DNA-free oligomers retained structural integrity, the quaternary association broke down, particularly in pentameric and dimeric units. While previous experimental studies have demonstrated the stability of geminiviral pentamers, our observations suggest that their resilience is likely linked to their association with DNA. Remarkably, the dimers lacking the bound DNA also display an atypical variation in curvature over time. Consequently, we propose that any trigger that loosens the association of the genome with the oligomers would be a prerequisite for the intersubunit contacts in the capsid to break and release the genome. We hypothesize that genomic DNA may interact with the pentamers to initiate capsid assembly, which may pave the way for the dimers and trimers to be integrated. The natural flexibility of the dimers could render it easier to provide the appropriate curvature and closure to the swiftly forming capsid. Thus, techniques that target DNA-protein interactions in geminiviruses could be the key to their effective management in fields.