RESUMO
The circular rep-encoding single-stranded DNA viruses (CRESS DNA viruses) are among the smallest, with 2-6 kb ssDNA genomes that encode for a coat protein (C) and a replication protein (R). To comprehend the complexity and divergence of the C and R proteins, we have created predictive structural models of representative viruses infecting unique hosts from each family using the neural network-based method AlphaFold2 and carried out molecular dynamic simulations to assess their stability. The structural characteristics indicate that differences in loops and amino-terminus may play a significant role in facilitating adaptations to multiple hosts and vectors. In comparison to the C, the Rs show a high degree of conservation and structural mimicry of the nuclease-helicase domains of plasmids. A phylogenetic analysis based on the structures and sequences of the C and R proteins reveals evolutionary variances. Our study also highlights the conservation of structural components involved in the interaction of R with the conserved intergenic region of the genome. Further, we envisage that the adaptability of R's central linker may be crucial for establishing interactions with multiple protein partners, including C. Supplementary Information: The online version contains supplementary material available at 10.1007/s13337-024-00858-x.
RESUMO
RNA-dependent RNA polymerases (RdRPs) represent a distinctive yet versatile class of nucleic acid polymerases encoded by RNA viruses for the replication and transcription of their genome. The structure of the RdRP is comparable to that of a cupped right hand consisting of fingers, palm, and thumb subdomains. Despite the presence of a common structural core, the RdRPs differ significantly in the mechanistic details of RNA binding and polymerization. The present review aims at exploring these incongruities in light of recent structural studies of RdRP complexes with diverse cofactors, RNA moieties, analogs, and inhibitors.
