Computational studies on rep and capsid proteins of CRESS DNA viruses

Abstract

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.

Keywords: Capsid and rep protein; Interaction; MD simulation; Phylogenetic analysis; Single-stranded DNA; Virus.

Fig. 1

Predicted structure of the (A) R and (B) C proteins of representative members of the ssDNA virus family. A: AADV, B: BCTV, C: CPbdV, D: HCYV5, E: HaGV, F: HLaVV, G: PhiMH2k, and H: SCSV. All structures have been coloured from N to C terminus using rainbow colors. All the Rs show a three-domain arrangement with an N-terminal endonuclease and C-terminal helicase domain connected by a central flexible linker of variable length. The Cs of all the viruses show the canonical jelly-roll fold (color figure online)

Fig. 2

Heatmaps showing the intra-molecular interactions in A the C protein and B the R protein of different viruses. It is worth noting that there are three and two major clades observed for the C and R proteins, respectively, similar to the structure-based phylogeny of the proteins

Fig. 3

Structure based phylogeny of A C and B R as determined by STRALCP [50]. Col_alpha3, ColG4, phi_X174, SpV4, and phiMH2K are shown in purple colour, MVM, B19V, AAV2, and AADV are indicated in blue, HaGV in cyan, SCSV and FBNSV in lime green, HLaVV in light maroon, CPbdV in light coral, and HCyV, DuCV, and PCV_2 in grey. The experimentally determined structures are indicated in maroon font color (color figure online)

Fig. 4

(A) Superposition of the modes of binding of various R with the IR region of ssDNA. (B) Mode of binding of various R with Respective C. A: AADV, B: BCTV, C: CPbdV, D: HCYV5, E: HUAGV, F: HLaVV, G: PhiMH2k, and H: SCSV. In panel A, the DNA is shown in yellow, while AADV is shown in purple, BCTV in blue, CPbdV in cyan, HCYV5 in green, HUAGV in olive, HLaVV in orange, PhiMH2K in red, and SCSV in pink, respectively. In panel B, all the R structures are shown in green, and the respective C structures are colored blue (color figure online)