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. 2018 May 22;9(1):2021.
doi: 10.1038/s41467-018-03713-y.

Hamiltonian path analysis of viral genomes

Reidun Twarock  1   2 , German Leonov  3   4 , Peter G Stockley  5
Affiliations

Hamiltonian path analysis of viral genomes

Reidun Twarock et al. Nat Commun. .
No abstract available

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Hamiltonian path representation of MS2 genome organisation. a Two consecutive PS sites in the linear genomic sequence are mapped on adjacent binding sites in the inner capsid surface. The stem loops (PDB ID: 5TC1) and the backbone connecting them were reported in ref. . The coat protein shell is shown as ribbons based on the icosahedrally averaged X-ray structure (PDB ID: 1ZDH). b These neighbouring PS contacts are represented by HPA as a short segment of an inscribed path connecting binding sites in the capsid interior, irrespective of their relative distance in the linear genomic RNA and the tertiary structure of the RNA fragment connecting them
Fig. 2
Fig. 2
PSs in the MS2 genome predicted by HPA analysis and confirmed by cryo-EM. The secondary structure of the MS2 genome is shown as a series of stem-loops (SLs), with the 15 SLs seen in the TR binding sites of the phage coat protein dimers in the asymmetric cryo-EM reconstruction, and predicted to be PSs via HPA (Dykeman et al), indicated by magenta boxes. Other SLs in the genome share characteristic MS2 coat protein recognition motifs with these 15 PSs, and were also proposed to be PSs. It is possible that at least some of these also contact coat protein dimers during PS-mediated assembly, but disengage thereafter and thus are not visible in the virion. Genomic SLs are numbered increasing in the 5′-to-3′ direction, preceded by their genetic locus, i.e. 5′UTR (untranslated region) (5U#), A protein (A#), CP (C#), replicase (R#) and 3′UTR (3U#).
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