Structural Effects of Single Mutations in a Filamentous Viral Capsid Across Multiple Length Scales

Viral mutations are a main source of resistance to medical treatment. By combining SAXS and magic-angle spinning (MAS) NMR we relate single-site mutations in the filamentous bacteriophage virus fd to structural changes over several length scales. The atomic-scale was examined by solving the quaternary structure of the phage[1], and by comparing NMR chemical shifts of three forms: wild-type, D12N, and Y21M. Inter-particle interactions experienced by different mutants on the nano-scale were studied by the SAXS osmotic pressure technique and the micron-scale, i.e. liquid crystal formation and phage alignment, was examined from SAXS and from optical birefringence.

We show that a single-site charge mutation (D12N – M13 virus) on the surface of the capsid, has a negligible effect on its structure however, a mutation in the hydrophobic packing region (Y21M) has a significant impact: it changes the symmetry, the subunit structure and the packing of the phage, and on the micron-scale it significantly alter the pitch of cholesteric liquid-crystals formed by the virus. Despite the fact that changes occurring in the atomic-scale propagate to the macroscopic scale, those changes skip the nano-scale; SAXS measurements we employed on the three forms of the virus (wt-fd, D12N, fd-Y21M) at different salt and osmotic pressure conditions suggest that inter-particle interactions are not significantly affected by the hydrophobic Y21M mutation. On the other hand, these interactions are significantly affected by the D12N charge mutation. Modelling of the SAXS data also allowed us to re-estimate the effective particle charge and show that the non-stoichiometric nucleotide-to-subunit ratio is the source of the net charge on the virus.

Since such mutation affect differently the organization of phage particles, our studies can direct smart design of phage-inspired bio- and nano-technology.

[1] Morag O, Sgourakis NG, Baker D, Goldbourt A, PNAS 27, 971-976 (2015).