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Viruses with icosahedral capsids

Small organisms have to economize upon their resources. This holds especially for viruses - if you allow for viruses being organisms. There is a whole range of minimalistic approaches, from rather naked genomes in viroids up to multilayered proteinous shells engulfing the genetic blueprint along with some enzymes. If you are posed to the problem of housing a genome with as few protein as possible (in terms of coding effort) the approach may be to use one protein which self-organizes to form the required capsule. The group of icosahedral viruses does so, by generating a capsid of 60 symmetry related subunits. The symmetry relations for this construction principle are outlined in the script "Symmetry relationships in icosahedral capsids".

Viruses of several taxonomic groups use this construction principle. So the genome may be coded by single or double stranded nucleic acid, either RNA or DNA. The protein subunits may be composed of 1, 2, 3, or 4 protein chains. Multiple chains may be derived from a single protein by different processing steps, thus allowing the individual types of chains to adopt different folding patterns according to their positions with respect to symmetry axes. In case of individually coded proteins similarities in the folding patterns indicate common ancesters.

The icosahedron lattice can be populated with more than 60 subunits giving rise to more complex capsids. An overview of icosahedral capsid structures with near atomic resolution is found in the web-based databank VIPER (Virus Particle Explorer).

Among the 'small' icosahedral viruses are well known human or animal pathogens causing e.g. poliomyelitis, cold (rhinovirus), hepatitis, foot and mouth disease or a variety of enteric diseases. Plant pathogens like the rice yellow mottle virus destroy region wide a year's harvest. Insect viruses or bacteriophages adopt the construction principle as well. The gallery below depicts some of these, with the colouring chosen just to give some depthcue. Their orientation (and relative size) is the same, you may easily find the major symmetry axes.

rhinovirus porcine parvovirus rice yellow mottle virus cricket paralysis virus bacteriphage phiX174
human rhinovirus porcine parvovirus rice yellow mottle virus cricket paralysis virus bacteriophage phiX174
images © VIPER (http://mmtsb.scripps.edu/viper/)

Because of their medical/healthcare and economic importance the picorna viruses were thoroughly investigated in the last decades. This resulted e.g. in the WHO's global polio eradication programme as well as in a wealth of structural information from the 1980s on. So interactions of the viruses with cellular receptors, neutralizing antibodies or antibiotics are now known at the molecular level. The structures of enzymes coded by the viruses (polymerases, proteases) are published too.

In the Chime-scripts on viral structures offered here do not expect to see complete viruses. Though the viruses are termed 'small', the atomic coordinate files for whole capsids are not. Chime was not designed to handle 30+ MB files on common PCs: the first picture would take more than 5 min to appear on the screen. Even with only some proteins displayed (as all ligands around a symmetry axis) the scenes may move not very smoothly.

poliovirus Scripts on poliovirus (if no link it's in preparation ;-)):

Literature:
DL Caspar & A Klug, Physical principles in the construction of regular viruses, Cold Spring Harbor Symp. Quant. Biol. 27 (1962) 1-24
MG Rossmann & JE Johnson, Icosahedral RNA virus structure, Annu. Rev. Biochem. 58 (1989) 533-573
JE Johnson & JA Speir, Quasi-equivalent viruses: a paradigm for protein assemblies, J. Mol. Biol. 269 (1997) 665-675
TS Baker et al, Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron microscopy, Microbiol. Mol. Biol. Rev. 63 (1999) 862-922
SC Harrison, The familiar and the unexpected in structures of icosahedral viruses, Curr. Opin. Struct. Biol. 11 (2001) 195-199
VS Reddy et al, Virus Particle Explorer (VIPER), a Website for virus capsid structures and their computational analysis, J. Virol. 75 (2001) 11943-11947
N Verdaguer et al, Structure of human rhinovirus serotype 2 (HRV2), J. Mol. Biol. 300 (2000) 1179-1194)
AA Simpson et al, The structure of porcine parvovirus: comparison with related viruses, J. Mol. Biol. 315 (2002) 1189-1198
C Qu et al, 3D domain swapping modulates the stability of members of an icosahedral virus group, Structure 8 (2000) 1095-1103
J Tate et al, The crystal structure of cricket paralysis virus: the first view of a new virus family, Nature Struct. Biol. 6 (1999) 765-774
R McKenna et al, Analysis of the single-stranded DNA bacteriophage phiX174, refined at a resolution of 3.0 Å, J. Mol. Biol. 237 (1994) 517-543

 


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