Quasi-equivalent packing

Structural versatility gives quasi-equivalent packing in T = 3 plant viruses... 

The molecular basis for quasi-equivalent packing was revealed by the very first structure determination to high resolution of a spherical virus, tomato bushy stunt virus. The structure of this T = 3 virus was determined to 2.9 A resolution in 1978 by Stephen Harrison and co-workers at Harvard University. The virus shell contains 180 chemically identical polypeptide chains, each of 386 amino acid residues. Each polypeptide chain folds into distinct modules an internal domain R that is disordered in the structure, a region (a) that connects R with the S domain that forms the viral shell, and, finally, a domain P that projects out from the surface. The S and P domains are joined by a hinge region (Figure 16.8). 

Tomato bushy stunt virus is a T = 3 plant virus with 180 chemically identical subunits. Each polypeptide chain is divided into several domains. The subunits preserve quasi-equivalent packing in most contact regions by conformational differences of the protein chains, especially a large change in... 

As examples of such quasi-equivalent arrangement of subunits, we will examine the T = 3 and T = 4 packing modes, both of which are found in known virus particles. In the T = 3 structure, which has 180 subunits (3 x 60),... 

Small spherical viruses have a protein shell around their nucleic acid that is constructed according to icosahedral symmetry. Objects with icosahedral symmetry have 60 identical units related by fivefold, threefold, and twofold symmetry axes. Each such unit can accommodate one or severed polypeptide chains. Hence, virus shells are built up from multiples of 60 polypeptide chains. To preserve quasi-equivalent symmetry when packing subunits into the shell, only certain multiples (T = 1, 3, 4, 7...) are allowed. 

The transformation from spheres to cyhnders is a peculiar example for the self-adjustment of the molecular conformation. The switching shape can be regarded as an example for the principle of quasi equivalency established by A. Klug for the self-assembly of biomolecules and viruses [145] for the sake of an improved intermolecular packing, the molecules adopt a conformation different from the minimum energy one. This also demonstrates that shape control does not mean a fully constrained structure. Similar to biomolecules, the combination of flexible macromolecules and self-assembly principles is a powerful strategy for preparation of molecules with well-defined but switchable shape [23]. 

In tomato bushy stunt virus, 180 identical protein subunits (Mr = 41,000) form a shell which surrounds a molecule of RNA containing 4,800 nucleotides. For geometrical reasons no more than 60 identical subunits can be positioned in a spherical shell in a precisely symmetrical way. This limits the volume, so, in order to accommodate a greater amount of RNA, a larger shell is needed. This can be achieved by relaxing the symmetry the subunits are divided into three sets of 60, each set packing with strict symmetry. However, the relationship between each set is different so that the overall packing is only quasi-equivalent. 

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