Capsid subunit arrangement

The other major type of symmetry found in oligomers, helical symmetry, also occurs in capsids. Tobacco mosaic virus is a right-handed helical filament made up of 2,130 identical subunits (Fig. 4-25b). This cylindrical structure encloses the viral RNA. Proteins with subunits arranged in helical filaments can also form long, fibrous structures such as the actin filaments of muscle (see Fig. 5-30). 

The complete, mature virus particle is known as a virion and usually has a regular shape. Many virions are icosahedral, that is, the capsid is formed from identical protein subunits (capsomeres) that combine to produce a solid with twenty faces, each of which is an equilateral triangle. The herpes viruses are of this type, as are the picomaviruses of which the polio viruses and rhinoviruses (cold viruses) are the bestknown members. The other common regular shape is that of a helix, and the tobacco mosaic virus is of this type. Its single helical strand of RNA is enclosed within a hollow tube, which comprises 2130 protein subunits arranged in a helix. Other viruses with a similar structure are the... 

The asymmetric unit contains one copy each of the subunits VPl, VP2, VP3, and VP4. VP4 is buried inside the shell and does not reach the surface. The arrangement of VPl, VP2, and VP3 on the surface of the capsid is shown in Figure 16.12a. These three different polypeptide chains build up the virus shell in a way that is analogous to that of the three different conformations A, C, and B of the same polypeptide chain in tomato bushy stunt virus. The viral coat assembles from 12 compact aggregates, or pen tamers, which contain five of each of the coat proteins. The contours of the outward-facing surfaces of the subunits give to each pentamer the shape of a molecular mountain the VPl subunits, which correspond to the A subunits in T = 3 plant viruses, cluster at the peak of the mountain VP2 and VP3 alternate around the foot and VP4 provides the foundation. The amino termini of the five VP3 subunits of the pentamer intertwine around the fivefold axis in the interior of the virion to form a p stmcture that stabilizes the pentamer and in addition interacts with VP4. 

Figure 16.18 A dimer is the basic unit that builds up the capsid of bacteriophage MS2. The two subunits (red and biue) are arranged so that the dimer has a p sheet of 10 antiparaliel strands on one side and the hairpins and a heiices on the other side. The heiices from one subunit pack against p strands from the other subunit and vice versa. (Adapted from a diagram provided by L. Liljas.)...

CPMV particles have an icosahedral symmetry with a diameter of approximately 28 nm (Figure 9.2), the protein shell of the capsid is about 3.9nm thick [72], The structure of CPMV is known to near-atomic resolution (Figure 9.3) [73], The virions are formed by 60 copies of two different types of coat proteins, the small (S) subunit and the large (L) subunit. The S subunit (213 amino acids) folds into one jelly roll P-sandwich, and the L subunit (374 amino acids) folds into two jelly roll P-sandwich domains. The three domains form the asymmetric unit and are arranged in a similar surface lattice to T = 3 viruses, except they have different polypeptide sequences therefore the particle structure is described as a pseudo T = 3 or P = 3 symmetry [74]. 

Of the insect virus families, the capsid proteins of members of the Nodaviridae family are similar to those of plant viruses such an SBMV and TBSV, which have the same T=3 arrangement of subunits (Hosur et al, 1987). The capsid protein of the T=4 virus NudaureEa capensis ut (NwV) (Fig. Id see Color Insert), belonging to the Tetraviridae family, also has a jelly-roll topology, but the EF loop contains a complete domain of the immunoglobulin type c topology that is located on the outside surface of the capsid (Munshi et al., 1996). The N and C termini form a separate helical domain on the inside of the protein shell. 

Fig. 5. Comparison of HSV-1 procapsid and capsid structures. Outside (A and B) and inside (C and D) views of reconstructions of the HSV-1 procapsid (A and C) and capsid (B and D). All views are shovm looking along a 3-fold icosahedral axis. Although it retains the same icosahedral symmetry, as shovm by the hexagonal arrangement of the capsomers apparent in the internal view (C), the procapsid subunits are much less clearly defined than those in the capsid. In addition, the contacts between individual subunits are much more tenuous and the continuous floor, formed by extensions from the bases of the capsomers, is not present. Note also the contrast in shape between the spherical procapsid and the polyhedral capsid. Scale bar 500 A. [Image supplied by Benes Trus.]...

Nature has found two basic ways of arranging the multiple capsid protein subunits and the viral genome into a nucleocapsid. In some viruses, multiple copies of a single coat protein form a helical structure that encloses and protects the viral RNA or DNA, which runs In a helical groove within the protein tube. Viruses with such a helical nucleocapsid, such as tobacco mosaic virus, have a rodlike shape. The other major structural type is based on the icosahedron, a solid, approximately spherical object built of 20 identical faces, each of which is an equilateral triangle. 

Supramolecular chirality is widely manifested in nature for example, the DNA double helix,the protein single helices and, in humans, rhinovirus 14, a member of the major rhinoviras receptor class, possesses a protein capsid that is composed of 60 protomers arranged in an icosahedrally symmetric arrayJ As shown previously in this book, at the molecular level, chirality is very important in asymmetric catalysis for the creation of novel chiral molecules however, more recently an increasing amount of attention has been drawn to chiral supramolecular assemblies. On the supramolecular level, chirality involves the nonsymmetric arrangement of molecular subunits in a noncovalent assembly via weak interactions such as hydrogen bonding, metal coordination and n-n interaction. 

---