Principles of Virology. Jane Flint
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(purple) are colored red, blue, green, yellow, and orange. The image was created by Jason Roberts, Doherty Institute, Melbourne, Australia. (B) The topology of the VP1 protein shown in a ribbon diagram, with the strands of the β-barrel jelly roll colored as in Fig. 4.12B. This β-barrel domain is perpendicular to the capsid surface. The C-terminal arm and α-helix shown in magenta is the invading arm from a different neighboring pentamer (not shown), which is clamped in place by extensive interactions of its β-strand with the N-terminal segment of the subunit shown. This subunit also interacts with the N-terminal arm from its anticlockwise neighbor in the same pentamer (not shown). (C) VP1 pentamer with each subunit shown in a different color, and one VP1 from a neighboring pentamer (colored magenta) showing the C-terminal arm invading the yellow VP1 of the neighboring pentamer. The structures shown in panels B and C are from PDB ID: 1SVA.
Simian virus 40 and poliovirus capsids differ in their surface appearance, in the number of structural units, and in the ways in which these structural units interact. Nevertheless, they share important features, including modular organization of the proteins that form the capsid shell and a common β-barrel domain as the capsid building block. Neither poliovirus nor simian virus 40 capsids conform to strict quasiequivalent construction: all contacts made by all protein subunits are not similar, and in the case of simian virus 40, the majority of VP1 pentamers are packed in hexameric arrays. Nevertheless, close packing with icosahedral symmetry is achieved by limited variations of the contacts, either among topologically similar, but chemically distinct, surfaces (poliovirus) or made by a flexible arm (simian virus 40).
Structurally simple icosahedral capsids in more-complex particles. Several viruses that are architecturally more sophisticated than those described in the previous sections nevertheless possess simple protein coats built from one or a few structural proteins. The complexity comes from the additional protein and lipid layers in which the capsid is enclosed (see “Viruses with Envelopes” below).
Structurally Sophisticated Capsids
Some naked viruses are considerably larger and more elaborate than the small RNA and DNA viruses described in the previous section. The characteristic feature of such virus particles is the presence of proteins devoted to specialized structural or functional roles. Despite such complexity, detailed pictures of the organization of this type of virus particle can be constructed by using combinations of biochemical and structural methods. Well-studied human adenoviruses and members of the Reoviridae exemplify these approaches. These two examples also illustrate distinct mechanisms by which large icosahedral capsids can be stabilized, via either specialized proteins that glue interactions among major capsid proteins or mutually reinforcing associations between protein layers.
Adenovirus. The most striking morphological features of the adenovirus particle (maximum diameter, 150 nm) are the well-defined icosahedral appearance of the capsid and the presence of long fibers at the 12 vertices (Fig. 4.15A). A fiber, which terminates in a distal knob that binds to the adenoviral receptor, is attached to each of the 12 penton bases located at positions of fivefold symmetry in the capsid. The remainder of the shell is built from 240 additional subunits, the trimeric hexons (Fig. 4.15B). Formation of this capsid depends on nonequivalent interactions among subunits: the hexons that surround pentons occupy a different bonding environment than those surrounded entirely by other hexons. The X-ray crystal structures of the trimeric hexon (the major capsid protein) established that each protein monomer contains two β-barrel domains, each with the topology of the β-barrels of the simpler RNA and DNA viruses described in the previous section (Fig. 4.15B). The very similar topologies of the two β-barrel domains of the three monomers facilitate their close packing to form the hollow base of the trimeric hexon. Interactions among the monomers are very extensive, particularly in the towers that rise above the hexon base and are formed by intertwining loops from each monomer. Consequently, the trimeric hexon is extremely stable.
Figure 4.15 Structural features of adenovirus particles. (A) The organization of human adenovirus type 5 is shown schematically to indicate the locations of the major (hexon, penton base, and fiber) and minor (IIIa, VI, VIII, and IX) capsid proteins and of the internal core proteins, V, VII, and μ. The locations of these proteins and some interactions were initially deduced from the composition of the products of controlled dissociation of viral particles and the results of cross-linking studies. This schematic is based on subsequent high-resolution structures of adenovirus particles. (B) Structure of the hexon homotrimer from PDB ID: 1P30. The monomer (left) is shown as a ribbon diagram, with gaps indicating regions that were not defined in the X-ray crystal structure at 2.9-Å resolution, and the trimer (right) is shown as a space-filling model with each monomer in a different color. The monomer contains two β-barrel jelly roll domains colored green and blue in the left panel. The trimers are stabilized by extensive interactions within both the base and the towers.
The adenovirus particle contains seven additional structural proteins (Fig. 4.15A). The presence of so many proteins and the large size of the particle made elucidation of adenovirus architecture a challenging problem. One approach that has proved generally useful in the study of larger viruses is the isolation and characterization of discrete subviral particles. For example, adenovirus particles can be dissociated into a core structure that contains the DNA genome, groups of nine hexons, and pentons. Analysis of the composition of such subassemblies identified two classes of proteins in addition to the major capsid proteins described above. One comprises the proteins present in the core, such as protein VII, the major DNA-binding protein. The remaining proteins are associated with either individual hexons or the groups of hexons that form an icosahedral face of the capsid, suggesting that they stabilize the structure.
The interactions of protein IX and other minor proteins with hexons and/or pentons were deduced initially by difference imaging (Fig. 4.5) and refined subsequently by X-ray crystallography and cryo-EM (Fig. 4.16A). The minor capsid proteins make numerous contacts with the major structural units. For example, on the outer surface of the capsid, a network formed by extensive interactions among the extended molecules of protein IX knit together the hexons that form the groups of nine (Fig. 4.16B). The function of protein IX as capsid “cement” has been confirmed by the much-reduced heat stability of altered particles that lack this protein. Other minor capsid proteins are restricted to the inner surface, where they reinforce the groups of nine hexons and their associations, or weld the penton base to its surrounding hexons. Not surprisingly, such protein “glues” also buttress other larger icosahedral structures, such as the herpes simplex virus nucleocapsid and the capsids of much larger viruses, such as Paramecium bursaria chlorella virus 1 (some 190 nm in diameter). During adenovirus assembly, interactions among hexons and other major structural proteins must be relatively weak, so that incorrect associations can be reversed and corrected. However, the assembled particle must be stable enough to survive passage from one host to another. It has been proposed that the incorporation of stabilizing proteins like protein IX allows these paradoxical requirements to be met.
Reoviruses. Reovirus particles exhibit an unusual architecture: they contain multiple protein shells. They are naked particles, 70 to 90 nm in diameter with an outer T = 13 icosahedral protein coat that contains the 10 to 12 segments of the double-stranded genome and the enzymatic machinery to synthesize viral mRNA. The particles of human reovirus (genus Orthoreovirinae