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Viral capsids

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The capsid is a complex structure made up of many identical subunits of viral protein – often termed a capsomer. The capsid functions to provide a protein shell in which the chemically labile viral genome can be maintained in a stable environment. The association of capsids with genomes is a complex process, but it must result in an energetically stable structure. While viruses can assume a range of shapes, some quite complex, given the dimensions of virus structure and the constraints of the capsomer's structural parameters, a very large number assume one of two regular shapes. The first is the helix, in which the capsomers associate with helical nucleic acid as a nucleoprotein – these can be either stiff or flexible depending upon the properties of the capsid proteins themselves. The other highly regular shape is the icosahedron, in which the capsomers form a regular solid structure enfolding the viral genome. Despite the frequency of such regular shapes, many viruses have more complex and/or less regular appearances; these include spindle, kidney, lemon, and lozenge shapes. Further, some viruses can assume different shapes depending upon the nature of the cells in which they mature, and some groups of viruses – notably the poxviruses – are distinguished by having a number of different shapes characterizing specific members of the group. Arrangement of the capsid around its viral genetic material is unique for each type of virus. The general properties of this arrangement define the shape of the capsid and its symmetry, and since each type of virus has a unique shape and structural arrangement based upon the precise nature of the capsids proteins and how they interact, capsid shape is a fundamental criterion in the classification of viruses.

The technique of x‐ray crystallography has been applied fruitfully to the study of capsid structures of some smaller icosahedral viruses, and structural solutions for human rhinovirus, poliovirus, foot and mouth disease virus, and canine parvovirus are available. In addition, the structures of a number of plant viruses have been determined. Since the method requires the ability to crystallize the subject material, it is not certain that it can be directly applied to larger, more complex viruses. Still, the structures of specific protein components of some viruses – such as the membrane‐associated hemagglutinin of influenza virus – have been determined.

The x‐ray crystallographic structure of Desmodium yellow mottle virus – a pathogen of beans – is shown in Figure 5.3, to illustrate the basic features of icosahedral symmetry. The icosahedral shell has a shape similar to a soccer ball, and the 12 vertices of this regular solid are arranged in a relatively simple pattern at centers of fivefold axes of symmetry. Each edge of the solid contains a twofold axis of symmetry, and the center of each of the 20 faces of the solid defines a threefold axis of symmetry. While a solid icosahedron can be visualized as composed of folded sheets, the virion structure is made up of repeating protein capsomers that are arrayed to fit the symmetry's requirements. It is important to see that the peptide chains themselves have their own distinct morphology, and it is their arrangement that makes up individual capsomers. The overall capsid structure reflects the next level of structure. Morphology of the individual capsomers can be ignored without altering the basic pattern of their arrangement. Further detail is shown in Figure 5.4, where the assembly of the single capsomer protein into two subunits of the capsid, a penton or a hexon, is shown.

Twelve pentons and 20 hexons assemble to form the capsid itself. The core of the capsid is filled with the viral genome, in this case RNA. This RNA is also arranged very precisely, with the bulk forming helical stretches and the regions coming in close contact with the inner surface of the capsid shell, forming open loops.

Basic Virology

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