Principles of Virology. Jane Flint

reduction in infectivity of poliovirus requires >250 days when particles suspended in water are incubated at room temperature at neutral pH. Certain picornaviruses are even resistant to very strong detergents. The highly folded nature of coat proteins and their dense packing to form shells render them largely inaccessible to proteolytic enzymes. Some viruses also possess an envelope, typically derived from cellular membranes, into which viral glycoproteins have been inserted. The envelope adds not only a protective lipid membrane but also an external layer of protein and sugars formed by the glycoproteins. Like the cellular membranes from which they are derived, viral envelopes are impermeable to many molecules and block entry of chemicals or enzymes in aqueous solution.

To protect the nucleic acid genome, virus particles must be stable. However, they must also attach to an appropriate host cell and deliver the genome to the interior of that cell, where the particle is at least partially disassembled. The protective function of virus particles depends on stable intermolecular interactions among their components during assembly, egress from the virus-producing cell, and transmission. On the other hand, these interactions must be reversed readily during entry and uncoating in a new host cell. In only a few cases do we understand the molecular mechanisms by which these apparently paradoxical requirements are met. Nevertheless, it is clear that contact of a virion with the appropriate cell surface receptor or exposure to a specific intracellular environment can trigger substantial conformational changes. Virus particles are therefore metastable assemblies that have not yet attained the minimum free energy conformation (Fig. 4.2). The latter state can be attained only once an unfavorable energy barrier has been surmounted, following induction of the irreversible conformational transitions that are associated with attachment and entry. Virions are not simply inert entities. Rather, they are molecular machines (nanomachines) that play an active role in delivery of the nucleic acid genome to the appropriate host cell and initiation of the reproductive cycle.

      PRINCIPLES Structure

       Virus particles are constructed to ensure protection and delivery of the genome.

       Virus structure can be studied at an atomic level of resolution.

       Principles of protein-protein interaction dictate construction of capsids from a small number of subunits.

       Rod-like and spherical viruses are built with helical and icosahedral symmetry, respectively.

       The primary determinant of capsid size is the number of subunits: the more subunits, the larger the capsid.

       There are multiple ways to achieve icosahedral symmetry, even among small viruses.

       Large icosahedral capsids contain dedicated stabilizing proteins or multiple protein shells that reinforce one another.

       While ordered RNA can be observed, how genomes are condensed and organized within virus particles is largely obscure.

       Some large viruses are built with structural elements recognizable from simpler viruses.

       Virus particles can contain nonstructural components, including enzymes, small RNAs, and cellular macromolecules.

Figure 4.1 Variation in the size and shape of virus particles. (A) Cryo-electron micrographs of mimivirus and, in the inset (upper left), the parvovirus adeno-associated virus type 4, shown to scale relative to one another to illustrate the ~50-fold range in diameter among viruses that appear roughly spherical. The mimivirus particle (A) is structurally complex: a large number of long, closely packed filaments project from its surface; and one vertex of the capsid carries a unique structure called the stargate, which opens in infected cells to release the viral genome. Rod-shaped viruses also exhibit considerable variation in size, ranging in length from <200 nm to ~2,000 nm. Photos reprinted from Xiao C et al. 2005. J Mol Biol 353:493–496, and Pardon E et al. 2005. J Virol 79:5047–5058, respectively, with permission. Courtesy of Y. Mustafi, National Institutes of Health, and M. Agbandje-McKenna, University of Florida, Gainesville. (B) Nonsymmetric shape of Acidianus bottle-shaped virus isolated from a hot spring in Italy. Adapted from Häring M et al. 2005. J Virol 79:9904–9911, with permission. Courtesy of D. Prangishvili, Institut Pasteur.

Table 4.1 Functions of virion proteins

Protection of the genome

Assembly of a stable protective protein shell

Specific recognition and packaging of the nucleic acid genome

Interaction with host cell membranes to form the envelope

Delivery of the genome

Binding to external receptors of the host cell

Transmission of signals that induce uncoating of the genome

Induction of fusion with host cell membranes

Interaction with internal components of the infected cell to direct transport of the genome to the appropriate site

Other functions

Interactions with cellular components for transport to intracellular sites of assembly

Interactions with cellular components to ensure an efficient infectious cycle

Figure 4.2 Free energy changes in virus particles. Mature virus particles occupy a free energy minimum (1); that is, they are stable, but have not attained the structure with the lowest free energy. Rather, they are primed during assembly and maturation to undergo irreversible conformational transitions (2) that overcome the energy barrier to that lower (more favorable) free energy state (3), and to disassemble at least partially. Such transitions are typically triggered by contact with a host cell receptor or coreceptor or such changes in the environment as a drop in pH. G, free energy; X, reaction coordinate (for example, time after addition of virus particles to susceptible host cells).

      As might be anticipated, elucidation of the structures of virus particles and individual structural proteins has illuminated the mechanisms of both assembly of viral nanomachines in the final stages of an infectious cycle and their entry into a new host cell. High-resolution structural information can also facilitate identification of targets for antiviral drugs, as well as the design of such drugs (Volume II, Chapter 8), and provide insights into the dynamic interplay between important viral pathogens and host adaptive immune responses (Volume II, Chapter 4). As we shall see, cataloguing of virus architecture has also revealed completely unanticipated relationships among viruses of different families that infect evolutionarily divergent hosts, and has suggested new principles of virus classification.

Nomenclature

Virus architecture is described in terms of structural units of increasing complexity, from the smallest biochemical unit (the polypeptide chain) to the infectious particle (or virion). These terms, which