Virion symmetry

Several methods of viral classification are in use. Classification based upon epidemiological criteria, such as enteric or respiratory viruses, is useful, but of more significance are schemes based upon the morphology of the virion (symmetry, envelope, etc.) and lype of nucleic acid (DNA, RNA, number of strands, polarity, etc.)... 

Enveloped viruses Many viruses have complex membranous structures surrounding the nucleocapsid. Enveloped viruses are common in the animal world (for example, influenza virus), but some enveloped bacterial viruses are also known. The virus envelope consists of a lipid bilayer with proteins, usually glycoproteins, embedded in it. Although the glycoproteins of the virus membrane are encoded by the virus, the lipids are derived from the membranes of the host cell. The symmetry of enveloped viruses is expressed not in terms of the virion as a whole but in terms of the nucleocapsid present inside the virus membrane. 

Complex viruses Some virions are even more complex, being composed of several separate parts, with separate shapes and symmetries. The most complicated viruses in terms of structure are some of the bacterial viruses, which possess not only icosahedral heads but helical tails. In some bacterial viruses, such as the T4 virus of Escherichia coli, the tail itself is a complex structure. For instance, T4 has almost 20 separate proteins in the tail, and the T4 head has several more proteins. In such complex viruses, assembly is also complex. For instance, in T4 the complete tail is formed as a subassembly, and then the tail is added to the DNA-containing head. Finally, tail fibers formed from another protein are added to make the mature, infectious virus particle. 

HIV protease is an homodimer of C2 symmetry. This enzyme specifically cleaves the precursor polyprotein and affords the proteins required for maturation of the virion and for virus replication. Some pseudosymmetric inhibitors have been conceived on this basis. For example, pseudosymmetric difluoroketones exhibit subnanomolar inhibitions and are active toward infected lymphocyte MT-4 cell lines. Nevertheless, simpler a-peptidyl fluoroketones are also good inhibitors (Figure 7.41). The difluorostanones developed by Merrell-Dow were very efficient toward infected cells. ... 

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]. 

The classification in Table 14.1 shows 16 groups of animal viruses and is based on (a) the nature of the nucleic acid, (b) the structural symmetry of the virus particle, (c) the presence of an envelope, and (d) the size of the virion. The classification is simplified from that of Fraenkel-Conrat (1974) and resembles that of Wildy (1971), but details of classifications differ as precise taxonomic relationships have not been established. 

Group Nucleic acid Average MW xlO6 Virion diam. (nm) Shape Symmetry env. eg-... 

A separate study investigated the function of the N-terminal region of the EHV coat protein in determining the geometry of the particle. It was postulated, on the basis of the position of the N terminus in the high-resolution structure of mature virions, that deletion of the first 31 residues would result in assembly of a particle with T = 1 symmetry containing 60... 

Reoviruses are nonenveloped virions with icosahedral symmetry and consist of two concentric protein shells, termed the outer capsid and core [15]. These virions encapsidate a genome of 10 double-stranded RNA gene segments. Reovirus strain type 1 Lang (TIL) has a diameter of 850 A and 600 projections composed of the uS protein [147]. uS interdigitates with a more internal layer composed of 600 copies of fil protein to form the outer capsid. At each icosahedral 5-fold axis, pentamers of 2.2 protein... 

Stewart et al.. Fig. 1. CryoEM reconstructions of reovirus TIL (A) virion, (B) infectious subvirion particle (ISVP), and (C) core viewed along a 2-fold symmetry axis. The capsid proteins crl, cr3, pi, and A2 are indicated. Note that the density from thin spikelike crl protein appears disconnected. The density is colored according to radial height as indicated by the color bar in order to accentuate the surface features. White scale bar 200 A. [Modified from the Journal of Cell Biology, 1993, Vol. 122, pp. 1023-1041 (Dryden et at, 1993) by copyright permission of the Rockefeller University Press.]... 

In addition to replication of the viral genome, a number of other structures associated with the complete virion also can be made. A number of viral proteins may be synthesized that have important functions in the structure, transmission, and survival of the virus. These proteins can protect the genetic material in the virus from destruction by nucleases, participate in the attachment process, and provide structure and symmetry to the virion. In addition, in certain cases where the virus requires an enzymatic process for which there is no host enzyme, a virion may include enzymes, such as RNA polymerases or a RT. Some viruses require a lipid envelope that contains transmembrane proteins specifically coded for by the virus and which envelopes the genetic material... 

Fig. 28-3. Structure of an alphavirus. Shown is the three-dimensional reconstruction of Sindbis virus at 28 A resolution from computer-processed images taken by electron cryomicroscopy, (a) The original electron micrograph shows virus particles in vitreous ice. (b) The surface view of the virus shows details of the 80 trimeric spikes, which are arranged in a T=4 icosahedron. Each spike protrudes 50 A from the virion surface and is believed to be composed of three E1-E2 glycoprotein heterodimers, (c) The cross-sectional view shows the outer surface spikes (yellow) and the internal nucleocapsid (blue), composed of the capsid and viral RNA. The space between the spikes and the nucleocapsid would be occupied by the lipid envelope. The green arrows mark visible points of interaction between the nucleocapsid and trans-membranal tails of the glycoprotein spikes, (d) The reconstructed capsid also exhibits a T=4 icosahedral symmetry. Computer models Courtesy of Angel M. Paredes, Cell Research Institute and Department of Microbiology, The University of Texas at Austin, Austin, Tex. Similar but not identical versions of these computer models were published in Paredes AM, Brown DT, Rothnagel R, et al. Three-dimensional structure of a membrane-containing virus. Proc Natl Acad Sci USA. 1993 90 9095-9099.

An icosahedron is defined by 20 triangular faces and 12 vertices related by two-, three-, and fivefold axes of rotational symmetry (Fig. 1). A spherical virion based on true icosahedral symmetry can be built from 60 copies of an identical coat protein subrmit. However, a virion based on true icosahedral symmetry severely restricts the size of the genome that can be packaged. In nature, most... 

The NV is a human calicivims and contains a single-stranded RNA genome.Particles of NV have T=3 icosahedral symmetry with an approximate outer diameter of 38 nm and an average inner diameter of the central cavity that ranges from 20-29 nm. These virions contain 180 molecules of identical capsid protein (56.6 kl/)a each), which has two principle domains, S and P. linked by a flexible hinge.These viruses arc difficult to cultivate in tissue culture systems or animals,"" making them difficult to study, and this factor limits their use as nanosynthctic reaction vessels. 

In 1959 Finch and Klug examined crystals of poliovirus by X-ray diffraction and concluded that the virion possessed icosahedral symmetry. Extrapolating from the experimental data, they also suggested that the capsid was made up on 60 identical asymmetric structure units with a diameter of 6O-65 Based upon the then accepted values of 6.7 x 10 for the particle weight of the virion and 2x10 for the molecular weight of the RUA, they calculated a molecular weight for the structure unit of 80,000 (28). 

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