Viruses subunit structure

Figure S.7 The subunit structure of the neuraminidase headpiece (residues 84-469) from influenza virus is built up from six similar, consecutive motifs of four up-and-down antiparallel fi strands (Figure 5.6). Each such motif has been called a propeller blade and the whole subunit stmcture a six-blade propeller. The motifs are connected by loop regions from p strand 4 in one motif to p strand 1 in the next motif. The schematic diagram (a) is viewed down an approximate sixfold axis that relates the centers of the motifs. Four such six-blade propeller subunits are present in each complete neuraminidase molecule (see Figure 5.8). In the topological diagram (b) the yellow loop that connects the N-terminal P strand to the first P strand of motif 1 is not to scale. In the folded structure it is about the same length as the other loops that connect the motifs. (Adapted from J. Varghese et al.. Nature 303 35-40, 1983.)...

In this chapter we will examine the construction principles of spherical viruses, the structures of individual subunits and the host cell binding properties of the surface of one of the picornaviruses, the common cold virus. 

One of the most striking results that has emerged from the high-resolution crystallographic studies of these icosahedral viruses is that their coat proteins have the same basic core structure, that of a jelly roll barrel, which was discussed in Chapter 5. This is true of plant, insect, and mammalian viruses. In the case of the picornaviruses, VPl, VP2, and VP3 all have the same jelly roll structure as the subunits of satellite tobacco necrosis virus, tomato bushy stunt virus, and the other T = 3 plant viruses. Not every spherical virus has subunit structures of the jelly roll type. As we will see, the subunits of the RNA bacteriophage, MS2, and those of alphavirus cores have quite different structures, although they do form regular icosahedral shells. 

Figure 16.13 The known subunit structures of plant. Insect, and animal viruses are of the jelly roll antiparallel p barrel type, described in Chapter 5. This fold, which is schematically illustrated in two different ways, (a) and (b), forms the core of the S domain of the subunit of tomato bushy stunt virus (c). [(b), (c) Adapted from A.J. Olson et al., /. Mol. Biol. 171 61-93, 1983.1...

The structures of many different plant, insect, and animal spherical viruses have now been determined to high resolution, and in most of them the subunit structures have the same jelly roll topology. However, a very different fold of the subunit was found in bacteriophage MS2, whose structure was determined to 3 A resolution by Karin Valegard in the laboratory of Lars Liljas, Uppsala. 

Figure 16.17 The subunit structure of the bacteriophage MS2 coat protein is different from those of other sphericai viruses. The 129 amino acid polypeptide chain is folded into an up-and-down antiparallei P sheet of five strands, P3-P7, with a hairpin at the amino end and two C-terminai a helices. (Adapted from a diagram provided by L. Liijas.)...

Such a subunit structure permits the construction of the virus partieles by a proeess in which the subunits self-assemble into structures held together by non-eovalent intermolecular forces as occurs in the process of erystallization. This eliminates the need for a sequenee of enzyme-catalysed reactions for coat synthesis. It also provides an automatic quality-control system, as subunits which may have major stmctural defects fail to become ineorporated into complete partieles. 

Zhou, Z. H., Prasad, B. V. V., Jakana, J., Rixon, F. J., and Chiu, W. (1994). Protein subunit structures in the herpes simplex virus A-capsid determined from 400kV spot-scan electron cryomicroscopy./. Mol. Biol. 242, 456-469. 

ROSENBERG, H., DISKIN, B., ORON, L. and TRAUB, A. Isolation and subunit structure of the polycytidylate-dependent RNA polymerase of encephalonQrocarditis virus. Proc. Nat. Acad. 

Another icosahedral plant virus used as a viral template is CCMV, a member of the Bromoviridae family. CCMV has a diameter of 28.6 nm and is comprised of a coat protein shell encapsulating a single strand of positive-sense RNA. Similar to CPMV, the genome of CCMV is comprised of multiple strands of RNA, with the three unique strands of RNA packaged individually into virus particles. The individual coat protein capsids of CCMV are composed of 190 amino acid residues and have a total mass of 19.8 kDa. Each coat protein subunit folds into the canonical virus -barrel structure. The protein shell of the virus is composed of 180 identical coat protein subunits. In contrast to CPMV, CCMV particles are stable at pH 5 but swell up to 10% in size when the pH is increased to 7. As illustrated in Figure 7, when the virus is swollen, pores are created within the protein shell, which permit the interior of the virns particles to be penetrated by small molecnles. The transition... 

Hence, the bottom-up procedures from a molecule to create new structures have become an important approach. This approach has already been used by Nature. Most of the structures of biological systems have been made by self-assembly and self-organization of specific molecules. The tobacco mosaic virus, for example, is rod-shaped—300 nm long and 18 nm in diameter—and has a mass of about 40,000 kDa [2]. The 2130 identical subunits in the protein coat are closely packed in a helical array around an RNA molecule consisting of 6390 nucleotides. Dissociated tobacco mosaic virus subunits and RNA can reassemble, under suitable conditions, into a virus that is identical with the original in structure and function. 

Two basic principles govern the arrangement of protein subunits within the shells of spherical viruses. The first is specificity subunits must recognize each other with precision to form an exact interface of noncovalent interactions because virus particles assemble spontaneously from their individual components. The second principle is genetic economy the shell is built up from many copies of a few kinds of subunits. These principles together imply symmetry specific, repeated bonding patterns of identical building blocks lead to a symmetric final structure. 

We have seen in the structure of this simple satellite virus that 60 subunits are sufficient to form a shell around an RNA molecule that codes for the subunit protein, but there is little room for additional genetic information. 

Can any number of identical subunits be accommodated in the asymmetric unit while preserving specificity of interactions within an icosahedral arrangement This question was answered by Don Caspar then at Children s Hospital, Boston, and Aaron Klug in Cambridge, England, who showed in a classical paper in 1962 that only certain multiples (1, 3, 4, 7...) of 60 subunits are likely to occur. They called these multiples triangulation numbers, T. Icosahedral virus structures are frequently referred to in terms of their trian-gulation numbers a T = 3 virus structure therefore implies that the number of subunits in the icosahedral shell is 3 x 60 = 180. 

As examples of such quasi-equivalent arrangement of subunits, we will examine the T = 3 and T = 4 packing modes, both of which are found in known virus particles. In the T = 3 structure, which has 180 subunits (3 x 60),... 

Figure 16.6 A T = 3 icosahedral virus structure contains 180 subunits in its protein shell. Each asymmetric unit (one such unit is shown in thick lines) contains three protein subunits A, B, and C. The icosahedral structure is viewed along a threefold axis, the same view as in Figure 16.5. One asymmetric unit is shown in dark colors.

Subunits VP2 and VP3 from different pentamers alternate around the threefold symmetry axes like subunits B and C in the plant viruses (Figure 16.12b). Since VP2 and VP3 are quite different polypeptide chains, they cannot be related to each other by strict symmetry, or even by quasi-symmetry in the original sense of the word. To a first approximation, however, they are related by a quasi-sixfold symmetry axis, since the folded structures of the cores of the subunits are very similar. 

The cleft where this drug binds is inside the jelly roll barrel of subunit VPl. Most spherical viruses of known structure have the tip of one type of subunit close to the fivefold symmetry axes (Figure 16.15a). In all the picor-naviruses this position is, as we have described, occupied by the VPl subunit. Two of the four loop regions at the tip are considerably longer in VPl than in the other viral coat proteins. These long loops at the tips of VPl subunits protrude from the surface of the virus shell around its 12 fivefold axes (Figure 16.15b). 

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