Protein coat

B Roux, TB Woolf. Molecular dynamics of Pfl coat protein in a phospholipid bilayer. In KM Merz Ir, B Roux, eds. Biological Membranes A Molecular Perspective from Computation and Experiment. Boston Birkhauser, 1996, pp 555-587. 

Antiparallel beta (P) structures comprise the second large group of protein domain structures. Functionally, this group is the most diverse it includes enzymes, transport proteins, antibodies, cell surface proteins, and virus coat proteins. The cores of these domains are built up by p strands that can vary in number from four or five to over ten. The P strands are arranged in a predominantly antiparallel fashion and usually in such a way that they form two P sheets that are joined together and packed against each other. 

The jelly roll barrel is thus conceptually simple, but it can be quite puzzling if it is not considered in this way. Discussion of these structures will be exemplified in this chapter by hemagglutinin and in Chapter 16 by viral coat proteins. 

Very few self-sufficient viruses have only 60 protein chains in their shells. The satellite viruses do not themselves encode all of the functions required for their replication and are therefore not self-sufficient. The first satellite virus to be discovered, satellite tobacco necrosis virus, which is also one of the smallest known with a diameter of 180 A, has a protein shell of 60 subunits. This virus cannot replicate on its own inside a tobacco cell but needs a helper virus, tobacco necrosis virus, to supply the functions it does not encode. The RNA genome of the satellite virus has only 1120 nucleotides, which code for the viral coat protein of 195 amino acids but no other protein. With this minimal genome the satellite viruses are obligate parasites of the viruses that parasitize cells. 

The asymmetric unit contains one copy each of the subunits VPl, VP2, VP3, and VP4. VP4 is buried inside the shell and does not reach the surface. The arrangement of VPl, VP2, and VP3 on the surface of the capsid is shown in Figure 16.12a. These three different polypeptide chains build up the virus shell in a way that is analogous to that of the three different conformations A, C, and B of the same polypeptide chain in tomato bushy stunt virus. The viral coat assembles from 12 compact aggregates, or pen tamers, which contain five of each of the coat proteins. The contours of the outward-facing surfaces of the subunits give to each pentamer the shape of a molecular mountain the VPl subunits, which correspond to the A subunits in T = 3 plant viruses, cluster at the peak of the mountain VP2 and VP3 alternate around the foot and VP4 provides the foundation. The amino termini of the five VP3 subunits of the pentamer intertwine around the fivefold axis in the interior of the virion to form a p stmcture that stabilizes the pentamer and in addition interacts with VP4. 

The coat proteins of many different spherical plant and animal viruses have similar jelly roll barrel structures, indicating an evolutionary relationship... 

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. 

The canonical jelly roll barrel is schematically illustrated in Figure 16.13. Superposition of the structures of coat proteins from different viruses show that the eight p strands of the jelly roll barrel form a conserved core. This is illustrated in Figure 16.14, which shows structural diagrams of three different coat proteins. These diagrams also show that the p strands are clearly arranged in two sheets of four strands each P strands 1, 8, 3, and 6 form one sheet and strands 2, 7, 4, and 5 form the second sheet. Hydrophobic residues from these sheets pack inside the barrel. 

In all jelly roll barrels the polypeptide chain enters and leaves the barrel at the same end, the base of the barrel. In the viral coat proteins a fairly large number of amino acids at the termini of the polypeptide chain usually lie outside the actual barrel structure. These regions vary considerably both in size and conformation between different coat proteins. In addition, there are three loop regions at this end of the barrel that usually are quite long and that also show considerable variation in size in the plant viruses and the... 

Figure 16.14 Schematic diagrams of three different viral coat proteins, viewed in approximately the same direction. Beta strands I through 8 form the common jelly roll barrel core, (a) Satellite tobacco necrosis virus coat protein, (b) Subunit VPl from poliovirus.

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). 

Since all members of this family of RNA phages have homologous coat proteins, their subunits are expected to have the same three-dimensional structure. It remains to be seen if the MS2 fold is also present in any other unrelated viruses. The fold is so far unique for the MS2 subunit, but similar structures have been observed in other proteins such as the major histocompatibility antigen, HLA, which was discussed in Chapter 15. 

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.)...

Figure 16.19 Schematic drawing illustrating the structure and sequence of the RNA fragment that is recognized and bound by the coat protein of bacteriophage MS2. The RNA fragment forms a base-paired stem with a bulge at base -10 and a loop of four bases. Bases that form sequence-specific Interactions with the coat protein are red. (Adapted from a diagram provided by L. Llljas.)...

Figure 16.21 Structure of one subunit of the core protein of Slndbls virus. The protein has a similar fold to chymotrypsin and other serine proteases, comprising two Greek key motifs separated by an active site cleft. The C-terminus of the protein is bound in the catalytic site, making the coat protein inactive (Adapted from S. Lee et al., Structure 4 531-541, 1996.)...

Each precursor protein molecule is cleaved only once to generate one molecule of the coat protein, and catalytic activity is restricted to the precursor protein. Why is the coat protein itself catalytically inactive The structure of the coat protein shows that its C-terminus is bound in the active site cleft and thereby prevents other proteins entering the cleft and being cleaved. Tbis arrangement allows the precursor protein to fulfill its function to generate the coat protein and prevents the coat protein from destroying other proteins in the infected cell, including other coat proteins. 

SV40 and polyomavirus shells are constructed from pentamers of the major coat protein with nonequivalent packing but largely equivalent interactions... 

Models also can assist in experimental design and the determination of the limits of experimental systems. For example, it is known that three proteins mediate the interaction of HIV with cells namely, the chemokine receptor CCR5, the cellular protein CD4, and the viral coat protein gpl20. An extremely useful experimental system to study this interaction is one in which radioactive CD4, prebound to soluble gpl20, is allowed to bind to cellular receptor CCR5. This system can be used to screen for... 

Assuming that all interactions of the species are possible, the system consists of the receptor CCR5 [R], radioligand CD4 [CD]), viral coat protein gpl20 [gp], and potential displacing ligand [B] ... 

Variance ratio, 239 Venn diagram, 177, 192f Viral coat protein, 44, 53 Volume of distribution, 165, 168... 

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