Jelly-roll structure

Figure S.18 Topological diagrams of the jelly roll structure. The same color scheme is used as in Figure 5.17.

The binding site is located at the tip of the subunit within the jelly roll structure (Figure 5.23). The sialic acid moiety of the hemagglutinin inhibitors binds in the center of a broad pocket on the surface of the barrel (Figure 5.24). In addition to this groove there is a hydrophobic channel that can accomodate large hydrophobic substituents at the C2 position of sialic acid (Figures 5.22 and 5.24). 

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 structures of ssDNA bacteriophages ( X174 and G4 have been reported in mature and provirus forms (Dokland et al, 1997 McKenna et al, 1992b, 1996). The mature viruses are T=1 with 60 copies each of the F, G, and (small J) proteins, and 12 copies of the H protein. Both the F and G proteins are classic viral jelly-roll structures. It is the F protein that occupies the positions homologous to the (+)ssRNA capsids. At 430 residues, the F protein is closest in size to the parvoviral capsids, and achieves its size through large loop insertions, primarily in the EF and HI... 

A. Gaskell, S. Crennell, and G. Taylor, The three domains of a baeterial sialidase A beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll. Structure, 3 (1995) 1197—1205. 

Such an internally fluid structure can be achieved by rolling the smectic layers into concentric cylinders (so-called "jelly roll" structure) (see Figure 2.19). 

Proposed "jelly-roll" structure of the banana smectic fibers. 

To illustrate how this rather complicated structure is built up, we will start by wrapping a piece of string around a barrel as shown in Figure S.16. The string goes up and down the barrel four times, crosses over once at the bottom and twice at the top of the barrel. This configuration is the basic pattern for the jelly roll motif. 

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. 

The number of possible ways to form antiparallel p structures is very large. The number of topologies actually observed is small, and most p structures fall into these three major groups of barrel structures. The last two groups—the Greek key and jelly roll barrels—include proteins of quite diverse function, where functional variability is achieved by differences in the loop regions that connect the p strands that build up the common core region. 

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

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 16.13 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 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). 

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. 

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