Jelly roll barrels

The Greek key motifs can form jelly roll barrels... 

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 jelly roll barrel is usually divided into two sheets... 

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... 

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). 

Figure 16.16 Schematic diagrams Illustrating the binding of an antiviral agent to human rhlnovirus strain 14. (a) The drug binds in a hydrophobic pocket of VPl below the floor of the canyon, (b) Schematic diagram of VPl Illustrating the pocket in the jelly roll barrel where the drug binds. (Adapted from T.J. Smith et al.. Science 233 1286-1293, 1986.)...

The biggest variations are in the loops—in size and additional secondary structural elements (or complete domains) that they contain. In the nonenveloped vertebrate viruses, it is the external loops that contain the antigenic sites (Rossmann et al, 1985 Tsao et al, 1991), with epitopes formed where several loops come together. The nomenclature BC is used to describe the loop between strands B and C. Generally, the BC, HI, DE, and EG loops that are close to the 5-fold/quasi-6-fold axes tend to be short, whereas the CD, EF, and GH loops tend to be longer. Whereas most of the jelly-roll / barrels are about 180 amino acids, they go up in size to 584 amino acids in parvoviruses with large insertions in the loops (Tsao et al, 1991). 

Antiparallel p sheets are, as was described earUer, twisted, and they can pack to form a barrel with a hydrophobic core. Three structures are commonly found for -proteins these are the up-and-down barrel (Figure 22a), the Greek key barrel (Figure 22b) and the jelly-roll barrel (Figure 22c). Another motif, shown in Figure 22(d), has been found in pectate lyase [119], even though it was thought too unstable to exist. 

Figure 22 Sheet motifs (a) the up-and-down barrel (b) the Greek key barrel (c) the jelly-roll barrel and (d) the structure in pectate lyase [119]...

Jelly roll barrels in which any even number of P strands (greater than four P strands) form a jelly roll barrel with equal number of connections across the top and bottom of the barrel. The antiparaUel up-and-down p barrel is the simplest organization. 

The p class contains the parallel and antiparallel p structures. The p strands are usually arranged in two p sheets that pack against each other and form a distorted barrel structure. Three major types of p barrels exist, the up-and-down barrels, the Greek key barrels,and the jelly roll barrels (see Figure 6). Most known antiparallel p structures, including the... 

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