P barrels, antiparallel

We saw in Chapter 2 that the Greek key motif provides a simple way to connect antiparallel p strands that are on opposite sides of a barrel structure. We will now look at how this motif is incorporated into some of the simple antiparallel P-barrel structures and show that an antiparallel P sheet of eight strands can be built up only by hairpin and/or Greek key motifs, if the connections do not cross between the two ends of the p sheet. 

Figure 9.18 Schematic digram of the structure of the DNA-binding domain of p53. (a) The DNA binding domain of p53 folds into an antiparallel p barrel with long loop regions—...

The polypeptide chain is folded into two domains (Figure 11.7), each of which contains about 120 amino acids. The two domains are both of the antiparallel p-barrel type, each containing six p strands with the same topology (Figure 11.8). Even though the actual structure looks complicated, the topology is very simple, a Greek key motif (strands 1-4) followed by an antiparallel hairpin motif (strands 5 and 6). 

Figure 11.8 Topology diagrams of the domain structure of chymotrypsin. The chain is folded into a six-stranded antiparallel p barrel arranged as a Greek key motif followed by a hairpin motif.

Each subunit of the trimeric porin molecule from R. capsulatus folds into a 16-stranded up and down antiparallel P barrel in which all p strands form... 

Figure 12.7 Ribbon diagram of one subunit of potin from Rhodobacter capsulatus viewed from witbin tbe plane of tbe membrane. Sixteen p strands form an antiparallel p barrel tbat traverses tbe membrane. Tbe loops at tbe top of tbe picture are extracellular whereas tbe short turns at tbe bottom face the periplasm. The long loop between p strands 5 and 6 (red) constricts the channel of the barrel. Two calcium atoms are shown as orange circles. (Adapted from S.W. Cowan, Curr. Opin. Struct. Biol. 3 501-507, 1993.)...

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...

POU regions bind to DNA by two tandemly oriented helix-turn-helix motifs Much remains to be learnt about the function of homeodomains in vivo Understanding tumorigenic mutations The monomeric p53 polypeptide chain is divided in three domains The oligomerization domain forms tetramers The DNA-binding domain of p53 is an antiparallel P barrel... 

A related family of proteins are represented by fatty acid-binding proteins1 ° and by the intracellular retinol- and retinoic acid-binding proteins (see also Box 22-A).p These are 10-stranded antiparallel P-barrels with two helices blocking an end (see Figure). 

The southern bean mosaic virus has an eight-stranded antiparallel P-barrel structure closely similar to that of the major domain of the bushy stunt viruses but lacking the second hinged domain. The problem of quasi-equivalence is resolved by the presence of an N-terminal extension that binds onto a subunit across the quasi-six-fold axis to give a set of three subunits (labeled C in Fig. 7-19) that associate with true three-fold symmetry and another set (B) with a slightly different conformation fitting between them. 2 The subunits A, which have a third conformation, fit together around the five-fold axis in true cyclic symmetry. 

Cyclophilin A, an antiparallel P-barrel formed by eight P-strands connected at the top and bottom by loops and a-helices (Figure 4), is an approximately spherical molecule 34 A in diameter.201 Cyclophilin s topology (+1, -3, -1, -2, +1, -2, -3) is unique, as is FKBP12 s. Unlike P-barrels found in some transport proteins, cyclophilin s core is filled with hydrophobic residues which preclude ligand binding in the barrel center.202... 

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