Topology diagrams

Topology diagrams are useful for classification of protein structures... 

Figure 2.11 Beta sheets are usuaiiy represented simply by arrows in topology diagrams that show both the direction of each (3 strand and the way the strands are connected to each other along the polypeptide chain. Such topology diagrams are here compared with more elaborate schematic diagrams for different types of (3 sheets, (a) Four strands. Antiparallel (3 sheet in one domain of the enzyme aspartate transcarbamoylase. The structure of this enzyme has been determined to 2.8 A resolution in the laboratory of William Lipscomb, Harvard University, (b) Five strands. Parallel (3 sheet in the redox protein flavodoxin, the structure of which has been determined to 1.8 A resolution in the laboratory of Martha Ludwig, University of Michigan, (c) Eight strands. Antiparallel barrel in the electron carrier plastocyanln. This Is a closed barrel where the sheet is folded such that (3 strands 2 and 8 are adjacent. The structure has been determined to 1.6 A resolution in the laboratory of Hans Freeman in Sydney, Australia. (Adapted from J. Richardson.)...

Figure 2.15 The Greek key motif is found in antiparallel p sheets when four adjacent p strands are arranged in the pattern shown as a topology diagram in (a). The motif occurs in many p sheets and is exemplified here by the enzyme Staphylococcus nuclease (b). The four p strands that form this motif are colored red and blue.

Figure 2.16 Suggested folding pathway from a hairpinlike structure to the Greek key motif. Beta strands 2 and 3 fold over such that strand 2 is aligned adjacent and antiparallel to strand 1. The topology diagram of the Greek key shown here is the same as in Figure 2.15a but rotated 180° in the plane of the page.

Figure 2.17 Two adjacent parallel p strands are usually connected by an a helix from the C-termlnus of strand 1 to the N-termlnus of strand 2. Most protein structures that contain parallel p sheets are built up from combinations of such p-a-P motifs. Beta strands are red, and a helices are yellow. Arrows represent P strands, and cylinders represent helices, (a) Schematic diagram of the path of the main chain, (b) Topological diagrams of the P-a-P motif.

Figure 2.21 Two sequentially adjacent hairpin motifs can be arranged in 24 different ways into a p sheet of four strands, (a) Topology diagrams for those arrangements that were found in a survey of all known structures in 1991. The Greek key motifs in (1) and (v) occurred 74 times, whereas the arrangement shown in (viii) occurred only once, (b) Topology diagrams for those 16 arrangements that did not occur in any structure known at that time. Most of these arrangements contain a pair of adjacent parallel P strands.

Figure 4.1 Alpha/beta domains are found in many proteins. They occur in different classes, two of which are shown here (a) a closed barrel exemplified by schematic and topological diagrams of the enzyme trlosephosphate isomerase and (b) an open twisted sheet with helices on both sides, as in the coenzymebinding domain of some dehydrogenases. Both classes are built up from p-a-p motifs that are linked such that the p strands are parallel. Rectangles represent a helices, and arrows represent p strands in the topological diagrams, [(a) Adapted from J. Richardson, (b) Adapted from B. Furugren.j...

Figure 4.14 Examples of different types of open twisted a/p structures. Both schematic and topological diagrams are given. In the topological diagrams, arrows denote strands of p sheet and rectangles denote a helices, (a) The FMN-binding redox protein flavodoxln. (b) The enzyme adenylate kinase, which catalyzes the reaction AMP +...

Where more than one a helix connects two P strands (for example, between strands 4 and S), they are represented as one rectangle in the topology diagram. (Adapted from T.N. Bhat et al., /. Mol. Biol. 1S8 699-709, 1982.)... 

Figure 4.19 Schematic and topological diagrams for the structure of the enzyme carboxypeptidase. The central region of the mixed p sheet contains four adjacent parallel p strands (numbers 8, 5, 3, and 4), where the strand order is reversed between strands 5 and 3. The active-site zinc atom (yellow circle) is bound to side chains in the loop regions outside the carboxy ends of these two p strands. The first part of the polypeptide chain is red, followed by green, blue, and brown. (Adapted from J. Richardson.)...

Figure 4.21 The polypeptide chain of the arabinose-binding protein in E. coli contains two open twisted a/P domains of similar structure. A schematic diagram of one of these domains is shown in (a). The two domains are oriented such that the carboxy ends of the parallel P strands face each other on opposite sides of a crevice in which the sugar molecule binds, as illustrated in the topology diagram (b). [(a) Adapted from J. Richardson.)...

Figure S.2 Schematic and topological diagrams of an up-and-down fi barrel. The eight p strands are all antiparallel to each other and are connected by hairpin loops. Beta strands that are adjacent in the amino acid sequence are also adjacent in the three-dimensional structure of up-and-down barrels.

Figure S.3 Schematic diagram of the structure of human plasma retinol-binding protein (RBP), which is an up-and-down P barrel. The eight antiparallel P strands twist and curl such that the structure can also be regarded as two p sheets (green and blue) packed against each other. Some of the twisted p strands (red) participate in both P sheets. A retinol molecule, vitamin A (yellow), is bound inside the barrel, between the two P sheets, such that its only hydrophilic part (an OH tail) is at the surface of the molecule. The topological diagram of this stmcture is the same as that in Figure 5.2. (Courtesy of Alwyn Jones, Uppsala, Sweden.)...

Figure S.6 Schematic and topological diagrams of the folding motif in neuraminidase from influenza virus The motif is built up from four antiparallel P strands joined by hairpin loops, an up-and-down open P sheet.

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.)...

The topological diagram of Figure 5.13 has been drawn to reflect the observation that the two (3 sheets are separate 3 strands 2 and 3 are not hydrogen bonded to each other, nor are strands 6 and 7. The connections... 

Figure S.13 A preliminary topological diagram of the structure of one domain of Y crystallin shown In Figure 5.12, Illustrating that the two P sheets ate separate within the domain.

Figure S.IS Schematic diagram (a) and topology diagram (b) for the y-crystallin molecule. The two domains of the complete molecule have the same topology each is composed of two Greek key motifs that are joined by a short loop region, [(a) Adapted from T. Blundell et ah. Nature 289 171-777, 1981.]...

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

Figure 8.S The three P strands of each subunit in lambda Cro are aligned in the dimer so that a six-stranded antiparallel p sheet is formed as shown in this topology diagram. The P strands are colored as in Figure 8.4.

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.

Figure 11.10 Topological diagram of the two domains of chymotrypsin, illustrating that the essential active-site residues are part of the same two loop regions (3-4 and 5-6, red) of the two domains. These residues form the catalytic triad, the oxyanion hole (green), and the substrate binding regions (yellow and blue) including essential residues in the specificity pocket.

Figure 11.15 Topology diagram of the a/p region of subtilisin illustrating that Pa-ae-Pa has a different hand than the other p-a-p units.

Figure 13.4 Schematic diagram (a) and topology diagram (b) of the polypeptide chain of cH-ras p21. The central p sheet of this a/p structure comprises six p strands, five of which are parallel a helices are green, p strands are blue, and the adenine, ribose, and phosphate parts of the GTP analog are blue, green, and ted, respectively. The loop regions that are involved in the activity of this protein are red and labeled Gl-GS. The Gl, G3, and G4 loops have the consensus sequences G-X-X-X-X-G-K-S/T, D-X-X-E, and N-K-X-D, respectively. (Adapted from E.R Pai et al., Nature 341 209-214, 1989.)...

Figure IS. 7 The constant domains of immunoglobulins are folded into a compressed antiparallel p banel built up from one three-stranded p sheet packed against a four-stranded sheet (a). A topological diagram (b) shows the connected Greek key motifs of this fold.

Figure 15.24 Ribbon diagram (a) and topology diagram (b) of the fibronectin type III domain, which is composed of a three-stranded and a four-stranded p sheet packed together as a compressed barrel.

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