Parallel topology diagram

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 2.17 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 4.19 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 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.)...

Fic. 90. Triosephosphate isomerase as an example of a singly wound parallel /3 barrel, (a) a-Carbon stereo, viewed from one end of the barrel (b) backbone schematic, viewed as in a (c) a-carbon stereo, viewed from the side of the barrel (d) backbone schematic, viewed as in c (e) topology diagram showing the + lx right-handed connections between the fi strands. 

Fig. 4-10 Topology diagram for (a) retinol binding protein (RBP) and (b) triosephosphate isomerase (TPI). The arrows represent p strands (numbered from N to C) and the dark boxes represent a helices. Note from Fig. 4-8 that both of these proteins form a barrel structure comprised of eight p strands with the first strand hydrogen bonded to last strand in order to "close the barrel. However, whereas the p strands are antiparallel in RBP, they are arranged in parallel in TPI and are surrounded by an outer layer of a helices which connect each p strand to the next in the barrel.

Figure 5.30 Schematic diagrams of the structure of the enzyme pectate lyase C, which has a three-sheet parallel P-helix topology.

Fig. 25. A topological schematic diagram of the connectivity in the parallel /3 sheet of flavodoxin. Arrows represent the /3 strands thin-line connections lie below the plane of the sheet and fat connections above it. No attempt is made to indicate the length or conformation of the connecting chains (most of them are helical) or the twist of the fi sheet. The topology can also be specified by a sequential list of the connection types in this case, - lx,+ 2x,+ lx,+ lx.

Although both diagrams appear similar at first glance, there are some important differences. In particular, in the reactive system all solid lines intersect at the origin. The dotted lines are parallel and change their orientation at the bisection line. Furthermore, the pathgrid of the reactive system is symmetric with respect to the bisection line due to the fact that both enantiomers behave the same. This topology has important implications for the construction of wave solutions as discussed in detail in Ref. [13]. 

Figure 7 Schematic diagrams of human telomeric quadruplex folding topologies. (A) The fold determined by NMR spectroscopy of the intramolecular G-quadruplex formed by d(AG3(T2AG3)s) in solution with only Na ions. Gray rectangles represent nucleosides with syn glycosidic torsion angles. For clarity, only G-bases are represented. (B) The G-quadruplex fold, with parallel GGG elements and external loops, as determined by X-ray crystallography for the same sequence crystallized in the presence of ions ...

The formation of mesostructured materials of the M41S family and of related materials is a very complex field. Synthesis field diagrams (SFDs), which list the conditions of formation of different structural topologies as a function of the concentrations of the surfactant and silica precursors, reveal interesting details about the synthesis process. For the construction of an SFD, it is necessary to perform 120 to 150 synthesis experiments. The time necessary to construct an SFD for a certain set of reaction conditions (temperature, reaction time, basicity of the solution) can be reduced drastically by using the approach of parallel synthesis. Here we present an autoclave array allowing the parallel synthesis of 24 samples and our results obtained with this invention. 

---