Topology helicity

MEMSAT [70] is a program for predicting the secondary structure and topology (helical orientation) of integral membrane proteins. 

In the history of helicity, DMA is probably the prototypical helical structure. Besides this natural constituent of living cells, this review surveys helical structures based on organ-ophosphorus derivatives. The first section contains phosphahelicenes constituted by a sequence of fused aromatic rings which can adopt a nonplanar screw-shaped topology. Helical structures can also arise from propeller-shaped molecules or by a succession of spirocycles illustrated consecutively. The last section reports systems where the helical arrangement comes from supramolecular organization. In this category fall acid... 

To date, RNA calculations have been performed on a variety of systems of different topologies including helical duplexes, hairpin loops, and single strands from tRNA, rRNA, and ribozymes. In a simulation of an RNA tetraloop of the GRNA type, which is very common and known to be remarkably stable, it was found that without imposing any external infonnation the simulation found the right confonnation even when it started from the wrong one [72]. Studies have used Ewald summation methods to handle the... 

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 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 +...

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.)...

Like other hormones in this class of cytokines, GH has a four-helix bundle structure as described in Chapter 3 (see Figures 3.7 and 13.18). Two of the a helices, A and D, are long (around 30 residues) and the other two are about 10 residues shorter. Similar to other four-helix bundle structures, the internal core of the bundle is made up almost exclusively of hydrophobic residues. The topology of the bundle is up-up-down-down with two cross-over connections from one end of the bundle to the other, linking helix A with B and helix C with D (see Figure 13.18). Two short additional helices are in the first cross-over connection and a further one in the loop connecting helices C and D. 

Figure 13.18 Ribbon diagram of the structure of human growth hormone. The fold is a four-helix bundle with up-up-down-down topology, and consequently there are two long cross-connections between helices A and B as well as between helices C and D. (Adapted from J. Wells et al., Annu. Rev. Biochem.

Studies of other members of the family have also added support to the topological model shown in the Fig. 3. In particular, chemical labelling of the native and mutated tetracycline transporter has confirmed the cytoplasmic location of the N-terminus and the loop connecting transmembrane helices 2 and 3 [231,232]. Protease digestion experiments on this protein have also provided preliminary evidence for the cyto-... 

FIGURE 3.1 Schematic representation of the transmembrane topology of the 4TM receptor family. Only TM2 show an a-helical structure in electron microscopic studies the remaining TM regions may fold in (5-sheet structures. Both the N-terminus (indicated by NH2) and the C-terminus are located extracellularly. The cytoplasmic loops between TM3 and TM4 are variable in size and contain putative phosphorylation sites. 

Over recent years a variety of new helical canal inclusion systems have been discovered and characterised, and an increasing awareness has developed of the roles played by canal topology and helicity in the function of certain biological systems. 

In the next section we consider some general questions about the occurrence, properties and experimental investigation of helical canal inclusion compounds, in relation to inclusion compounds with different topologies. In subsequent sections we describe the properties of specific systems. 

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