Open twisted

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 4.2 A p-a-p motif is a right-handed structure. Two such motifs can be joined into a four-stranded parallel p sheet in two different ways. They can be aligned with the a helices either on the same side of the p sheet (a) or on opposite sides (b). In case (a) the last p strand of motif I (red) is adjacent to the first p strand of motif 2 (blue), giving the strand order 1 2 3 4. The motifs are aligned in this way in barrel structures (see Figure 4.1a) and in the horseshoe fold (see Figure 4.11). In case (b) the first p strands of both motifs are adjacent, giving the strand order 4 3 12. Open twisted sheets (see Figure 4.1b) contain at least one motif alignment of this kind. In both cases the motifs ate joined by an ct helix (green).

Figure 4.5 The polypeptide chain of the enzyme pyruvate kinase folds into several domains, one of which is an a/p barrel (red). One of the loop regions in this barrel domain is extended and comprises about 100 amino acid residues that fold into a separate domain (blue) built up from antiparallel P strands. The C-terminal region of about 140 residues forms a third domain (green), which is an open twisted a/p structure.

In the next class of a/p structures there are a helices on both sides of the p sheet. This has at least three important consequences. First, a closed barrel cannot be formed unless the p strands completely enclose the a helices on one side of the p sheet. Such structures have never been found and are very unlikely to occur, since a large number of p strands would be required to enclose even a single a helix. Instead, the p strands are arranged into an open twisted p sheet such as that shown in Figure 4.1b. 

Figure 4.13 (a) The active site in open twisted a/p domains is in a crevice outside the carboxy ends of the P strands. This crevice is formed by two adjacent loop regions that connect the two strands with a helices on opposite sides of the P sheet. This is illustrated by the curled fingers of two hands (b), where the top halves of the fingers represent loop regions and the bottom halves represent the P strands. The rod represents a bound molecule in the binding... 

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 4.15 Schematic diagram of the enzyme tyrosyl-tRNA synthetase, which couples tyrosine to its cognate transfer RNA. The central region of the catalytic domain (red and green) is an open twisted a/p stmcture with five parallel p strands. The active site is formed by the loops from the carboxy ends of P strands 2 and S. These two adjacent strands are connected to a helices on opposite sides of the P sheet.

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.)...

Upha/beta (a/p) structures are the most frequent and most regular of the pro-kein structures. They fall into three classes the first class comprises a central core of usually eight parallel p strands arranged close together like the staves pf a barrel, surrounded by a helices the second class comprises an open twisted parallel or mixed p sheet with a helices on both sides of the p sheet and Ihe third class is formed by leucine-rich motifs in which a large number of parallel p strands form a curved p sheet with all the a helices on the outside bfthis sheet. 

Analogously to the ATD dimer, the 7TM level of the mGluR homodimer oscillates between inactive and active conformations (90). The 7TMs-7TMs equilibrium is regulated by the equilibrium between the inactive and active ATD homodimer conformations, which in turn is regulated by the equilibrium between the open and the closed ATD (Fig. 9B). Both the closed-open/twisted and closed-closed/twisted ATD homodimer conformations could be capable of stabilizing an active 7TM conforma-... 

Figure 4.9 (a) Triose phosphate isomerase (TIM), has a (3-a-(3 structure made up of eight P-a motifs terminating in a final a-helix, which form a barrel-like structure, (b) An open twisted P-sheet with helices on both sides, such as the coenzyme-binding domain of many dehydrogenases. (From Branden and Tooze, 1991. Reproduced by permission of Garland Publishing, Inc.)... 

The folding of a/jS-proteins falls into two major classes, illustrated in Figure 23 the closed ( a)g barrel (the subject of this article) and the open twisted sheet which has a helices on both sides of it. They both involve parallel p sheets that are connected in most cases by an a heUx (the )3a/J-motif described earlier). 

Figure 23 Some a/ -motifs (a) the barrel and (b) the open twisted sheet...

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