Parallel strands

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.)...

The interiors of protein molecules contain mainly hydrophobic side chains. The main chain in the interior is arranged in secondary structures to neutralize its polar atoms through hydrogen bonds. There are two main types of secondary structure, a helices and p sheets. Beta sheets can have their strands parallel, antiparallel, or mixed. 

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 4.11 Schematic diagram of the structure of the ribonuclease inhibitor. The molecule, which is built up by repetitive P-loop-a motifs, resembles a horseshoe with a 17-stranded parallel p sheet on the inside and 16 a helices on the outside. The P sheet is light red, a helices are blue, and loops that are part of the p-loop-(x motifs are orange. (Adapted from B. Kobe et al.. Nature 366 7S1-756,...

In these p-helix structures the polypeptide chain is coiled into a wide helix, formed by p strands separated by loop regions. In the simplest form, the two-sheet p helix, each turn of the helix comprises two p strands and two loop regions (Figure 5.28). This structural unit is repeated three times in extracellular bacterial proteinases to form a right-handed coiled structure which comprises two adjacent three-stranded parallel p sheets with a hydrophobic core in between. 

O Shea, E.K., et al. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254 539-544, 1991. 

Parallel /3-sheets tend to be more regular than antiparallel /3-sheets. The range of (f) and i/t angles for the peptide bonds in parallel sheets is much smaller than that for antiparallel sheets. Parallel sheets are typically large structures those composed of less than five strands are rare. Antiparallel sheets, however, may consist of as few as two strands. Parallel sheets characteristically distribute... 

Another important parallel /3-array is the eight-stranded parallel j8-barrel, exemplified in the structures of triose phosphate isomerase and pyruvate kinase (Figure 6.30). Each /3-strand in the barrel is flanked by an antiparallel a-helix. The a-helices thus form a larger cylinder of parallel helices concentric with the /3-barrel. Both cylinders thus formed have a right-handed twist. Another parallel /3-structure consists of an internal twisted wall of parallel or mixed /3-sheet protected on both sides by helices or other substructures. This structure is called the doubly wound parallel j8-sbeet because the structure can be... 

FIGURE 6.41 The quaternary structure of liver alcohol dehydrogenase. Within each subunit is a six-stranded parallel sheet. Between the two subunits is a two-stranded antiparallel sheet. The point in the center is a C9 symmetry axis. (Jane Richardson)... 

Most dehydrogenases that use NAD or NADP bind the cofactor in a conserved protein domain called the Rossmann fold (named for Mchael Rossmann, who deduced the structure of lactate dehydrogenase and first described this structural motif). The Rossmann fold typically consists of a six-stranded parallel /3 sheet and four associated a helices (Fig. 13-16). 

RGURE 13-16 The nucleotide binding domain of the enzyme lactate dehydrogenase, (a) The Rossmann fold is a structural motif found in the NAD-binding site of many dehydrogenases It consists of a six-stranded parallel /3 sheet and four a helices inspection reveals the arrangement to be a pair of structurally similar motifs... 

Fig. 63. Dependence of (S2)1 on M for fibrin initiated by thrombin at 37 °C (- -) curve 1 gives the theoretical dependence for a single strand, curve 3 shows the behavior of fibres with many strands parallel, and curve 2 is the best fit224 ...

Thus, a peptide sequence that was originally designed to form a two-stranded parallel coiled coill50 was later identified from X-ray crystallographic data as a triple-helix coiled coil)51 A synthetic peptide with lie in all five d positions and Leu in all five a positions was a four-stranded coiled coil)12 while a similar peptide with only three lie residues in the middle d positions was two-stranded)32 In addition, a 35-residue peptide with Leu at all the a and d positions was two-stranded in the reduced form, but the disulfide-bridged coiled coil became four-stranded)32 Analogues of the Rop protein, where the hydrophobes in the interface were... 

Therefore, de novo designed two-stranded parallel and antiparallel coiled coils become ideal model systems to study the factors that contribute to our understanding of protein folding and assembly. 

Although the amino acid sequences have no identity (except at the active serine), the two enzymes show a similar architectural framework consisting of a central five-stranded parallel /3-sheet structure. The catalytic groups are positioned on this /3-sheet structure in a strikingly similar way, though there are also some significant differences. 

Fig. 7 Dark currents for aligned DNA-lipid complex films measured under three conditions DNA strands are perpendicular to the two electrodes in atmosphere (a) and in a vacuum at 0.1 mmHg (b), contrasting with DNA strands parallel to the two electrodes (c). Reproduced with permission from [28]...

Both the coiled coil domain and the TRAF-G domain mediate TRAF domain trimerization. The three-stranded parallel coiled coil structure is stabilized by hydrophobic residues at positions A and D of the... 

Flo. 4. Diagrammatic representation of the NAD -binding domain showing the six-stranded parallel p sheet flanked by helices (4S, 6S). 

NA (1) N-terminal membrane attachment domain of unknown structure (2) propeller of six blades, each a four-stranded parallel (3 sheet... 

The structure of human rhinovirus 16 (HRV16) was pursued at higher resolution (2.15 A) than most, and revealed interesting structures around the 5-fold axis (Hadfield et al., 1997). These were composed in part of residues that had been disordered in prior rhinoviral crystal structures, but had been seen in type 3 poliovirus (Filman et al, 1989). N termini of five symmetry-equivalent VPS come together to form a five-stranded parallel /3 barrel, plugging a gap between the five VPl jelly-roll domains. Each of 5 VP4 N termini contributes a / hairpin to a 10-stranded antiparallel /3 barrel closer to the virus center. In both rhino- and polioviruses VP4 is N-terminally myristoylated and these elements of structure are thought to be intimately involved with conformational transitions that occur on cell entry and uncoating. 

The first structure determined for a sialyltransferase (Cstll from Campylobacter jejuni of family GT42 see O Fig. 8c) revealed an unusual variant of the GT-A fold [350]. The protein displays a similar t) e of fold as the canonical GT-A fold, but with some differences in the connectivity of /3-strands (parallel /3-sheet of topology 8712456) and it has no DxD motif. Therefore the Cstll structure represents a new type of fold. Another prokaryotic sialyltransferase has, though, a GT-B fold (see O Table 2). 

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