Parallel hairpin

Furthermore, D- and L-prolyl-(l,l-dimefhyl)-l,2-diaminoethyl (Pro-DADME) segments have been used successfully to connect two y9-peptide strands via their C-termini and to promote the formation of a parallel hairpin (e.g. 123) in both solution (CD3OH) and solid state (Fig. 2.32) [196]. 

Fig. 2. 32 Parallel hairpin formation in a j3-peptide by incorporation of a D-Pro-DADME turn segment [195]. Summary of the long-range NOE observed by NMR in CD3OH which is consistent with a hairpin conformation together with the structure of 123 in the...

Hairpins, because they consist of a normal duplex topped by a small single-stranded loop, are not readily distinguished from double-stranded DNA by external probes. In one study, unusual hairpin structures were formed from single-stranded DNAs with the normal antiparallel double-stranded stem and with a parallel-stranded stem [319] (Fig. 4.31). The dye Hoechst 33258 bound to the normal hairpins (in the stems) and fluoresced as usual, but showed very little emission with the parallel-stranded hairpins [319]. Interestingly, ethidium bromide fluoresced when bound to both kinds of hairpins and emitted twice as brightly when bound to the parallel hairpins [319]. 

The hairpin motif is a simple and frequently used way to connect two antiparallel p strands, since the connected ends of the p strands are close together at the same edge of the p sheet. How are parallel p strands connected If two adjacent strands are consecutive in the amino acid sequence, the two ends that must be joined are at opposite edges of the p sheet. The polypeptide chain must cross the p sheet from one edge to the other and connect the next p strand close to the point where the first p strand started. Such CTossover connections are frequently made by a helices. The polypeptide chain must turn twice using loop regions, and the motif that is formed is thus a p strand followed by a loop, an a helix, another loop, and, finally, the second p strand. 

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.

Connections between /3-strands are of two types—hairpins and cross-overs. Hairpins, as shown in Figure 6.27, connect adjacent antiparallel /3-strands. Cross-overs are necessary to connect adjacent (or nearly adjacent) parallel /3-strands. Nearly all cross-over structures are right-handed. Only in subtilisin and phosphoglucoisomerase have isolated left-handed cross-overs been identi-... 

Figure 10-4A(2). Multitube hairpin fintube heat exchangers. The individual shell modules can be arranged into several configurations to suit the process parallel and/or series flow arrangements. The shell size range is 3-16 in. (Used by permission Brown Fintube Co., A Koch Engineering Co., Bui. B-30-1.)...

To prevent insolubility resulting from uncontrolled aggregation of extended strands, two adjacent parallel or antiparallel yS-peptide strands can be connected with an appropriate turn segment to form a hairpin. The / -hairpin motif is a functionally important secondary structural element in proteins which has also been used extensively to form stable and soluble a-peptide y9-sheet arrangements in model systems (for reviews, see [1, 4, 5] and references therein). The need for stable turns that can bring the peptide strands into a defined orientation is thus a prerequisite for hairpin formation. For example, type F or II" turns formed by D-Pro-Gly and Asn-Gly dipeptide sequences have been found to promote tight a-pep-tide hairpin folding in aqueous solution. Similarly, various connectors have been... 

The vasa recta are modified peritubular capillaries. As with the peritubular capillaries, the vasa recta arise from efferent arterioles. However, these vessels are associated only with the juxtamedullary nephrons and are found only in the medullary region of the kidney. The vasa recta pass straight through to the inner region of the medulla, form a hairpin loop, and return straight toward the cortex. This structure allows these vessels to lie parallel to the Loop of Henle and collecting ducts. 

Proteins containing a large amount of antiparallel /3-sheet usually show negative ROA bands in the range 1340—1380 cm-1, especially if the /3-sheet is extended as in a sandwich or barrel, which appear to originate in tight turns of the type found in /3-hairpins. One example is the band at 1345 cm-1 in jack bean concanavalin A (Fig. 4). These bands do not appear in the ROA spectra of a/// proteins, since these contain only parallel /6-sheet with the ends of the parallel /6-strands connected by a-helical sequences rather than tight turns (Barron etal., 2000). 

Strand-turn-strand motifs in /1-solenoids differ fundamentally from those found in globular proteins. In globular structures, two adjacent strands with an intervening /l-turn form an antiparallel structure called a /1-hairpin (Fig. 10A). In /1-solenoids, the polypeptide chain also folds back on itself, but the flanking /1-strands make contact via their side chains rather than interacting via H-bonds of the backbone (Fig. 10A). As a result, consecutive strands find themselves in two different, parallel, /1-sheets. The latter strand-turn-strand structure is called a /1-arch, and its turn, a /1-arc (Hennetin et at., 2006 Yoder and Jurnak, 1995). In /1-solenoids, /1-arches stack in-register to form /1-arcades which have two parallel /1-sheets assembled from corresponding strands in successive layers. 

Fig. 17. Models of A/ (l-40) fibrils, viewed down the fibril axis. (A, B) Cartoon representations of the hairpin model proposed by Petkova et al. (2002). (A) The proposed /1-strands span residues 9-24 and 30-40, with a main-chain bend spanning residues 25-29. Aspartate 23 and lysine 28 are proposed to form a salt bridge (dotted line) based on distance constraints provided by ssNMR. The hairpins stack in-register to form two parallel //-sheets. (B) Two hairpin stacks pack together to form the smallest observed fibrils, or protofilaments, burying the hydrophobic residues of the C-terminal strand. Two or more protofilaments may pack together to form thicker fibrils. (C) Cartoon representation of the parallel /i-helix-like model proposed byj. T. Guo and Y. Xu (unpublished model shown in Fig. 1 of Shivaprasad and Wetzel, 2004). The gray oval highlights residues 17 and 34, proposed to sit in close proximity.

Figure 4.8 Super-secondary structures found in proteins (a) P-a-P motifs (b) anti-parallel P-sheets connected by hairpin loops (c) a-a motifs. (From Voet and Voet, 2004. Reproduced with permission from John Wiley Sons., Inc.)...

Fibroin, the fibrous protein found in silk, has a secondary structure called a beta- (/8-) pleated sheet, in which a polypeptide chain doubles back on itself after a hairpin bend. The two sections of the chain on either side of the bend line up in a parallel arrangement held together by hydrogen bonds (Figure 24.8). Although not as common as the a-helix, small pleated-sheet regions are often found in proteins. 

The orthogonal-plane PIV technique is recently proposed for investigating the 3D characteristics of the coherent structures in a turbulent boundary layer flow (Hambleton et al., 2006 Kim et al., 2006). The hardware components and principle of this technique are the same as polarization-based dual-plane PIV. The only difference is to set up both laser sheets mutually perpendicular to each other instead of parallel to each other in the dual-plane PIV system. This allows for measuring velocity distributions in both streamwise-spanwise and streamwise-wall-normal planes simultaneously, so that the salient features of the coherent structures in a turbulent boundary layer flow as the legs and the head of the hairpin vortices can be detected (Hambleton et al., 2006 Kim et al., 2006). 

A high-resolution structure has been determined for the BI IgG-binding domain of protein G. The structure comprises of four stranded /3-sheet made up of two antiparallel j8-hairpins connected by an a-helix. The two central strands of the sheet are parallel and comprise the N- and C-terminal residues. Comparison of the protein A and protein G IgG-binding domain architectures reveals no immediately obvious region that could take the place of the two interacting helices of protein A and protein G complex. 

---