Hairpin loop

A hairpin consists of a helix bridged by a loop of unpaired nucleotides (Fig. 1.1). The hairpin loop is a frequent target for protein interactions and also functions as nucleation site for RNA folding. In particular the tetraloop hairpins, a group of loop sequences, UNCG, GNRA and CUUG, exhibit unusual thermodynamic stability. 

---

Use of D-amino acids in the synthesis of a hairpin loop portion from the CD4 receptor provides a stable CD4 receptor mimic, which blocks experimental allergic encephalomyelitis (144). This synthetic constmct is not simply the mirror image or enantiomer of the CD4 hairpin loop, but rather an aH-D-constmct in the reverse sequence, thus providing stereochemicaHy similar side-chain projections of the now inverted backbone (Fig. 11). This peptide mimetic, unlike its aH-L amino acid counterpart, is resistant to en2yme degradation. As one would expect, the aH-D amino acid CD4 hairpin loop, synthesi2ed in the natural direction, the enantiomer of the natural constmct, is inactive. 

Fig. 11. Use of D-amino acids in the synthesis of a hairpin loop portion from the CD4 receptor (a) all L-Ser—Lys—Ala tripeptide constmcted in the natural...

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 2.8 Adjacent antiparallel P strands are joined by hairpin loops. Such loops are frequently short and do not have regular secondary structure. Nevertheless, many loop regions in different proteins have similar structures, (a) Histogram showing the frequency of hairpin loops of different lengths in 62 different proteins, (b) The two most frequently occurring two-residue hairpin loops Type I turn to the left and Type II turn to the right. Bonds within the hairpin loop are green, [(a) Adapted from B.L. Sibanda and J.M. Thornton, Nature 316 170-174, 1985.]...

Figure S.2 Schematic and topological diagrams of an up-and-down fi barrel. The eight p strands are all antiparallel to each other and are connected by hairpin loops. Beta strands that are adjacent in the amino acid sequence are also adjacent in the three-dimensional structure of up-and-down barrels.

Figure S.6 Schematic and topological diagrams of the folding motif in neuraminidase from influenza virus The motif is built up from four antiparallel P strands joined by hairpin loops, an up-and-down open P sheet.

The major stmctural feature of the HAz chain (blue in Figure 5.20) is a hairpin loop of two a helices packed together. The second a helix is 50 amino acids long and reaches back 76 A toward the membrane. At the bottom of the stem there is a i sheet of five antiparallel strands. The central i strand is from HAi, and this is flanked on both sides by hairpin loops from HAz. About 20 residues at the amino terminal end of HAz are associated with the activity by which the vims penetrates the host cell membrane to initiate infection. This region, which is quite hydrophobic, is called the fusion peptide. 

A closer examination of these essential residues, including the catalytic triad, reveals that they are all part of the same two loop regions in the two domains (Figure 11.10). The domains are oriented so that the ends of the two barrels that contain the Greek key crossover connection (described in Chapter 5) between p strands 3 and 4 face each other along the active site. The essential residues in the active site are in these two crossover connections and in the adjacent hairpin loops between p strands 5 and 6. Most of these essential residues are conserved between different members of the chymotrypsin superfamily. They are, of course, surrounded by other parts of the polypeptide chains, which provide minor modifications of the active site, specific for each particular serine proteinase. 

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. 

Stem A stretch of double-stranded RNA Loop A loop of RNA Hairpin loop A very short loop... 

Integral membrane proteins with one transmembrane domain may have soluble domains at either or both surfaces. An example of a monotopic protein, cytochrome b5 has a single hydrophobic segment that forms a hairpin loop, acting as an anchor to the cytoplasmic surface but probably not totally penetrating the bilayer. 

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.)...

Rho-independent termination occurs when the newly formed RNA folds back on itself to form a GC-rich hairpin loop closely followed by 6-8 U residues. These two structural features of the newly synthesized RNA promote dissociation of the RNA from the DNA template. This is the type of terminator shown in Figure 1-3-4. 

As anticipated from their sequence similarity, the (non-catalytic) a- and the (catalytic) P-type subunits have the same fold (Lowe et al. 1995 Groll et al. 1997) a four-layer a+p structure with two antiparallel five-stranded P sheets, flanked on one side by two, on the other side by three a helices. In the P-type subunits, the P-sheet sandwich is closed at one end by four hairpin loops and open at the opposite end to form the active-site cleft the cleft is oriented towards the inner surface of the central cavity. In the a-type subunits an additional helix formed by an N-terminal extension crosses the top of the P-sheet sandwich and fills this cleft. Initially, the proteasome fold was believed to be unique however it turned out to be prototypical of a new superfamily of proteins referred to as Ntn (N-terminal nucleophile) hydrolases (Brannigan et al. 1995). 

---