Protein hairpin loops

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.]...

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.)...

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). 

The P structure is one of the most important secondary structures in proteins. It occurs in about 80% of the soluble globular proteins whose structures have been determined. In many cases almost the entire protein is made up of P structure. Single strands of extended polypeptide chain are sometimes present within globular proteins but more often a chain folds back on itself to form a hairpin loop. A second fold may be added to form an antiparallel "P meander"102 and additional folds to form P sheets. Beta structures are found in silk fibers (Box 2-B) as well as in soluble proteins. 

In all tRNAs the bases can be paired to form "clover-leaf" structures with three hairpin loops and sometimes a fourth as is indicated in Fig. 5-30.329 331 This structure can be folded into the L-shape shown in Fig. 5-31. The structure of a phenylalanine-carrying tRNA of yeast, the first tRNA whose structure was determined to atomic resolution by X-ray diffraction, is shown.170/332 334 An aspartic acid-specific tRNA from yeast,335 and an E. coli chain-initiating tRNA, which places N-formyl-methionine into the N-terminal position of proteins,336,337 have similar structures. These molecules are irregular bodies as complex in conformation as globular proteins. Numerous NMR studies show that the basic... 

It had often been assumed that a hydrophobic signal sequence, perhaps folded into a hairpin loop, spontaneously inserts itself into an ER membrane to initiate translocation. However, study of the genetics of protein transport suggests otherwise. Over 50 different genetic loci affect the translocation of proteins in yeast.31/32/33d Products of these secretory genes,... 

Parts of the 2569-nucleotide sequence for the RNA of phage MS2498 are shown in Fig. 29-17. The 5 end (upper left center) still bears the triphosphate group of the initiating GTP. Following a number of hairpin loops there is a ribosome-protected region, which begins with the initiation codon GUG for the A protein... 

What is the nature of the insoluble forms of the prion protein They are hard to study because of the extreme insolubility, but the conversion of a helix to (3 sheet seems to be fundamental to the process and has been confirmed for the yeast prion by X-ray diffraction.11 It has been known since the 1950s that many soluble a-helix-rich proteins can be transformed easily into a fibrillar form in which the polypeptide chains are thought to form a P sheet. The chains are probably folded into hairpin loops that form an antiparallel P sheet (see Fig. 2-ll).ii-11 For example, by heating at pH 2 insulin can be converted to fibrils, whose polarized infrared spectrum (Fig. 23-3A) indicates a cross-P structure with strands lying perpendicular to the fibril axis >mm Many other proteins are also able to undergo similar transformation. Most biophysical evidence is consistent with the cross-P structure for the fibrils, which typically have diameters of 7-12 rnn."-11 These may be formed by association of thinner 2 to 5 nm fibrils.00 However, P-helical structures have been proposed for some amyloid fibrils 3 and polyproline II helices for others. 1 11... 

The cystatins, which are a superfamily of proteins that inhibit papain-like cysteine proteases, are a classic example of these inhibitors. The cystatins (Fig. 3) insert a wedge-hke face of the inhibitor that consists of the protein N-terminus and two hairpin loops into the V-shaped active site of a cysteine protease. The N-terminal residues bind in the S3-S1 pockets in a substrate-like manner, but the peptide then turns away from the catalytic residues and out of the active site. The two hairpin loops bind to the prime side of the active site, which provides most of the binding energy for the interaction. Thus, both the prime and the nonprime sides of the active site are occupied, but no interactions are actually made with the catalytic machinery of the enzyme (23). 

The carboxyl-terminal 469 amino acids of NompC resemble a class of ion channel proteins called TRP (transient receptor potential) channels. This region includes six putative transmembrane helices with a porelike region between the fifth and sixth helices. The amino-terminal 1150 amino acids consist almost exclusively of 29 ankyrin repeats (Figure 32.35). Ankyrin repeats are structural motifs formed by 33 amino acids folded into a hairpin loop followed by a helix-tum-helix. Importantly, in other proteins, regions with tandem arrays of these motifs mediate protein-protein interactions, suggesting that these arrays couple the motions of other proteins to the activity of the NompC channel. 

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