Hairpin loop interaction

The contact surface between the a and /3 subunits is very broad ( 1100 A2) and is mostly hydrophobic in character.7 The a subunit loops following strands 2,3,4, and 5 (Fig. 7.2) make important contacts with the /3 subunit. The 50-residue subdomain of the /3 subunit (residues 260-310) comprised of several long /3 hairpin loops makes several contacts with the a subunit (Fig. 7.5).7 Contacts in this region probably prevent tryptic cleavage of the /3 subunit in the 02/82 complex.34-35 The fact that the sites of tryptic cleavage of the /3 subunit (Lys-272, R-275, and K-283) are close to the a/(3 contact surface may explain why proteolytically cleaved /3 subunit does not associate with the a subunit.59-106 In contrast, cleavage of the /3 subunit by proteinase K at Glu-296, a residue at a position in the subdomain (residues 260-310) that does not make direct contact with the a subunit, yields an enzymatically active nicked f3 subunit that interacts weakly with a subunits.61 ... 

The major subunit of the FH complex is a small (Mr = 5,400) polypeptide referred to as proteolipid because of the high proportion of phospholipid bound to it. This proteolipid, now sequenced from a number of sources, forms a hairpin loop that traverses the inner mitochondrial membrane and has unique hydrophobic amino acid sequences flanking a central, short, highly charged segment that interacts with the OSCP or with F, component 5. 

B18. Bjork, I., Brieditis, I., Raub-Segall, E., Pol, E., Hakansson, K., and Abrahamson, M., The importance of the second hairpin loop of cystatin C for proteinase binding. Characterization of the interaction of Trp-106 variants of the inhibitor with cysteine proteinases. Biochemistry 35(33),... 

Fig. 2 Secondary, tertiary, and quantenary structures of streptavidin. a Amino acid residues interacting with biotin, b Anti-parallel p sheets with dotted lines showing hydrogen bonds, c Folded apostreptavidin subunit with an extended hairpin loop near the carboxyl terminus, d Formation of streptavidin dimer through the interaction between the extended hairpin loops of the monomeric subunits, e Formation of streptavidin tetramer through the weak interaction of two stable dimer subunits (biotin is shown in pink) N N-terminus, C C-terminus. (a taken from [14]. b taken from [15]. e taken from http //www.scrippslabs.com/graphics/pdfs/Strept.pdf)...

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. 

Figure 32.35 Ankyrin repeat structure. One ankyrin domain is shown in red in this series of four ankyrin repeats. Notice the hairpin loop followed by a helix-turn-helix motif in the red-colored ankyrin unit. Ankyrin domains interact with other proteins, primarily through their loops. [Drawn from lAWC,pdb.]...

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. 

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