P-Hairpin formation

Haque TS, Little JC, Gelhnan SH (1994) Mirror image reverse turns promote p-hairpin formation. J Am Chem Soc 116 4105-4106... 

The intended role of the glycylalanine repeats in this design is the formation of p-sheet crystalline stems,7.8 while residues X and Y are chosen to form reverse tums.9,10 In each case, the selection of local sequence elements was based on information about the conformational properties of known polypeptides poly(glycylalanine) has been reported to form p-sheet crystals, , and Sibanda and Thornton have identified five X,Y pairs that appear to favor p-hairpin formation in globular proteins.9,10 As of this writing, we have expressed six different sequence variants of 1, and several chain-length variants as well. Detailed structural analysis by x-ray scattering and spectroscopic methods is underway and will be repotted elsewhere. 

V. Munoz, P. A. Thompson, J. Hofrichter, and W. A. Eaton, Folding dynamics and mechanism P-hairpin formation. Nature 390, 196-199 (1997). 

There is a natural hierarchy in proteins (see Figure 15.1) which allows the complex three-dimensional structure to be simplified and categorized as combinations of smaller motifs. At the atom level there are patterns of side-chain interactions at the backbone level we see formation of secondary structure (a helix, P sheet and yS turn) and loop families these combine to give supersecondary structures (e.g. P hairpins) and motifs (e.g. Greek key) and ultimately the whole tertiary and quaternary structure. In this chapter we present an overview of current patterns which are observed... 

Figure 35 Multiblock copolymers consisting of a PEG soft block and a tetrapeptide Gly-Ala-Gly-Ala, crystalline hard block in two variants (a) templated system in which an aromatic hairpin turn is used to force parallel p-sheet formation and (b) nontemplated system in which peptide segments are free to form parallel and/or antiparallel p-sheets. Reprinted with permission from Rathore, 0. Sogah, D. Y. Macromolecules 34,1477-1486, Copyright 2001 American Chemical Society. ...

Gloaguen E, Pollet R, Piuzzi F, Tardivel B, Mons M (2009) Gas phase folding of an (Ala)4 neutral peptide chain spectroscopic evidence for the formation of a p-hairpin H-bonding pattern. Phys Chem Chem Phys 11 11385... 

The situation is very different for p-sheet structures. Until recently, experimental studies of these structures have been mostly unsuccessful, largely due to the fact that short peptides which fold into a p-sheet conformation tend to aggregate in solution [125]. These difficulties have Anally been overcome with the recent discoveries of designed sequences, such as Beta-nova [132] and others [133,134], as well as the second p-hairpin fragment of Protein G (residues 41-56) [135], thus opening the door to a proper study of p-haiipin and p-sheet formation [136-144]. Our ongoing efforts to analyze the Protein G fragment (41-56) will be discussed in Section IV.E. 

S. Honda, N. Kobayashi, and E. Munekata, Theormodynamics of a P-hairpin structure Evidence for cooperative formation of folding nucleus. J. Mol. Biol. 295(2), 269-278 (2000). 

Figure 37-6. The predominant bacterial transcription termination signal contains an inverted, hyphenated repeat (the two boxed areas) followed by a stretch of AT base pairs (top figure). The inverted repeat, when transcribed into RNA, can generate the secondary structure in the RNA transcript shown at the bottom of the figure. Formation of this RNA hairpin causes RNA polymerase to pause and subsequently the p termination factor interacts with the paused polymerase and somehow induces chain termination.

Most p-independent terminators have two distinguishing features. The first is a region that produces an RNA transcript with self-complementary sequences, permitting the formation of a hairpin structure (see Fig. 8-2la) centered 15 to 20 nucleotides before the projected end of the RNA strand. The second feature is a highly conserved string of three A residues in the template strand that are transcribed into U residues near the 3 end of the hairpin. When a polymerase arrives at a termination site with this structure, it pauses (Fig. 26-7). Formation of the hairpin structure in the RNA disrupts several A=U base pairs in the RNA-DNA hybrid segment and may disrupt important interactions... 

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)...

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