C terminal a-helix

Figure 8.21 Richardson-type diagram of the structure of one suhunit of the lac repressor. The polypeptide chain is arranged in four domains, an amino terminal DNA-hinding domain (red) with a helix-tum-helix motif, a hinge helix (purple), a large core domain which has two subdomains (green and hlue) and a C-terminal a helix. (Adapted from M. Lewis et al.. Science 271 1247-1254, 1996.)...

The polypeptide chain of the lac repressor subunit is arranged in four domains (Figure 8.21) an N-terminal DNA-hinding domain with a helix-turn-helix motif, a hinge helix which binds to the minor groove of DNA, a large core domain which binds the corepressor and has a structure very similar to the periplasmic arablnose-binding protein described in Chapter 4, and finally a C-terminal a helix which is involved in tetramerization. This a helix is absent in the PurR subunit structure otherwise their structures are very similar. 

Figure 9.22 Most tumorigenic mutations of pS3 are found in the regions of the polypeptide chain that are involved in protein-DNA interactions. These regions are loops L2 (green) and L3 (red) and a region called LSH (blue) which comprises part of p strand 9 as well as the C-terminal a helix.

A160G mutant (open circles) against temperature. (A) Alal03 (C-D loop), (B) Ala39 (helix B), 168 (helix F), (C) Ala228, 233 (C-terminal a-helix), D-F (transmembrane a-helices). From Ref. 192 with permission. 

From the spin label studies we were able to conclude that NPY associates specifically with its hydrophobic side of the C-terminal a-helix parallel to the membrane surface. 

The 36-residue pancreatic polypeptide is a hormone of uncertain functions. The crystalline polypeptide has at the N terminus an 8-residue collagenlike helix that lies parallel to a C-terminal a helix (Fig. 30-5). The overall shape resembles that of both insulin and glucagon.107 108 This PP-fold includes also neuropeptide Y, which is considered in the next section,109 and neuropeptide YY.110... 

The fact that both N- and C-terminal a-helix induction was achieved using the same concept raised the question of whether it would be possible to combine the N- and C-cap concepts, by generating a position-independent template that stabilizes (J-helical conformations not only from N-terminal or C-terminal ends but also from internal positions. 

Figure 15.7 Binding cavity of BmPBP. In the crystal structure of the BmPBP-bombykol complex (B-form) the pheromone. In the unligated acidic form of the protein (A-form), C-terminal a-helix occupies the binding pocket. This figure was prepared by Fred Damberger by using the program molmol (Koradi et al., 1996).

Figure 15.8 Schematic representation of the proposed mechanisms for mode of action of OBPs in the perireceptor events. Pheromone (or other semiochemicals) enters the sensillar lymph through cuticular openings (pore tubules), is solubilized by an odorant-binding protein, transported to the olfactory receptors, and protected from degrading enzymes. Interaction with negatively charged sites at the surface of the dendrites triggers a conformational change that leads to the formation of a C-terminal a-helix. The insertion of this helix into the binding cavity ejects the pheromone to the olfactory receptors.

A leucine zipper has a leucine every seventh amino acid and forms an a-helix with the leucines presented on the same side of the helix every second turn, giving a hydrophobic surface. Two transcription factor monomers can interact via the hydrophobic faces of their leucine zipper motifs to form a dimer. The helix-loop-helix (HLH) motif contains two a-helices separated by a nonhelical loop. The C-terminal a-helix has a hydrophobic face two transcription factor monomers, each with an HLH motif, can dimerize by interaction between the hydrophobic faces of the two C-terminal a-helices. 

Yang, W., Shimaoka, M., Chen, J. F., and Springer, T. A. (2004a). Activation of integrin / subunit Hike domains by one-turn C-terminal a-helix deletions. Proc. Natl. Acad. 

The secondary site of eco binds to the protease over 20 A away from the active site and forms up to 30 van der Waals interactions and up to five additional hydrogen bonds. An additional important source of binding energy and association, the secondary site is composed of the 60 s and lOO s loops of eco and a hydrophobic patch near the protease residues 91 to 94 and the C-terminal a helix amino acids 236 to 242. This patch and helix separated from the 80 s loop accounts for the fold specificity of eco. Each inhibitor molecule forms an interaction with both proteases of the tetramer in a clamp configuration that can be adapted to fit most serine proteases. 

The structure of collagenase and eco highlights an important aspect of the eco-protease interaction-flexibility. The eco dimer is extremely accommodating of the differences between serine protease molecules because it binds at two relatively invariant regions, the substrate binding deft and the C-terminal a helix-90 s loop. 

Each member of this family contains some 70 residues, about 30 of which form a three-stranded, anti-parallel p-sheet scaffold on to which is folded a C-terminal a-helix and an aperiodic N-terminal segment that is disulfide-bonded to the p-sheet domain [27 -32]. All known natural a-chemokines self-associate as dimers or tetramers. Dimers form by extension of monomer p-sheet domains to form a six-stranded sheet, called the AB-dimer, exemplified by IL-8. In native PF4, two AB- dimers are sandwiched together to form a tetramer. 

Fig. (10). Representation of the functional determinants of fowIicidin-1. The C-terminal a-helix (Glyl6 - lie 23) is required for the three activities of the peptide antibacterial, cytolitic, and LPS-binding. The N-terminal unstructured region (VaI5-Pro7) comprises the second determinant that is importantly implicated in citotoxicity and LPS-binding. The a-helix (Leu8-AIal5) also most likely enables the interaction of the C-terminal helix with lipid membranes. Reprinted with permission from [148]. Copyright (2006) Blackwell Publishing.

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