Helical dimer

FIGURE 10.41 (a) Gramicidin forms a double helix in organic solvents a helical dimer is the preferred strnctnre in lipid bilayers. The strnctnre is a head-to-head, left-handed helix, with the carboxy-termini of the two monomers at the ends of the strnctnre. (b) The hydrogen-bonding pattern resembles that of a parallel /3-sheet. 

Cabon 13 NMR has been used to confirm the presence of a double helical dimer model87. 

With somewhat the same idea, Minoura [44] used the formation of a crown ether sandwich complex with K+ to force the association of helical dimers of C-terminal modified poly-benzylglutamate (52). Although no structural data were provided, he observed by viscosimetry the reversible formation of a K+ sandwich complex with two 15-crown-5 modified peptides. 

The native state conformation of the freely diffusing polypeptide is seen to be a helical dimer (Cf. Fig. 3). Assuming that the donor-acceptor distance R is given by the end-to-end distance, the corresponding distribution of R clearly shows that surface-immobilization does not affect the conformations in the folded state, regardless of whether the surface is repulsive or attractive (Cf. Fig. 4). This can be explained by the fact that the two helices are held together by the attractive nonbonding B-B interactions so that the B residues form a hydrophobic core, and therefore cannot effectively interact with the surface. 

The bicyclic guanidinium tetramer 43 was first reported as a possible binder for helical oligonucleotides. Initial studies with 43 and sulfate anions showed that the tetramer formed double-helical dimers around sulfate counterions [69]. Despite the initial proposal of using this receptor for membrane transport of oligonucleotides, all subsequent work on 43 has been conducted on helical peptides. For example, the binding of 43 with several synthetic peptides caused an increase in the helicity and helical stability of the peptides in 10% water/methanol [70]. The peptide containing four Asp derivatives showed the... 

Fig. 8. Amino acid sequence of the BChl c-binding (antenna) polypeptide of the chlorosomes from Chloroflexus aurantiacus (A) and the proposed a-helix model of this antenna polypeptide (B) with possible BChl c binding sites (Gin 12,15,22,26,33, Asn 30,41) via the central Mg atom. (C) Chlorosome subunit ( globular subunit ) (light-harvesting BChl c-protein complex of C. aurantiacus) composed of 12 polypeptide chains (a-helices) of the BChl c-binding polypeptide. Pairs of a-helices (dimeric basic units) are tilted to expose the areas for BChl c binding (hatched areas). (D) Chlorosome model (cross-section, C. aurantiacus) containing the chlorosome subunits of the rod-shaped elements in the chlorosome core region (taken from Refs. 69 and 72).

The first double-helical metal complex described was the tetrahedral bis(zinc formylbiliverdinate) (Figure 5.34). The helical dimer forms spontaneously, if the planar monomeric zinc complex, which carries an axial water ligand, is dehydrated by HCl" . 

Alignment of procollagen VII into cysteine cross-linked hexamers (triple helical dimers)... 

Several studies suggest that the conformation (double-stranded helix or helical monomer) of gramicidin inserted into the membrane is that found in solution (36-39). Upon heating, the membrane-bound, antiparallel, double-stranded helix converts to a helical dimer (37). Subsequent studies have suggested that the initially inserted double-stranded helical forms are unlikely to have any conductance capabilities (40). 

Figure 2. Schematic models of gramicidin A dimers (A) head-to-head helical dimer (B) tail-to-tail helical dimer (C) antiparallel double-stranded helix (D) parallel double-stranded helix. (Reproduced with permission from reference 301. Copyright 1986 Biophysical Society.)...

Leucine zippers also function as dimers to regulate gene transcription (see Fig. 16.16B). The leucine zipper motif is an a-helix of 30 to 40 amino acid residues that contains a leucine every seven amino acids, positioned so that they align on the same side of the helix. Two helices dimerize so that the leucines of one helix align with the... 

Figure 6.2.16 Schematic x-ray structures of (a) zinc octaethylformylbiliverdinate monohydrate and (b) its dehydrated, bis-helical dimer. (From Struckmeier et al., 1976.)...

Figure 6.5.1 Irradiation of benzene solutions of magnesium octaethylporphyrinate under air leads to the short-lived dioxetane and then to the formylbiliverdinate in quantitative yield as shown by the spectroscopic changes within 30 minutes. The zinc ion in the center carries an axial pyridine or water ligand. Upon acidification with HCl, this ligand is removed and a bis-helical dimer is formed in quantitative yield. Back-titration with sodium hydroxide reforms the monomer. (From Wasser and Fuhrhop, 1973 Struckmeier et al, 1976.) Chlorophyll oxidation in nature also leads to formylbiliverelin derivatives (Krautler and Matile, 1999).

This figure gives evidence of ionic selectivity, which appears in the coil conformation first and is associated with ion pair formation, as demonstrated using ultrasound absorption [17], The ion pair formation with reduces the net charge of the polymer and favours the helical dimer formation. 

The gramicidin channel, formed by dimerization of two molecules in a loose helical conformation (Fig. 3), has been studied extensively as a model system. The helical dimer spans the membrane to produce a channel through the hollow center of the helix with anionic sites or regions to facilitate cation transport. The channel transmits only univalent cations. Divalent calcium ion blocks ion flow through the channel. The channel exhibits the anomalous mole fraction effect. Both univalent thallous ion and sodium ion are very permeable when gramicidin dimers... 

---