Coiled Coils and Helix Bundles
The hybridization of two molecules to form a complex with a defined structure can serve to build a larger suprastructure with additional properties and functions the individual molecules might not possess even if they already do have a defined structure in the absence of their hybridization partner. A classical example for hybridization of structured molecules from Nature is the leucine zipper (Fig. 4.3). Two a-helical peptides of ca. 30 amino acid length with a leucine in every seventh position of the strand dimerize in a parallel orientation . This way the hydro-phobic leucine residues can interact with each other, thereby glueing the two helices together via hydrophobic contacts. Even though each helix on its own is structured only the dimerization forms a Y-shaped tweezer which allows the specific interaction with a third molecule in this case DNA. Leucine zippers are a common motif found in DNA transcription factors.
The dimerization, besides forming the binding site needed for the interaction with the DNA, also offers additional means of controlling the interaction via the more pronounced concentration dependence of the dimerization . The leu-cine zipper is an example of a more general motif found in peptide self-assembly
called coiled-coil motif, in which normally two or three a-helices formed from the repeat of a heptad with hydrophobic residues in position 1 and 4 interdigitate to form a stable aggregate .
Based on such natural coiled-coil motifs several modifications within artificial peptides have been introduced to modify the structure or stability of the resulting aggregates. For example, Tirrell  and coworkers incorporated trifluoroleucine into the leucine zipper protein A1 using in vivo expression (Fig. 4.4).
The secondary structures of both the fluorinated and the wild type protein were identical as determined by CD-spectroscopy (ca. 90% helical) and both proteins formed stable dimers with Kdiss < 10 mM. However, thermal denaturation studies showed that the fluorination significantly increased the stability of the dimer (ATm = +13 °C, AAG = 2.4 kcal mol-1) most likely due to the specific interactions of the fluorinated side chains at the dimer interface within the modified protein. The same could be shown with a urea titration. The concentration of urea needed for denaturation of the protein increased within increasing content of incorporated trifluoroleucine into the protein . The increased stability due to fluorinated alkyl groups relative to nonfluorinated ones can also nicely be demonstrated by incorporating semi- or perfluorinated alkyl chains into self-assembling dendrimers [21, 22]. The higher thermal stability of the corresponding supramolecular system is based on the lower flexibility of a fluorinated chain and the larger van der Waals radius offluorine compared to hydrogen. The resulting overall increased van der Waals volume of fluorinated chains and their lower polarizability give rise to an increase in both hydrophobic and lypophobic character of a fluorinated molecule relative to a hydrocarbon .
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