Using a coiled coil heterodimeric model system and substitutions focused to the hydrophobic core, we have shown that the impact of size and polarity of the fluorinated building blocks highly depends upon the immediate environment of the substitution. Coiled coils are α-helical assemblies that possess a (pseudo-) repetitive primary sequence (abcdefg)n, in which hydrophobic side chains generally occupy the a- and d-positions (Figure 3). At central a positions, where the Cα-Cβ bond vectors point out of the hydrophobic core and into solution, stability is mainly determined by side chain volume. At central d positions, however, the destabilizing impact of fluorine-induced polarity prevails, since here the Cα-Cβ bond vectors point directly into the hydrophobic core (Salwiczek, Chem. Eur. J., 2009).
To efficiently screen for preferred interaction partners of the four aminobutyric acid analogues, phage display was carried out (Vagt, Org. Biomol. Chem., 2010). The predetermined secondary and tertiary structure of coiled coils are the features of our system that allow this technology to be exploited. Thus, fluorinated amino acids are incorporated into the hydrophobic positions of one strand of the heterodimer, and the residues of the other strand expected to directly interact with the nonnatural analogues are randomized to create a library that is displayed on bacteriophage. Despite the polarity that is induced by partial fluorination, the interaction profiles of all four fluoroalkylated amino acids studied so far are similar to that of aminobutyric acid. Moreover, independent of the respective microenvironment, incorporating fluorinated aminobutyric acids into a central a- or d-position of a parallel heterodimeric coiled coil leads to pairing characteristics that are similar to their canonical analogues (Nyakatura, RSC Advances, 2013).