Side Chain Packing Fluorinated Amino Acids

Our laboratory, that of David Tirrell and others, has independently shown that appropriate patterning of protein surfaces with fluorinated amino acids results in stable folds with enhanced thermal and chemical stability (Bilgiger et al. 2001; Tang et al. 2001). Coiled coils are helical bundles formed by the supercoiling of individual strands. Their primary sequences contain a heptad repeat (abcdefg) with hydrophobic side chains at the a and d positions that align on one face of the helix. Exclusion of nonpolar side chains away from water provides the primary driving force for assembly. In order to make coiled-coil assemblies with fluorinated interfaces, we replaced the core residues of the dimerization domain of the yeast transcriptional activator GCN4 with trifluorovaline (1) and trifluoroleucine (2) at the a and d positions, respectively. (For structures of these and other unnatural amino acids mentioned in this chapter, see Figure 9.2). The resulting peptide ensemble was thermally and chemically more stable than the native one. The increased stability could be directly attributed to the higher hydrophobicities of the trifluoromethyl over methyl groups shielded from solvent water in the hydrophobic core. By substituting amino acids containing CF3 groups, the hydrophobicity of the monomers is increased beyond what is available in the canon of the naturally occurring ones.

The phase separation proclivity of perfluorocarbons in both water and hydrocarbons suggests that fluorinated amino acids should be able to direct specific proteinprotein interactions. A parallel coiled coil (HH) with seven leucines and a single asparagine on each strand in the core and a fluorinated version (FF) where all seven leucines were replaced with hexafluoroleucine (3) served as the test system (Bilgiger and Kumar 2002). A disulfide exchange assay was used to evaluate the self-sorting cf3 ^ HQ F.. F.

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