We report the first successful design of a self-associating antiparallel coiled coil, APH. The simultaneous application of Coulombic and hydrophobic components results in a decided preference for the antiparallel alignment as judged by HPLC, sedimentation equilibrium, and chemical denaturation data. The designed peptide is of comparable stability to naturally occurring leucine zipper peptides and can be expressed in bacteria. These properties of APH suggest potential in vivo protein fusion and biomaterials applications.

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Basic-region leucine zipper (bZip) proteins contain a bipartite DNA-binding motif consisting of a leucine zipper dimerization domain and a basic region that directly contacts DNA. In all naturally occurring bZip proteins, the basic region is positioned N-terminal to the leucine zipper. We have designed a series of model bZip peptides in which the basic region of the yeast transcriptional activator GCN4 is placed C-terminal to its leucine zipper. DNA-binding studies demonstrate that the optimal reverse GCN4 (rGCN4) peptide is able to bind specifically and with wild-type affinity to DNA despite this unnatural arrangement of the two subdomains. These results suggest that a thermodynamic basis for the observed N-terminal positioning of the basic region relative to the dimerization domain is unlikely.

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