Finally, and with wider implications, we have compiled a method for predicting interaction of parallel, dimeric coiled coils, using our T m data as a training set, and applying it to 59 bZIP proteins previously reported. Our algorithm, unlike others to date, accounts for helix propensity, which is found to be integral in coiled coil stability. Indeed, in applying the algorithm to these 59 2 bZIP interactions, we were able to correctly identify 92% of all strong interactions and 92% of all noninteracting pairs.bioinformatics ͉ protein design ͉ protein stability ͉ protein-protein interaction ͉ dominant negative T he dimeric transcription factor activator protein-1 (AP-1) comprises Jun, Fos, activating transcription factor, and musculoaponeurotic fibrosarcoma families. Chief mammalian cell AP-1 constituents, Jun and Fos, contain a transactivation domain, a basic region for recognizing a DNA consensus sequence and a leucine zipper [coiled coil (CC)] region (see Fig. 1). The latter, in dimerizing, permits the two basic domains to bind to their consensus sequence. Such transcription factors, known as basic-zipper or bZIP proteins, are found at the closing stages of mitogen-activated protein kinase signaling cascades (e.g., the RAS pathway). AP-1 is implicated in various cancers where it can become up-regulated or overexpressed (1), and has been shown to be important in cell growth initiation, with c-Jun and c-Fos identified as cellular counterparts to viral oncoproteins v-Jun and v-Fos, thus establishing their role in tumorigenesis (2). Indeed, they are central in numerous oncogenic pathways and could therefore be prime candidates in anticancer drug design. However, AP-1 can also have antiproliferative properties, depending on subunit composition, transcription level, posttranslational modification (e.g., phosphorylation), and interaction with other proteins (e.g., Jun N-terminal kinase); this is manifested by the preponderance of different AP-1 family members in different types of tissue cancer. . Alternative residue options were included at e and g positions, and were aimed at varying electrostatic attraction levels at the dimeric interface. Other alternative residues, largely taken from homologues (see key), were introduced to the library pool at the solvent exposed b, c, and f positions. Wild-type residues removed from libraries are struck through in green, newly introduced amino acids are marked red, and wildtype positions left in the library are marked blue. Library winner selections are circled green. Position c1 E (marked red) is for additional N-cap stability, whereas b3 Y assists with concentration determination. Capping motifs have also been added.
