Systematic Analysis Of Coiled-coil Domains In Budding Yeast

Eukaryotic proteins are usually constructed in a cassette-like fashion using domains and motifs as building blocks that mediate specific molecular interactions. Among such domains, the coiled coil has been frequently found in mediating protein-protein interactions.To analyze the interaction specificity between coiled coils, we developed a multi-step strategy that combines computation and experiment to identify specific coiled-coil interactions. In step 1, all coiled coils were predicted for the proteome of sacchromyses cerevisiae. The proteins that contain coiled coils are denoted as coiled-coil proteins. In step 2, a coiled-coil protein interaction network was obtained by only considering interactions between coiled-coil proteins in the known protein-protein interactions in yeast. In step 3, a computational program based on SVM was used to predict the potential coiled-coil interactions. In step 4, the potential coiled-coil pairs were subject to a yeast two-hybrid assay. In total, we analyzed the interactions for 4149 coiled-coil pairs, 478 of them are positives involving 202 coiled-coil.domains.Furthermore, we attempted to explore the functional role of coiled coils. When a coiled coil that is involved in methione metabolic pathways was knocked out, yeast exhibited methionine auxotroph, indicating the essential role of coiled coil in such biological pathway. Meanwhile, we develop new techniques to systematically detect coiled-coil interactions in vivo and in vitro, and promise to explore the architectural pattern of life in domain level.