A Game of Bait and Prey: The Effects of the Intrinsically Disordered Loops of Fpr4 on Mediating Protein Interactions

Abstract

The shape of a protein is a critical determinant of its function. Shape is constituted both by ordered regions like alpha helices and beta sheets, but also by intrinsically disordered regions (IDRs) whose significance we have examined in this study. Since the function of a protein is often mediated through interactions with other proteins, we have sought to determine the extent to which the IDRs of Fpr4 are needed for its binding to other proteins. Fusing TURBO-ID to the c-terminal end of Fpr4 has allowed us to separate the proteins that Fpr4 transiently, or in the long-term, interacts with, based on the ability of TURBO-ID to biotinylate proximal interactors which, by this basis of biotinylation, have been pulled down by a streptavidin resin and Western blotted. The changes in this protein profile in response to deletions of the disordered loops have included both gains and losses of interactors. Furthermore, we have demonstrated that the IDRs of Fpr4 are not essential for its interaction with its paralog, Fpr3. Fpr4 is a protein in yeast that negatively regulates protein-coding genes in the nucleus and ribosomal rRNAs genes in the nucleolus.