Scanning mutagenesis of the Arc repressor as a functional probe of operator recognition

Protein-DNA and protein-protein interactions are central to most biological regulation, and yet our understanding of these macromolecular recognition events is still incomplete. Both types of interactions are critical for the function of the Arc repressor. The functional importance of residues in or near its operator DNA-binding surface and dimer-dimer interaction surface has been probed by alanine-scanning mutagenesis. Mutations in three categories cause large binding defects: beta-sheet side chains that directly interact with DNA bases; side chains that link different DNA-binding regions of Arc, and side chains required to maintain the active DNA-binding conformation.