Inhibition of Protein Interactions with the β₂ Sliding Clamp of Escherichia coli DNA Polymerase III by Peptides from β ₂-Binding Proteins

The sliding clamp of the Escherichia coli replisome is now understood to interact with many proteins involved in DNA synthesis and repair. A universal interaction motif is proposed to be one mechanism by which those proteins bind the E. coli sliding clamp, a homodimer of the β subunit, at a single site on the dimer. The numerous β₂-binding proteins have various versions of the consensus interaction motif, including a related hexameric sequence. To determine if the variants of the motif could contribute to the competition of the β-binding proteins for the β₂ site, synthetic peptides derived from the putative β₂-binding motifs were assessed for their abilities to inhibit protein-β₂ interactions, to bind directly to β₂, and to inhibit DNA synthesis in vitro. A hierarchy emerged, which was consistent with sequence similarity to the pentameric consensus motif, QL(S/D)LF, and peptides containing proposed hexameric motifs were shown to have activities comparable to those containing the consensus sequence. The hierarchy of peptide binding may be indicative of a competitive hierarchy for the binding of proteins to β₂ in various stages or circumstances of DNA replication and repair.