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

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journal contribution
posted on 2004-05-18, 00:00 authored by Gene Wijffels, Brian P. Dalrymple, Pavel Prosselkov, Kritaya Kongsuwan, V. Chandana Epa, Penelope E. Lilley, Slobodan Jergic, Jens Buchardt, Susan E. Brown, Paul F. Alewood, Philip A. Jennings, Nicholas E. Dixon
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.