title: Inhibition of protein interactions with the beta 2 sliding clamp of Escherichia coli DNA polymerase III by peptides from beta 2-binding proteins.
abstract: 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 beta subunit, at a single site on the dimer. The numerous beta(2)-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 beta-binding proteins for the beta(2) site, synthetic peptides derived from the putative beta(2)-binding motifs were assessed for their abilities to inhibit protein-beta(2) interactions, to bind directly to beta(2), 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 beta(2) in various stages or circumstances of DNA replication and repair.
authors.affiliation: CSIRO Livestock Industries, St. Lucia, Queensland 4067, Australia. gene.wijffels@csiro.au
authors.forename: Gene
authors.initials: G
authors.lastname: Wijffels
authors.forename: Brian P
authors.initials: BP
authors.lastname: Dalrymple
authors.forename: Pavel
authors.initials: P
authors.lastname: Prosselkov
authors.forename: Kritaya
authors.initials: K
authors.lastname: Kongsuwan
authors.forename: V Chandana
authors.initials: VC
authors.lastname: Epa
authors.forename: Penelope E
authors.initials: PE
authors.lastname: Lilley
authors.forename: Slobodan
authors.initials: S
authors.lastname: Jergic
authors.forename: Jens
authors.initials: J
authors.lastname: Buchardt
authors.forename: Susan E
authors.initials: SE
authors.lastname: Brown
authors.forename: Paul F
authors.initials: PF
authors.lastname: Alewood
authors.forename: Philip A
authors.initials: PA
authors.lastname: Jennings
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Dixon
mesh_terms: D020816:Amino Acid Motifs; D001667:Binding, Competitive; D002352:Carrier Proteins / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D016384:Consensus Sequence; D004258:DNA Polymerase III / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D004269:DNA, Bacterial / Q000037:antagonists & inhibitors / Q000096:biosynthesis; D019281:Dimerization; D029968:Escherichia coli Proteins / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry* / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods; D021122:Protein Subunits / Q000737:chemistry* / Q000378:metabolism; D020349:Surface Plasmon Resonance
chemical_list: D002352:Carrier Proteins; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D009842:Oligopeptides; D021122:Protein Subunits; D004258:DNA Polymerase III