Inhibition of protein interactions with the beta 2 sliding clamp of Escherichia coli DNA polymerase III by peptides from beta 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 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.
Wijffels
Gene
G
CSIRO Livestock Industries, St. Lucia, Queensland 4067, Australia. gene.wijffels@csiro.au
Dalrymple
Brian P
BP
Prosselkov
Pavel
P
Kongsuwan
Kritaya
K
Epa
V Chandana
VC
Lilley
Penelope E
PE
Jergic
Slobodan
S
Buchardt
Jens
J
Brown
Susan E
SE
Alewood
Paul F
PF
Jennings
Philip A
PA
Dixon
Nicholas E
NE
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
D002352:Carrier Proteins; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D009842:Oligopeptides; D021122:Protein Subunits; D004258:DNA Polymerase III