Inhibition of protein interactions with the beta 2 sliding clamp of Escherichia coli DNA polymerase III by peptides from beta 2-binding proteins

Biochemistry. 2004 May 18;43(19):5661-71. doi: 10.1021/bi036229j.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Binding, Competitive
  • Carrier Proteins / chemistry*
  • Carrier Proteins / metabolism
  • Computer Simulation
  • Consensus Sequence
  • DNA Polymerase III / antagonists & inhibitors*
  • DNA Polymerase III / chemistry
  • DNA Polymerase III / metabolism
  • DNA, Bacterial / antagonists & inhibitors
  • DNA, Bacterial / biosynthesis
  • Dimerization
  • Escherichia coli Proteins / antagonists & inhibitors*
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism
  • Models, Molecular
  • Oligopeptides / chemistry*
  • Oligopeptides / metabolism
  • Protein Interaction Mapping* / methods
  • Protein Subunits / chemistry*
  • Protein Subunits / metabolism
  • Surface Plasmon Resonance


  • Carrier Proteins
  • DNA, Bacterial
  • Escherichia coli Proteins
  • Oligopeptides
  • Protein Subunits
  • DNA Polymerase III