Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• Escherichia coli single-stranded DNA binding (SSB) protein is crucial for DNA replication, repair, and recombination.
• SSB protein exhibits multiple binding modes on single-stranded DNA (ssDNA).
• Protein-protein interactions involving SSB regulate its function.

Purpose of the Study:

• To provide direct evidence for fluctuations between major SSB binding modes.
• To investigate the influence of salt concentration on SSB binding dynamics.
• To explore the role of SSB's C-terminus in regulating binding modes.

Main Methods:

• Single molecule analysis was employed to study SSB-ssDNA interactions.
• The study focused on the (SSB)(35) and (SSB)(65) binding modes on a (dT)(70) oligonucleotide.
• Experiments involved varying NaCl concentrations to assess electrostatic effects.

Main Results:

• Direct evidence of interconversion between (SSB)(35) and (SSB)(65) modes was observed.
• Interconversion rates showed a significant salt concentration dependence, with up to a 200-fold change for a fourfold change in NaCl.
• Deletion of SSB's acidic C-terminus shifted equilibrium towards the (SSB)(35) mode without altering salt dependence.
• A novel, low-abundance binding configuration was identified.

Conclusions:

• The SSB-ssDNA complex exists in a dynamic equilibrium of multiple states.
• Electrostatic interactions, modulated by salt concentration, are critical for controlling SSB binding modes.
• Interactions with other proteins via the C-terminus may regulate SSB binding mode transitions.
• SSB expression levels and protein interactions offer precise control over SSB function in vivo.