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

Rahul Roy, Alexander G Kozlov, Timothy M Lohman, Taekjip Ha

Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, IL 61801, USA.

Journal of molecular biology 2007 Jun 22

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Escherichia coli single-stranded (ss)DNA binding (SSB) protein binds ssDNA in multiple binding modes and regulates many DNA processes via protein-protein interactions. Here, we present direct evidence for fluctuations between the two major modes of SSB binding, (SSB)(35) and (SSB)(65) formed on (dT)(70), with rates of interconversion on time scales that vary as much as 200-fold for a mere fourfold change in NaCl concentration. Such remarkable electrostatic effects allow only one of the two modes to be significantly populated outside a narrow range of salt concentration, providing a context for precise control of SSB function in cellular processes via SSB expression levels and interactions with other proteins. Deletion of the acidic C terminus of SSB, the site of binding of several proteins involved in DNA metabolism, does not affect the strong salt dependence, but shifts the equilibrium towards the highly cooperative (SSB)(35) mode, suggesting that interactions of proteins with the C terminus may regulate the binding mode transition and vice versa. Single molecule analysis further revealed a novel low abundance binding configuration and provides a direct demonstration that the SSB-ssDNA complex is a finely tuned assembly in dynamic equilibrium among several well-defined structural and functional states.

Citation

Rahul Roy, Alexander G Kozlov, Timothy M Lohman, Taekjip Ha. Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein. Journal of molecular biology. 2007 Jun 22;369(5):1244-57