title: A model for the binding of E. coli single-strand binding protein to supercoiled DNA.
abstract: A model is proposed for the binding of E. coli single strand binding protein (SSB) to supercoiled DNA. The basic tetrameric binding units of SSB are assumed to bind in pairs to the complementary single strands of a locally melted region. The cooperativity of the binding includes contributions from both protein-protein and base-pair stacking interactions. Each bound SSB tetramer is assumed to unwind l = 34 bp, which implies an unwinding angle of 3.27 turns. The resulting loss of superhelical strain is the essential driving force for binding SSB to supercoiled DNAs. All molecular parameters entering into the theory are estimated from available data, except for the composite binding constant (Ka), which is adjusted to best-fit the theory to the fluorescence quenching (FQ) and diffusion coefficient (D0) data of Langowski et al. Very good fits are obtained with optimum values of Ka that are consistent with estimates from other data. This binding model predicts several noteworthy features. (1) SSB binds essentially always in a single contiguous stack on a supercoiled plasmid, and relative fluctuations in stack length are quite small, in agreement with results of electron microscopy studies. (2) The progressive loss of superhelical strain with increasing bound ligand decreases the affinity of the DNA for SSB. This anti-cooperativity offsets the cooperativity of the binding and causes apparent saturation of the binding at rather low binding ratios. Consequently, over the limited span of the measurements, the FQ data can also be satisfactorily fitted by a non-cooperative model comprising a small number of independent sites. (3) When SSB binds to a population of different topoisomers, the distribution of linking differences of the resulting complexes is extremely narrow. Thus, SSB acts to level any differences in superhelical strain in a population of topoisomers. Finally, the effects of restricting binding to a region comprising only part of the plasmid are assessed.
authors.affiliation: Department of Chemistry, University of Washington, Seattle 98195.
authors.forename: J B
authors.initials: JB
authors.lastname: Clendenning
authors.forename: J M
authors.initials: JM
authors.lastname: Schurr
mesh_terms: D001665:Binding Sites; D004278:DNA, Superhelical / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism*; D007700:Kinetics; D046911:Macromolecular Substances; D008961:Models, Structural; D008962:Models, Theoretical; D013816:Thermodynamics
chemical_list: D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D046911:Macromolecular Substances