COOPERATIVITY IN BINDING OF PROTEINS TO DNA

Three different, linear, three-site binding models are presented for t he binding of proteins, such as a repressor, to DNA. The first model a ssumes that the DNA is rigid and all correlations between the Ligands are due to direct ligand-ligand interactions. In the second and third models conformational changes in the DNA are induced by the binding pr ocess. In these models we find both direct and indirect correlations b etween the ligands. Examination of the indirect correlation reveals tw o characteristic features that, in general, are negligible in the dire ct correlation. (1) Long range correlation, between nonadjacent sites. (2) Nonadditivity of the triplet correlations. It is shown that these two features cannot be neglected in the indirect correlations. The ar guments for explaining these features are similar to those which expla in long range and nonadditivies of correlations in the liquid state. ( C) 1997 American Institute of Physics. [S0021-9606(97)52046-0].