Ion‐exchange reactions of proteins during DNA binding

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Abstract
The equilibrium association constant observed for many DNA/protein interactions in vitro (Kobs) is strongly dependent on the salt concentration of the reaction buffer ([MX]). This dependence is often used to estimate the number of ionic contacts between protein and DNA by assuming that displacement of cations from the DNA is the predominant form of the involvement of ions in the binding reaction. With this assumption, the graph of log Kobs versus log [MX] is predicted to have a constant slope proportional to the number of ions displaced from the DNA upon protein binding [Record, M. T., Lohman, T. M. & deHaseth, P. L. (1976) J. Mol. Biol. 107, 145–158]. Experimental data often deviate from linearity, however, at lower salt concentrations. Such deviations can be due to differential cation binding, anion binding or changes in macromolecular hydration, or differential screening effects of the electrolyte on protein and/or DNA charges. Here the theoretical effects on Kobs of a simple form of ion–protein interaction are examined. A model for binding interactions is used that includes a mass balance of ions bound to both protein and DNA as the protein is transferred from the salt concentration of bulk solvent to the typically higher cation and lower anion concentrations characteristic of the volume adjacent to the DNA. We show that models in which the cation and anion stoichiometries of a protein change as it associates with DNA are consistent with the curvature of plots of log Kobs versus log [MX]. Such mechanisms could reduce the sensitivity of gene‐regulatory interactions to changes in environmental salt concentration.