14] Structural-perturbation approaches to thermodynamics of site-specific protein—DNA interactions

Abstract

This chapter presents the structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions. The conceptual foundation of structural perturbation methods derives from the idea of a thermodynamic cycle, referred to as a pseudocycle because some of the constituent steps represent imaginary chemical transformations. In structural-perturbation methods, values of K obs are determined for the normal DNA site and for one or more modified DNAs or modified proteins. As an introduction to the kinds of information that may be derived from structural-perturbation methods, the energetic factors that may contribute to the interaction between a protein and its DNA recognition site is enumerated. The set of structural perturbation methods discussed, when used in concert with a variety of measures of thermodynamic, kinetic, and structural parameters, allows gaining significant insights into the behavior of protein- DNA complexes. Determination of either thermodynamic or kinetic parameters of DNA-protein interactions requires accurate knowledge of the molar concentration of active protein.