Quantitative determination of equilibrium binding isotherms for multiple ligand-macromolecule interactions using spectroscopic methods

Abstract

Thermodynamic studies provide information that is necessary in order to understand the forces that drive the formation of ligand-macromolecule complexes. Knowledge of the energetics of these interactions is also indispensable for characterization of functionally important structural changes that occur within the studied complexes. Quantitative examination of the equilibrium interactions are designed to provide the answers to the questions: What is the stoichiometry of the formed complexes? How strong or how specific are the interactions? Are there any cooperative interactions among the binding sites and/or the bound ligand molecules? Are the binding sites intrinsically heterogeneous? What are the molecular forces involved in the formation of the studied complexes, or, in other words, how do the equilibrium binding and kinetic parameters depend on solution variables (temperature, pressure, pH, salt concentration, etc.)? Equilibrium isotherms for the binding of a ligand to a macromolecule represent the relationship between the degree of ligand binding (moles of ligands bound per mole of a macromolecule) and the free ligand concentration. A true thermodynamic binding isotherm is model-independent and reflects only this relationship. Only then, when such an isotherm is obtained, can one proceed to extract physically meaningful interaction parameters that characterize the free energies of interaction. This is accomplished by comparing the experimental isotherms to theoretical predictions based on specific binding models that incorporate known molecular aspects, such as intrinsic binding constants, cooperativity parameters, allosteric equilibrium constants, discrete character of the binding sites or overlap of potential binding sites, etc. (see below). Any method used to quantitatively study ligand binding to a macromolecule must relate the extent of the complex formation to the free ligand concentration in solution. Numerous techniques have been developed to study equilibrium properties of specific and non-specific ligand-macromolecule interactions in which binding is directly monitored, including equilibrium dialysis, ultrafiltration, column chromatography, filter binding assay and gel electrophoresis (1-6). These direct methods are very straightforward; however, they are usually time consuming and some, like filter binding or gel shift assays, are non-equilibrium techniques which require many controls before the reliable equilibrium binding data can be obtained.