Solvation Free Energy in Governing Equations for DNA Hybridization, Protein–Ligand Binding, and Protein Folding

Abstract

ABSTRACTThis work examines the thermodynamics of model biomolecular interactions using a governing equation that accounts for the participation of bulk water in the balanced reaction. In the first example, the binding affinities of two model DNA duplexes, one of nine and one of ten base pairs in length, are measured and characterized by isothermal titration calorimetry as a function of concentration. The results indicate that the change in solvation free energy that accompanies duplex formation (ΔGS) is large and unfavorable. When normalized to the number of base pairs, the duplex with the larger number of G:C pairings yields the largest change in solvation free energy, ΔGS= +460 kcal/mol/base pair at 25 °C. A modelling study demonstrates how the solvation free energy alters the output of a typical titration experiment. Hybridization measurements are completed at four different temperatures, however a van’t Hoff analysis of the data is complicated by the varying degree of intramolecular base stacking within each DNA strand as a function of temperature. The same thermodynamic framework is applied to a model protein– ligand interaction, the binding of ribonuclease A with the nucleotide inhibitor 3’-UMP, and to a conformational equilibrium, the change in tertiary structure of α-lactalbumin in molar guanidinium chloride solutions. The ribonuclease study yields a value of ΔGS= +160 kcal/mol, whereas the folding equilibrium yields ΔGS≈ 0, an apparent characteristic of hydrophobic interactions. These examples complement previous applications of the governing equation to the interaction of smaller molecules and demonstrate the importance of solvation energy in biothermodynamics.