Theoretical Calculations of Relative Affinities of Binding

This chapter presents the theoretical calculations of relative affinities of binding. Modern experimental techniques allow for the specific replacement of amino acid residues in enzymes by genetic manipulation. These techniques open the way for the systematic study of the role of individual residues in binding of ligands to enzymes and in catalysis, as well as for the design of tailor-made enzymes that have specific catalytic properties. These changes can also be made in a computer model. For the calculation of relative binding constants, methods have been developed for the evaluation of free energy differences from molecular simulations. Computer simulations, therefore, have become an increasingly important tool in the analysis and prediction of properties of modified enzymes as well as of modified substrates or inhibitors. The chapter also discusses two methods for calculating differences in free energy—namely, the perturbation and thermodynamic integration techniques. The perturbation method in its general form can be used with any representative ensemble of configurations for some reference state and with any perturbation. The thermodynamic integration technique corresponds to the general idea of the way free energy changes are measured when some parameter is reversibly changed.