This book provides the first systematic treatment of the thermodynamic theory of site-specific effects in biological macromolecules. It describes the phenomenological and conceptual bases required to allow a mechanistic understanding of these effects from analysis of experimental data. The thermodynamic theory also results in novel experimental strategies that enable the derivation of information on local, site-specific properties of a macromolecular system from analysis of perturbed global properties. The treatment focuses on binding phenomena, but is amenable to extension both conceptually and formally to the analysis of other cooperative processes, such as protein folding and helix-coil transitions. Much attention is devoted to the analysis of mutational perturbations used as probes of site-specific energetics. The arrangement of various sections in the book allows its use both as a reference work on cooperative binding phenomena for any scientist involved in structure-function studies of biological macromolecules, and as a text for graduate students in biochemistry and biophysics.