Domain motions are central to the biological functions of many proteins. The energetics of the motions, however, is often difficult to characterize when motions are coupled with the ligand binding. Here, we determined the thermodynamic parameters of individual domain motions and ligand binding of enzyme I (EI) using strategic domain-deletion mutants that selectively removed particular motions. Upon ligand binding, EI employs two large-scale domain motions, the hinge motion and the swivel motion, to switch between conformational states of distinct domain2domain orientations. Calorimetric analysis of the EI mutants separated the free energy changes of the binding and motions, demonstrating that the unfavorable hinge motion (DG 5 1.5 kcal mol 21 ) was driven by the favorable swivel motion (DG 5 25.2 kcal mol 21 ). The large free energy differences could be explained by the physicochemical nature of the domain interfaces associated with the motions; the hinge motion employed much narrower interface than the swivel motion without any hydrogen bonds or salt bridges. The small heat capacity further suggested that the packing of the domain interfaces associated with the hinge motion was less compact than that commonly observed in proteins. Lastly, thermodynamic analysis of phosphorylated EI suggests that the domain motions are regulated by the ligand binding and the phosphorylation states. Taken together, the thermodynamic dissection approach illustrates how multiple motions and ligand binding are energetically connected during the functional cycle of EI.Keywords: calorimetry; domain motions; free energy evolution; ligand binding; thermodynamics Outline Enzyme I employs a hinge motion and a swivel motion upon ligand binding to accomplish its autophosphorylation reaction. We have characterized the free energy changes of each motion and binding separately using calorimetric analysis of domaindeletion mutants. The thermodynamic parameters demonstrate the free energy loss and gain of individual motions in a quantitative manner, and illustrate how free energies evolve along a series of binding and motions in multidomain proteins.