Thermodynamic dissection of large-scale domain motions coupled with ligand binding of enzyme I

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 domain-domain orientations. Calorimetric analysis of the EI mutants separated the free energy changes of the binding and motions, demonstrating that the unfavorable hinge motion (ΔG = 1.5 kcal mol(-1)) was driven by the favorable swivel motion (ΔG = -5.2 kcal mol(-1)). 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.