Local perturbations by ligand binding of hydrogen deuterium exchange kinetics in a four-helix bundle protein, acyl coenzyme A binding protein (ACBP).

Amide hydrogen exchange kinetics of the individual amides in a four-helix bundle protein, acyl-coenzyme A binding protein, have been studied by nuclear magnetic resonance spectroscopy. The kinetics of amides with exchange rate constants in the range of 10(-25) to 10(-6.5) S-1 at pH 6.65 in free protein and the ligand-protein complex have been measured, and the effect of binding the ligand, palmitoyl-coenzyme A, on individual exchange rates has been analysed. Specific correlations between exchange kinetics and the structural properties of the individual amides known from the three-dimensional structure of acyl-coenzyme A binding protein have been examined. Furthermore, an analysis has been performed comparing the structural perturbations of the protein-ligand interactions known from the three dimensional structure of the complex of palmitoyl-coenzyme A and acyl-coenzyme A binding protein with the ligand-induced perturbations on the amides exchange kinetics. Finally, the ligand-induced perturbations on hydrogen exchange have been compared with those on 15N relaxation. The results suggest that hydrogen exchange kinetics in the individual sites of acyl-coenzyme A binding protein are primarily determined by local structural features; they show that ligand binding gives rise mainly to changes localized at the sites of interaction between protein and ligand; they imply that the perturbation of exchange kinetics caused by ligation can be either, as in one example a local stabilisation of the pre-exchange equilibrium induced by formation of a hydrogen bond, or as seen here in several examples a reduction of the dynamic processes that lead to the opening and closing processes of the pre-exchange equilibrium. The results seem not to indicate changes in the rate of the final chemical exchange step.