Dynamics of Protein Ligand Binding on Multiple Time Scales: NADH Binding to Lactate Dehydrogenase

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Abstract
Although the importance of atomic motion to how proteins function has been conjectured for several decades, the characterization of protein dynamics on multiple time scales is scant. This is because of severe experimental and theoretical difficulties, particularly characterizing the nanosecond to millisecond time scales. Here, we apply advanced laser-induced temperature-jump relaxation spectroscopic techniques to examine the kinetics of NADH binding to lactate dehydrogenase over this time scale. The bimolecular rate process, at about 290 μs, is easily observed as are multiple faster events (with relaxation times of 200 ns, 3.5 μs, and 24 μs), revealing a rich dynamical nature of the binding step. The results show that there are multiple structures of bound enzyme−ligand complexes, some of which are likely to be far from the catalytically productive structure. The results have important implications for interpretations of the binding thermodynamics of ligands to LDH and, by extension, to other proteins. The observed processes likely play a role in the dynamics of the chemistry that is catalyzed by lactate dehydrogenase.

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