Abstract
Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. Recently, we have demonstrated that the heat capacity of catalysis, ΔCP‡, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions at the active site can affect long-range protein dynamics and link to enzyme temperature activity. Here, we use a model promiscuous enzyme (glucose dehydrogenase from Sulfolobus solfataricus) to chemically map how individual substrate interactions affect the temperature dependence of enzyme activity and the network of motions throughout the protein. Utilizing a combination of kinetics, red edge excitation shift (REES) spectroscopy, and computational simulation, we explore the complex relationship between enzyme–substrate interactions and the global dynamics of the protein. We find that changes in ΔCP‡ and protein dynamics can be mapped to specific substrate–enzyme interactions. Our study reveals how subtle changes in substrate binding affect global changes in motion and flexibility extending throughout the protein.
Highlights
Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis
We have previously applied a model for understanding the temperature dependence of enzyme catalysis, which explicitly incorporates the difference in heat capacity between the ground state and transition state, ln k
We have recently developed the understanding of the protein red edge excitation shift (REES) phenomenon, a quantification of the effect, which allows subtle changes in protein dynamics to be tracked.[25−28] We term this quantification Quantitative Understanding of Bimolecular Edge Shift, QUBES.[29]
Summary
Uncovering the role of global protein dynamics in enzyme turnover is needed to fully understand enzyme catalysis. We have demonstrated that the heat capacity of catalysis, ΔCP‡, can reveal links between the protein free energy landscape, global protein dynamics, and enzyme turnover, suggesting that subtle changes in molecular interactions at the active site can affect long-range protein dynamics and link to enzyme temperature activity. Recent studies have begun to elucidate the relationship between global and local protein dynamics and enzyme turnover.[1−6] There is a range of computational and experimental evidence that variation in the normal distribution of vibrational modes remote from the active site volume can affect the observed rate and temperature dependence of enzyme turnover. In the absence of alternative sources of nonlinearity, the magnitude of ΔCP‡ is a useful experimental window into the difference in rigidity between the ground state and the transition state and the difference in the distribution of vibrational modes
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