Correlating Protein Dynamics and Catalytic Activity of a Model Hydrogenase Using Paramagnetic and Biological Nuclear Magnetic Resonance Spectroscopy

Rational catalyst design remains a significant challenge, with electronic structure, steric, and electrostatic effects known to contribute to activity. Recently, dynamics has been recognized as another factor that impacts catalysis, though identifying and predicting these effects have remained out of reach. Nickel-substituted rubredoxin (NiRd), a protein-based mimic of a hydrogenase enzyme, serves as a model catalytic system in which dynamics can be systematically investigated with respect to activity. While over 30 secondary-sphere mutants of NiRd have been shown to be catalytically active, no significant correlation has been observed between the rates and catalytic overpotential or electronic structure, prompting questions about the protein-derived factors that modulate activity. In this work, NMR spectroscopy was used to investigate the roles of substrate accessibility, protein dynamics, and protein stability in controlling catalysis. Significant paramagnetic effects from the nickel center (<i>S</i> = 1) isolate the methylene proton resonances of the metal-coordinating cysteine residues. The sensitivity of resonance positions and line widths to local environment offers an opportunity to study dynamic molecular changes around the metal center with high resolution. Machine learning algorithms were employed to identify correlations between the catalytic activity and the paramagnetic NMR spectra. These analyses revealed spectroscopic features of specific cysteine protons that report on catalytic overpotential and increased turnover rates, which are further supported by the results obtained using high-field NMR techniques. Collectively, these studies indicate the potential for multifrequency NMR techniques to resolve key contributors to catalytic activity and highlight the importance of local and outer-sphere dynamics.