Dynamic Proton Sharing and Second-Sphere Gating Control Catalytic States in [NiFe] Hydrogenase

Area of Science:

• Biochemistry
• Computational Chemistry
• Spectroscopy

Background:

• [NiFe] hydrogenases are crucial for reversible hydrogen oxidation.
• Spectroscopic heterogeneity in Ni-L and Ni-R intermediates has hindered mechanistic understanding.

Purpose of the Study:

• To elucidate the structural and electronic origins of spectroscopic heterogeneity in [NiFe] hydrogenase intermediates.
• To reconcile long-standing models of Ni-L/Ni-R heterogeneity.

Main Methods:

• Multiscale quantum mechanics/molecular mechanics (QM/MM) calculations.
• Long-time scale molecular dynamics (MD) simulations.
• Quantum cluster models.
• Electron paramagnetic resonance (EPR) and infrared (IR) spectroscopy simulations.

Main Results:

• Spectroscopic heterogeneity arises from Cys546-protonated and Glu34-protonated configurations.
• The Glu34-protonated form is thermodynamically favored.
• A conserved Cys546-Glu34 proton-sharing motif, modulated by second-sphere residues, governs proton localization.
• Experimental EPR and IR data are quantitatively reproduced by Glu34-protonated models.

Conclusions:

• The Cys-Glu proton-sharing motif and its gating mechanism are likely conserved in Group 1 [NiFe] hydrogenases.
• Second-sphere dynamics play a critical role in gating proton transfer.
• Findings provide design principles for bioinspired hydrogen-evolution catalysts.