A microscopic model for gas diffusion dynamics in a [NiFe]-hydrogenase.

Area of Science:

• Biocatalysis
• Enzyme kinetics
• Computational biophysics

Background:

• [NiFe]-hydrogenase enzymes are promising catalysts for biofuel cells.
• Carbon monoxide (CO) and oxygen (O2) inhibit these enzymes.
• Understanding gas diffusion within the enzyme is key to overcoming inhibition.

Purpose of the Study:

• To develop and apply a microscopic model for calculating gas diffusion rates in [NiFe]-hydrogenase.
• To investigate the diffusion pathways of CO, O2, and H2 within the enzyme.
• To provide insights for engineering gas selectivity into hydrogenase enzymes.

Main Methods:

• Coarse-grained master equation approach to model diffusive hopping.
• Transition rates estimated using equilibrium and non-equilibrium pulling simulations.
• Propagation of the rate matrix to determine diffusion probabilities.

Main Results:

• The model accurately predicts the effective diffusion rate constant for CO, matching experimental data.
• Carbon monoxide preferentially diffuses through a hydrophobic channel.
• Oxygen and hydrogen exhibit exploration of larger protein fractions compared to CO.

Conclusions:

• The developed model is effective for simulating gas diffusion in [NiFe]-hydrogenase.
• Differential diffusion pathways of gases highlight potential for engineering selectivity.
• Findings contribute to the design of more robust and efficient hydrogenase-based biofuel cells.