Proton Transfer Pathways in Nitrogenase with and without Dissociated S2B

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Nitrogenase is the sole enzyme capable of biological nitrogen fixation, converting atmospheric nitrogen (N2) into ammonia (NH3).
• Crystallographic data indicates the active-site FeMo cluster's S2B sulfide ligand can be displaced by inhibitors (e.g., CO, OH-) and may be involved in the natural reaction cycle.

Purpose of the Study:

• To investigate potential proton transfer pathways within the FeMo cluster during N2 to NH3 conversion.
• To determine the role of the S2B ligand's presence or absence in these proton transfer mechanisms.

Main Methods:

• Employed combined quantum mechanical and molecular mechanical (QM/MM) calculations.
• Utilized TPSS and B3LYP density functionals to model proton transfer pathways.
• Assessed proton entry at S3B, S4B, or S5A sulfide ions and subsequent substrate transfer.

Main Results:

• Calculated reaction barriers were found to be reasonable when the S2B ligand remained bound to the FeMo cluster.
• Prohibitive energy barriers were observed when the S2B ligand was assumed to have dissociated.
• Proton transfer pathways are feasible with S2B intact but highly unfavorable if S2B dissociates.

Conclusions:

• The S2B ligand likely remains bound to the FeMo cluster during the normal nitrogenase reaction cycle.
• Reversible dissociation of the S2B ligand is unlikely due to the significantly high energy barriers it would impose.
• The structural integrity of the FeMo cluster, including the S2B ligand, is critical for efficient nitrogen fixation.