N₂H₂ binding to the nitrogenase FeMo cluster studied by QM/MM methods

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Nitrogenase is a crucial enzyme catalyzing nitrogen fixation.
• Understanding the mechanism of nitrogen (N₂) binding and reduction is key to improving nitrogen fixation efficiency.
• Previous studies have explored various intermediates in the nitrogenase catalytic cycle.

Purpose of the Study:

• To systematically investigate the possible structures of the N₂ bound state in nitrogenase using combined quantum mechanical and molecular mechanical (QM/MM) methods.
• To determine the preferred binding mode and orientation of N₂ within the enzyme's active site.
• To elucidate the role of protein environment in stabilizing N₂ binding.

Main Methods:

• Employed a systematic combined quantum mechanical and molecular mechanical (QM/MM) approach.
• Investigated protonated N₂H₂ states, considering both end-on and side-on binding modes.
• Utilized TPSS and B3LYP density-functional theory (DFT) methods for structural and energetic analysis.

Main Results:

• The binding of N₂H₂ is significantly influenced by interactions and steric effects with the surrounding protein residues.
• The most stable binding mode identified is trans-HNNH terminally bound to Fe2, stabilized by pi-stacking with His-195 and Ser-278.
• Several other structures, including cis-HNNH and HNNH₂ bound to different iron sites, were found to be energetically competitive, with variations depending on the DFT functional used.

Conclusions:

• Protein-ligand interactions and steric factors play a dominant role in determining the preferred N₂ binding conformation within nitrogenase.
• The trans-HNNH binding mode at Fe2 represents a highly stable intermediate in the nitrogenase catalytic cycle.
• Computational QM/MM studies provide valuable insights into the complex mechanisms of enzymatic nitrogen fixation.