Computational Studies of Nitrogenase

Project: DissertationIndividual research project

Research areas and keywords

UKÄ subject classification

  • Natural Sciences

Keywords

  • nitrogenase, QM/MM, quantum refinement, FeMo cluster, E4 state, N2 binding, V-nitrogenase, P-cluster, S2B dissociation, broken-symmetry state, homocitrate, DFT, protonation state, disorder, ComQumX-2QM, pMMO, Cu, additive or subtractive QM/MM

Description

Nitrogenase is the only enzyme that can convert the inert nitrogen molecule to ammonia, so that it can be used in biosynthetic pathways. It contains a complicated acitve site, composed of eight metal ions, nine sulfur ions and one carbide ion (the FeMo cluster). Although it has been thoroughly studied with experimental and computational methods, the reaction mechanism is still not known and many conflicting hypotheses have been presented. To solve some of these problems, we have performed a thorough and systematic study of nitrogenase with various computational approaches. We have:
• Decided the protonation states of eight key amino acid residues around the active site and showed that the homocitrate ligand is singly prontated on the hydroxide group.
• Studied how the the broken-symmetry (BS) state for the FeMo cluster depends on the QM method, the basis sets, the surrounding protein and the protonation and oxidation state of the cluster.
• Predicted the most stable protonation state for the E0–E4 states of nitrogenase with two density functional theory (DFT) methods.
• Showed that different DFT methods give relative eneriges that can differ by >600 kJ/mol for nitrogenase. This is the main reason for the diverging computational results.
• Showed that the most stable E4 structure obtained with pure functionals has two hydride ions bridging between two pairs of iron ions, in agreement with experiments.
• Predicted that the most stable binding mode of N2H2 to nitrogenase involves trans-HNNH binding to Fe2.
• Suggested an alternating reaction mechanism for nitrogenase with a dissociated S2B ligand.
• Decided the most stable BS states for the P-cluster in four oxidation states and decided the protonation state of the one-electron oxidised state.
• Developed a novel quantum-refinement approach allowing for disorder in the QM system and applied it to the P-cluster in two crystal structures of nitrogenase.
• Shown by quantum refinement that a recent crystal structure of V-nitrogenase does not involve a N-derived ligand, but rather a hydride-inhibited state.
StatusFinished
Effective start/end date2016/01/042020/06/30

Participants

Related research output

Lili Cao & Ulf Ryde, 2020 Apr 7, In : Journal of Biological Inorganic Chemistry. 25, 3, p. 521-540 20 p.

Research output: Contribution to journalArticle

Lili Cao & Ulf Ryde, 2019, In : Physical Chemistry Chemical Physics. 21, 5, p. 2480-2488 9 p.

Research output: Contribution to journalArticle

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