Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement

Spatzal, Thomas; Schlesier, Julia; Burger, Eva; Sippel, Daniel; Zhang, Limei; Andrade, Susana L. A.; Rees, Douglas C.; Einsle, Oliver

doi:10.1038/ncomms10902

Cited by 138 publications

(167 citation statements)

References 44 publications

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“…As concluded in the last section, only the [MoFe 7 S 9 C] 1-charge is likely to be the resting state based on this new geometric analysis that is in agreement with the most recent analysis of the Mössbauer properties 32 as well as the recent spatially resolved anomalous dispersion refinement (SpReAD) study 78 . All of our QM/MM calculations have used broken-symmetry SCF solutions (with M S =3/2) using the broken-symmetry solution known as BS7 as proposed by Noodleman 11 .…”

Section: B Qm/mm Femoco Geometry: Effect Of Broken-symmetry Spin Isosupporting

confidence: 88%

“…Finally, it is important to note that the BS7-235 broken-symmetry solution and our picture of FeMoco involving specific delocalized pairs/localized Fe(II)/Fe(III) sites (see Figure 5) is not inconsistent with the results that came from spatially resolved anomalous dispersion refinement 78 (SpReAD) where 3 Fe atoms (no. 1, 3 and 7) were found to be more reduced (similar to the P-cluster) than the others.…”

Section: B Qm/mm Femoco Geometry: Effect Of Broken-symmetry Spin Isosupporting

confidence: 61%

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QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

2017

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Nitrogenase is one of the most fascinating enzymes in nature, being responsible for all biological nitrogen reduction. Despite decades of research it is among the enzymes in bioinorganic chemistry whose mechanism is the most poorly understood. The MoFe protein of nitrogenase contains an iron-molybdenum-sulfur cluster, FeMoco, where N 2 reduction takes place. The resting state of FeMoco has been characterized by crystallography, multiple spectroscopic techniques and theory (broken-symmetry density functional theory) and all heavy atoms are now characterized. The cofactor charge, however, has been controversial, the electronic structure has proved enigmatic and little is known about the mechanism. While many computational studies have been performed on FeMoco, few have taken the protein environment properly into account. In this study, we put forward QM/MM models of the MoFe protein from Azotobacter vinelandii, centered on FeMoco. By a detailed analysis of the FeMoco geometry and comparing to the atomic resolution crystal structure we conclude that only the [MoFe 7 S 9 C] 1-charge is a possible resting state charge. Further we find that, of the 3 lowest energy broken-symmetry solutions of FeMoco the BS7-235 spin isomer (where 235 refers to Fe atoms that are "spin-down") is the only one that can be reconciled with experiment. This is revealed by a comparison of the metal-metal distances in the experimental crystal structure, a rare case of spin-coupling phenomena being visible through the molecular structure. This could be interpreted as the enzyme deliberately stabilizing a specific electronic state of the cofactor, possibly for tuning specific reactivity on specific metal atoms. Finally, we show that the alkoxide group on the Mo-bound homocitrate must be protonated under resting state conditions; the presence of which has implications regarding the nature of FeMoco redox states as well as for potential substrate reduction mechanisms.3

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Section: B Qm/mm Femoco Geometry: Effect Of Broken-symmetry Spin Isosupporting

confidence: 88%

Section: B Qm/mm Femoco Geometry: Effect Of Broken-symmetry Spin Isosupporting

confidence: 61%

QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

2017

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“…This also appears consistent with recent spatially resolved anomalous dispersion (SpReAD) studies by Spatzal et al, which favor a Mo(III):4Fe(III):3Fe(II) assignment. 82 We emphasize, however, that the SpReAD data indicate only that three irons appear “more reduced” than the other four, and the possibility that this reflects contributions from mixed-valent iron sites cannot be ruled out. On the basis of the results presented here, however, the lack of a shift in the rising edge on going from the P-cluster to FeMoco could be rationalized if FeMoco is composed of localized Fe 2+ –Fe 3+ sites as opposed to delocalized Fe 2.5+ dimer configurations.…”

Section: Discussionmentioning

confidence: 76%

X-ray Absorption and Emission Spectroscopic Studies of [L₂Fe₂S₂]ⁿ Model Complexes: Implications for the Experimental Evaluation of Redox States in Iron–Sulfur Clusters

et al. 2016

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Herein, a systematic study of [L2Fe2S2]n model complexes (where L = bis(benzimidazolato) and n = 2-, 3-, 4-) has been carried out using iron and sulfur K-edge X-ray absorption (XAS) and iron Kβ and valence-to-core X-ray emission spectroscopies (XES). These data are used as a test set to evaluate the relative strengths and weaknesses of X-ray core level spectroscopies in assessing redox changes in iron–sulfur clusters. The results are correlated to density functional theory (DFT) calculations of the spectra in order to further support the quantitative information that can be extracted from the experimental data. It is demonstrated that due to canceling effects of covalency and spin state, the information that can be extracted from Fe Kβ XES mainlines is limited. However, a careful analysis of the Fe K-edge XAS data shows that localized valence vs delocalized valence species may be differentiated on the basis of the pre-edge and K-edge energies. These findings are then applied to existing literature Fe K-edge XAS data on the iron protein, P-cluster, and FeMoco sites of nitrogenase. The ability to assess the extent of delocalization in the iron protein vs the P-cluster is highlighted. In addition, possible charge states for FeMoco on the basis of Fe K-edge XAS data are discussed. This study provides an important reference for future X-ray spectroscopic studies of iron–sulfur clusters.

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“…16 The oxidation states of the iron atoms shown here are from X-ray absorption and anomalous dispersion studies. 17,18 The belt iron sites are colored red.…”

Section: Figurementioning

confidence: 99%

Insight into the Iron–Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands

2016

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Nitrogenase enzymes are used by microorganisms for converting atmospheric N2 to ammonia, which provides an essential source of N atoms for higher organisms. The active site of the molybdenum-dependent nitrogenase is the unique carbide-containing iron-sulfur cluster called the iron-molybdenum cofactor (FeMoco). On the FeMoco, N2 binding is suggested to occur at one or more iron atoms, but the structures of the catalytic intermediates are not clear. In order to establish the feasibility of different potential mechanistic steps during biological N2 reduction, chemists have prepared iron complexes that mimic various structural aspects of the iron sites in FeMoco. This reductionist approach gives mechanistic insight, and also uncovers fundamental principles that could be used more broadly for small molecule activation. Here, we review recent results and highlight directions for future research. In one direction, synthetic iron complexes have now been shown to bind N2, break the N-N triple bond, and produce ammonia catalytically. Carbon and sulfur based donors have been incorporated into the ligand spheres of Fe-N2 complexes to show how these atoms may influence the structure and reactivity of the FeMoco. Hydrides have been incorporated into synthetic systems, which can bind N2, reduce some nitrogenase substrates, and/or reductively eliminate H2 to generate reduced iron centers. Though some carbide-containing iron clusters are known, none yet have sulfide bridges or high-spin iron atoms like the FeMoco.

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Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement

Cited by 138 publications

References 44 publications

QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

X-ray Absorption and Emission Spectroscopic Studies of [L₂Fe₂S₂]ⁿ Model Complexes: Implications for the Experimental Evaluation of Redox States in Iron–Sulfur Clusters

Insight into the Iron–Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands

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Nitrogenase FeMoco investigated by spatially resolved anomalous dispersion refinement

Cited by 138 publications

References 44 publications

QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site

X-ray Absorption and Emission Spectroscopic Studies of [L2Fe2S2]n Model Complexes: Implications for the Experimental Evaluation of Redox States in Iron–Sulfur Clusters

Insight into the Iron–Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands

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X-ray Absorption and Emission Spectroscopic Studies of [L₂Fe₂S₂]ⁿ Model Complexes: Implications for the Experimental Evaluation of Redox States in Iron–Sulfur Clusters