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Density functional study of the catalytic cycle of nickel–iron [NiFe] hydrogenases and the involvement of high-spin nickel(II)

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Abstract

In light of recent experiments suggesting high-spin (HS) Ni(II) species in the catalytic cycle of [NiFe] hydrogenase, a series of models of the Ni(II) forms Ni-SI(I,II), SI-CO and Ni-R(I,II,III) were examined in their high-spin states via density functional calculations. Because of its importance in the catalytic cycle, the Ni–C form was also included in this study. Unlike the Ni(II) forms in previous studies, in which a low-spin (LS) state was assumed and a square–planar structure found, the optimized geometries of these HS Ni(II) forms resemble those observed in the crystal structures: a distorted tetrahedral to distorted pyramidal coordination for the NiS4. This resemblance is particularly significant because the LS state is 20–30 kcal/mol less stable than the HS state for the geometry of the crystal structure. If these Ni(II) forms in the enzyme are not high spin, a large change in geometry at the active site is required during the catalytic cycle. Furthermore, only the HS state for the CO-inhibited form SI-CO has CO stretching frequencies that match the experimental results. As in the previous work, these new results show that the heterolytic cleavage reaction of dihydrogen (where H2 is cleaved with the metal acting as a hydride acceptor and a cysteine as the proton acceptor) has a lower energy barrier and is more exothermic when the active site is oxidized to Ni(III). The enzyme models described here are supported by a calibrated correlation of the calculated and measured CO stretching frequencies of the forms of the enzyme. The correlation coefficient for the final set of models of the forms of [NiFe] hydrogenase is 0.8.

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Notes

  1. Linear regression analysis just using the CO values yields: ν exp=0.948ν calc, R 2=0.77.

  2. Nearly all of the models without a third bridging Ni–Fe ligand have longer Ni–Fe distances than those observed for the crystal structures. The discrepancies are most likely due to our simplified model, which lacks a complete protein backbone. However, fixing the Ni–Fe distance to the experimental value (2.9 Å) has little geometric or energetic effect on the states of these species. For example, the freely optimized HS SII form is 1.72 kcal/mol more stable than the freely optimized LS one, and the dihedral angles of the NiS  unit are 87.4° (HS) and 16.6° (LS). For the optimized geometries with a fixed Ni–Fe distance, the HS SII form is 2.0 kcal/mol more stable than the corresponding LS one, and the dihedral angles of the NiS4 unit are 88.6° (HS) and 19.1° (LS). Furthermore, fixing the Ni–Fe distance in SII models only raises the energies of these two forms by 2.78 (HS) and 2.20 (LS) kcal/mol. Similar changes are found for the partially optimized Ni-R form witha fixed Ni–Fe distance. Thus, reasonable models for the energies, frequencies and geometries of other ligands can be obtained without the full constraint provided by the protein.

  3. Although a recent study suggests that there is a second (reduced by one electron) CO-inhibited form, the (SI-CO)red form, we will not study this form because this species occurs due to the cluster reduction [31].

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Acknowledgements

The authors gratefully acknowledge the National Science Foundation (Grant No. 9800184 CHE and MRI 02-16275), The Welch Foundation (Grant No. A-648) and The Spanish Ministry of Science and Technology (BQU2003-04221) for financial support of this work.

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Authors and Affiliations

  1. Instituto de Catalisis, CSIC, c/ Marie Curie s/n, Campus de Cantoblanco, 28049, Madrid, Spain

    Alejandro Pardo, Antonio L. De Lacey & Víctor M. Fernández

  2. Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, TX, 77843-3255, USA

    Hua-Jun Fan, Yubo Fan & Michael B. Hall

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  1. Alejandro Pardo
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Correspondence to Michael B. Hall.

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Pardo, A., De Lacey, A.L., Fernández, V.M. et al. Density functional study of the catalytic cycle of nickel–iron [NiFe] hydrogenases and the involvement of high-spin nickel(II). J Biol Inorg Chem 11, 286–306 (2006). https://doi.org/10.1007/s00775-005-0076-3

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