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

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.

Intermediates in the Catalytic Cycle of [NiFe] Hydrogenase: Functional Spectroscopy of the Active Site

“…The (Ni-SI r ) II and Ni-SI a states have been reported to have within the spectral resolution identical FTIR spectra in the case of A. vinosum, [41,81] whereas for other oxygen-sensitive enzymes only the active Ni-SI a (or Ni-SI II according to some authors) is proposed. [91][92][93] Regarding the spin state of the divalent nickel ion, only a high-spin Ni 2 + species with a distorted tetrahedral geometry is in agreement with the one-electron reduced Ni-SI r/a states according to calculations [37,94] considering a four-coordinated nickel centre. This is further supported by Ni L-edge X-ray circular magnetic dichroism (XCMD) measurements on D. desulfuricans and D. gigas.…”

Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach

“…For each of these [NiFeSe] center redox states, the continuum electrostatics calculations were performed with all ISCs oxidized and with all ISCs reduced. It is worth pointing out that the nomenclature of the states is not uniform in the literature, and the two mechanistic studies quoted here are no exception; Ni-SI in the first model [42] and Nia-S in the second model [41] are the same state, but with different designations.…”

“…Since there is no consensual mechanism, we considered two different recent hypotheses in the literature. From the mechanism proposed by Pardo et al [42] in 2006, we used the states SI I and SI II , cleavage reaction product C and the intermediate Ni(I) (the mechanism is illustrated in Fig. S1a).…”

“…However, the chemical identities of these states as well as the catalytic mechanism of hydrogenases are still under debate. Quantum mechanics studies provide the most detailed insight into the mechanism and its intermediates [40][41][42][43][44], but no detailed study exists for [NiFeSe] hydrogenases. Therefore, in this work, we chose to assume that the mechanism and the intermediates proposed for [NiFe] hydrogenases can be transposed to [NiFeSe] hydrogenases, given their similarity.…”

A Threonine Stabilizes the NiC and NiR Catalytic Intermediates of [NiFe]-hydrogenase

“…NiSI and NiR are observed in different protonation states (NiSI I and NiSI II ; NiR I and NiR II ) (2,6). A NiR III state has also been detected in Allochromatium vinosum hydrogenase (noted Ni a -SR 1913 ) (7) and attributed to a NiR state with two fewer protons than NiR I (8). NiL, a state observed upon irradiation of NiC, is sometimes seen as a putative reaction intermediate as proposed for Hyd-1 from Escherichia coli in which NiC could not be detected (9).…”