Hydride bridge in [NiFe]-hydrogenase observed by nuclear resonance vibrational spectroscopy

Abstract

The metabolism of many anaerobes relies on [NiFe]-hydrogenases, whose characterization when bound to substrates has proven non-trivial. Presented here is direct evidence for a hydride bridge in the active site of the 57Fe-labeled fully reduced Ni-R form of Desulfovibrio vulgaris Miyazaki F (DvMF) [NiFe]-hydrogenase. A unique ‘wagging’ mode involving H− motion perpendicular to the Ni(μ-H)57Fe plane was studied using 57Fe-specific nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations. Upon Ni(μ-D)57Fe deuteride substitution, this wagging causes a characteristic perturbation of Fe–CO/CN bands. Spectra have been interpreted by comparison with Ni(μ-H/D)57Fe enzyme mimics [(dppe)Ni(μ-pdt)(μ-H/D)57Fe(CO)3]+ and DFT calculations, which collectively indicate a low-spin Ni(II)(μ-H)Fe(II) core for Ni-R, with H− binding Ni more tightly than Fe. The present methodology is also relevant to characterizing Fe–H moieties in other important natural and synthetic catalysts.

Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides

“…On the other hand, high energy vibrations, such as M–H/D stretches, see the metal move only very slightly, as the mass of M is large relative to that of H or D. Pure ν MH modes are thus difficult—although not impossible—to observe. 103 …”

“…89 The hydrido binds Ni (1.58 Å) somewhat tighter than Fe (1.78 Å), and its presence has since been verified by 57 Fe NRVS, with the observation of a characteristic δ NiHFe bending vibration at 675 cm −1 . 103,312 …”

NRVS for Fe in Biology: Experiment and Basic Interpretation

“…Besides non-Rieske [2Fe2S] 22 and [3Fe4S] 23 proteins and [4Fe4S] 24 proteins, It is important to note that 57 Fe NRVS has been expanded to study electron transfer in larger enzymes and their catalytic metallocofactors such as (but not comprehensively) the NiFe site in [NiFe] hydrogenase, 3, 25–26 the diiron site in [FeFe] hydrogenase, 27–28 the P [8Fe7S]- and M [7Fe9SMo]- clusters of Mo-Nitrogenase, 29–32 heme systems, 33–34 non-heme systems, 35–36 and nitric-oxide sensing [4Fe4S] clusters. 37 Further as the systems of interest have become more complicated, with multiple FeS clusters of differing composition, innovative strategies of site-specific 57 Fe labeling have been implemented that target maturation 28 or a modified cofactor insertion.…”

“…As such, the extreme specificity of 57 Fe NRVS for only 57 Fe motion, makes the perfect tool to study vibrational dynamics of the critical Fe-containing components of the biomolecule. Without contribution from the biological sample background, NRVS enjoys very little spectroscopic noise, even modes of Fe hydrides within enzymes 3–4 have been observed – which are typically difficult to directly identify with other techniques. 5–6 The selection rules – or comparatively lack thereof – allows for 57 Fe NRVS to reveal both IR- and Raman- active modes that contain 57 Fe motion – thus providing a complete picture for Fe vibration.…”

Chemical energy storage: Part of a systemic solution

“…The exact nature [12] of the separation of charges and ions is different in these devices. We have learned much about the way in which nature does this reaction during photosynthesis [13] and we can use this knowledge for designing technical devices. We have to abstain from the idea to copy the biological process as it is way too complex for technical realization and it is also not efficient enough on the basis of hydrogen production per catalyst atom: the used enzymes are extremely complex and require continuous self-repair to remain operational.…”