Resonance Raman Spectroscopy as a Tool to Monitor the Active Site of Hydrogenases

Siebert, Elisabeth; Horch, Marius; Rippers, Yvonne; Fritsch, Johannes; Frielingsdorf, Stefan; Lenz, Oliver; Escobar, Francisco Velázquez; Siebert, Friedrich; Paasche, Lars; Kuhlmann, Uwe; Lendzian, Friedhelm; Mroginski, Maria‐Andrea; Zebger, Ingo; Hildebrandt, Peter

doi:10.1002/anie.201209732

Cited by 60 publications

(112 citation statements)

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“…Trace G shows a spectrum of a H 2 -reduced single MBH crystal for comparison. 15 The Journal of Physical Chemistry B Article even crystals of the as-isolated MBH seem to contain minor contributions from the Ni-L state, recently detected to be photochemically formed in RR experiments of H 2 -reduced MBH crystals. 15 This raises the question of the origin of the electrons required for the corresponding reduction of the asisolated MBH.…”

Section: Articlementioning

confidence: 92%

“…As shown previously, the RR spectrum of the H 2 -reduced [NiFe] active site almost exclusively represents the Ni-L state, which is formed photochemically in the course of the RR experiment (Figure 1). 15 The QM model for the Ni-L state of the [NiFe] active site includes the [NiFe] center, the CN − and CO ligands, and the coordinating cysteine residues (75, 78, 597, and 600), with Cys597 being protonated. 15 Furthermore, the model comprises the adjacent amino acids Arg530, Thr553, and His82 ( Figure S2).…”

Section: The Journal Of Physical Chemistry Bmentioning

confidence: 99%

“…15 The QM model for the Ni-L state of the [NiFe] active site includes the [NiFe] center, the CN − and CO ligands, and the coordinating cysteine residues (75, 78, 597, and 600), with Cys597 being protonated. 15 Furthermore, the model comprises the adjacent amino acids Arg530, Thr553, and His82 ( Figure S2). Taking into account that the resonance enhancement is derived from the Fe → CO metal-to-ligand charge-transfer transition, Raman intensities of the individual modes were scaled according to the contributions from the Fe−CO stretching and bending coordinates as described previously.…”

Section: The Journal Of Physical Chemistry Bmentioning

confidence: 99%

“…Despite a low resonance enhancement, RR bands of modes including Fe−CO and Fe− OH coordinates have been observed for the H 2 -reduced [NiFe] center and the superoxidized [4Fe-3S] 5+ cluster of the MBH, respectively. 6,15 The corresponding Fe−CO and Fe−CN modes were identified also for the oxidized and reduced [NiFe] active site of the regulatory hydrogenase (RH) from R. eutropha. 16 All these modes are located in the same frequency range between 450 and 650 cm −1 , and this holds true for all detectable redox states of the active site.…”

Section: ■ Introductionmentioning

confidence: 99%

“…The comparison of experimental RR spectra with calculated spectra, obtained by quantum mechanics/molecular mechanics (QM/ MM) hybrid methods, allows for a reliable determination of the structure and electronic configuration of various cofactor states and may further support a structural refinement of the crystallographic models. 15 ■ MATERIALS AND METHODS Materials. Purification of the heterodimeric MBH from R. eutropha H16 has been described previously.…”

Section: ■ Introductionmentioning

confidence: 99%

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Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O₂-Tolerant Membrane-Bound Hydrogenase in the Crystalline State

et al. 2015

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We have applied resonance Raman (RR) spectroscopy on single protein crystals of the O2-tolerant membrane-bound [NiFe] hydrogenase (MBH from Ralstonia eutropha) which catalyzes the splitting of H2 into protons and electrons. RR spectra taken from 65 MBH samples in different redox states were analyzed in terms of the respective component spectra of the active site and the unprecedented proximal [4Fe-3S] cluster using a combination of statistical methods and global fitting procedures. These component spectra of the individual cofactors were compared with calculated spectra obtained by quantum mechanics/molecular mechanics (QM/MM) methods. Thus, the recently discovered hydroxyl-coordination of one iron in the [4Fe-3S] cluster was confirmed. Infrared (IR) microscopy of oxidized MBH crystals revealed the [NiFe] active site to be in the Nir-B [Ni(III)] and Nir-S [Ni(II)] states, whereas RR measurements of these crystals uncovered the Nia-S [Ni(II)] state as the main spectral component, suggesting its in situ formation via photodissociation of the assumed bridging hydroxyl or water ligand. On the basis of QM/MM calculations, individual band frequencies could be correlated with structural parameters for the Nia-S state as well as for the Ni-L state, which is formed upon photodissociation of the bridging hydride of H2-reduced active site states.

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Section: Articlementioning

confidence: 92%

Section: The Journal Of Physical Chemistry Bmentioning

confidence: 99%

Section: The Journal Of Physical Chemistry Bmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O₂-Tolerant Membrane-Bound Hydrogenase in the Crystalline State

et al. 2015

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NAD ⁺ ‐Reducing [ NiFe ]‐Hydrogenase

Shomura

Higuchi

2019

Encyclopedia of Inorganic and Bioinorganic Chemistry

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Hydrogenases catalyze the decomposition and synthesis of molecular hydrogen (H 2 ) and play crucial roles in microbial H 2 metabolism. They are divided into evolutionarily independent three classes based on the metal content of the active sites: the [Fe]‐, [FeFe]‐, and [NiFe]‐hydrogenases. The NAD + ‐reducing [NiFe]‐hydrogenases contain the Ni–Fe cluster at the active site in the heterodimeric hydrogenase unit, HoxHY, which forms a complex with the heterodimeric NADH diaphorase unit, HoxFU, harboring FMN as a cofactor for the oxidation and reduction of pyridine nucleotides. The members from photosynthetic bacteria and Geobacter spp. further contain the HoxE subunit as a component of the diaphorase unit, which is termed the heteropentamer types. The active sites of the hydrogenase in HoxH and the diaphorase in HoxF are connected via several Fe–S clusters for electron transfer.

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Computational Insights into the Reaction Mechanisms of Nickel‐Catalyzed Hydrofunctionalizations and Nickel‐Dependent Enzymes

Zhang

Chung

2018

Asian J Org Chem

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For several decades, transition-metal catalysis has been ap opular methodf or many functional group transformations in organicc hemistry.R ecent developments in sustainability and applicationso fe arth-abundant metals have resulted in as ynthetic renaissance and have attracted considerable interest in less toxic and inexpensive first-row transition-metal catalysts such as nickel. Herein, we highlight some recent computationali nsights into the reactionm ech-anismso fN i-catalyzed hydrofunctionalizations (i.e.,h ydrogenation,h ydrovinylation, hydroacylation, hydroheteroarylation, hydrosilylation, and hydroalkoxylation) and Ni-dependent enzymes (i.e.,l actater acemase, methyl-CoM reductase, and [NiFe]-hydrogenase). These computational studies provide insightsi nto these reactionm echanisms and thus assist in the developmentand design of sustainable catalysts.Scheme3.Ni-catalyzed asymmetric hydrogenationofb-amino nitroolefins (TFE = 2,2,2-trifluoroethanol, TON = turnover number).Scheme4.Computedf avorable catalytic cycle for the Ni-catalyzed asymmetric hydrogenation in the presence of the (S)-binapine ligand. Relative Gibbs free energy valuesare shown.Scheme5.Computedf ree energies of proposed key catalyticcycle for the Ni-catalyzed hydrogenation in the presence of ad imeric Ni speciesa nd the (S)-binapine ligand (only the key transition states were computed).Scheme6.[Si II (Xant)Si II ]Ni(h 2 -1,3-cod)-catalyzedolefin hydrogenation.Scheme20. The proposed proton-coupled electron transfer mechanism for lactate racemization (see Ref.[35]). Scheme21. (a) Methane formation reaction catalyzed by MCR and (b) the active-site structure of F 430 .Scheme22. Different proposed mechanisms for methanef ormation catalyzed by MCR (see Ref. [49]).

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Resonance Raman Spectroscopy as a Tool to Monitor the Active Site of Hydrogenases

Cited by 60 publications

References 20 publications

Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O₂-Tolerant Membrane-Bound Hydrogenase in the Crystalline State

Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O₂-Tolerant Membrane-Bound Hydrogenase in the Crystalline State

NAD ⁺ ‐Reducing [ NiFe ]‐Hydrogenase

Computational Insights into the Reaction Mechanisms of Nickel‐Catalyzed Hydrofunctionalizations and Nickel‐Dependent Enzymes

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Resonance Raman Spectroscopy as a Tool to Monitor the Active Site of Hydrogenases

Cited by 60 publications

References 20 publications

Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O2-Tolerant Membrane-Bound Hydrogenase in the Crystalline State

Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O2-Tolerant Membrane-Bound Hydrogenase in the Crystalline State

NAD + ‐Reducing [ NiFe ]‐Hydrogenase

Computational Insights into the Reaction Mechanisms of Nickel‐Catalyzed Hydrofunctionalizations and Nickel‐Dependent Enzymes

Contact Info

Product

Resources

About

Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O₂-Tolerant Membrane-Bound Hydrogenase in the Crystalline State

Resonance Raman Spectroscopic Analysis of the [NiFe] Active Site and the Proximal [4Fe-3S] Cluster of an O₂-Tolerant Membrane-Bound Hydrogenase in the Crystalline State

NAD ⁺ ‐Reducing [ NiFe ]‐Hydrogenase