Reaction Coordinate Leading to H2 Production in [FeFe]-Hydrogenase Identified by Nuclear Resonance Vibrational Spectroscopy and Density Functional Theory

Crystallographic and spectroscopic assignment of the proton transfer pathway in [FeFe]-hydrogenases

The unmatched catalytic turnover rates of [FeFe]-hydrogenases require an exceptionally efficient proton-transfer (PT) pathway to shuttle protons as substrates or products between bulk water and catalytic center. For clostridial [FeFe]-hydrogenase CpI such a pathway has been proposed and analyzed, but mainly on a theoretical basis. Here, eleven enzyme variants of two different [FeFe]-hydrogenases (CpI and HydA1) with substitutions in the presumptive PT-pathway are examined kinetically, spectroscopically, and crystallographically to provide solid experimental proof for its role in hydrogen-turnover. Targeting key residues of the PT-pathway by site directed mutagenesis significantly alters the pH-activity profile of these variants and in presence of H₂ their cofactor is trapped in an intermediate state indicative of precluded proton-transfer. Furthermore, crystal structures coherently explain the individual levels of residual activity, demonstrating e.g. how trapped H₂O molecules rescue the interrupted PT-pathway. These features provide conclusive evidence that the targeted positions are indeed vital for catalytic proton-transfer.

[FeFe]-hydrogenases catalyze H₂-evolution and -oxidation at very high turnover-rates. Here the authors provide experimental evidence for the proposed proton-transfer (PT) pathway by kinetically, spectroscopically, and crystallographically characterizing eleven mutants from the two [FeFe]-hydrogenases CpI and HydA1.

The Molecular Proceedings of Biological Hydrogen Turnover

Over the past two decades, the bioinorganic chemistry of hydrogenases has attracted much interest from basic and applied research. Hydrogenases are highly efficient metalloenzymes that catalyze the reversible reduction of protons to molecular hydrogen (H₂) in all domains of life. Their iron- and nickel-based cofactors represent promising blueprints for the design of biomimetic, synthetic catalysts. In this Account, we address the molecular proceedings of hydrogen turnover with [FeFe]-hydrogenases. The active site cofactor of [FeFe]-hydrogenases ("H-cluster") comprises a unique diiron complex linked to a [4Fe-4S] cluster via a single cysteine. Since it was discovered that a synthetic analogue of the diiron site can be incorporated into apoprotein in vitro to yield active enzyme, significant progress has been made toward a comprehensive understanding of hydrogenase catalysis. The diiron site carries three to four carbon monoxide (CO) and two cyanide (CN^-) ligands that give rise to intense infrared (IR) absorption bands. These bands are sensitive reporters of the electron density across the H-cluster, which can be addressed by infrared spectroscopy to follow redox and protonation changes at the cofactor. Synthetic variation of the metal-bridging dithiolate ligand at the diiron site, as well as site-directed mutagenesis of amino acids, provides access to the proton pathways toward the cofactor. Quantum chemical calculations are employed to specifically assign IR bands to vibrational modes of the diatomic ligands and yield refined H-cluster geometries. Here, we provide an overview of recent research on [FeFe]-hydrogenases with emphasis on experimental and computational IR studies. We describe advances in attenuated total reflection Fourier transform infrared spectroscopy (ATR FTIR) and protein film electrochemistry, as well as density functional theory (DFT) calculations. Key cofactor species are discussed in terms of molecular geometry, redox state, and protonation. Isotope editing is introduced as a tool to evaluate the cofactor geometry beyond the limits of protein crystallography. In particular, the role of proton-coupled electron transfer (PCET) in the generation of catalytically relevant redox species is addressed. We propose that site-selective protonation of the H-cluster biases surplus electrons either to the [4Fe-4S] cluster or to the diiron site. Protonation of the [4Fe-4S] cluster prevents premature reduction at the diiron site and stabilizes a reactive, terminal hydride. The observed H-cluster species are assigned to rapid H₂ conversion or to reactions possibly involved in activity regulation and cellular H₂ sensing. In the catalytic cycle of [FeFe]-hydrogenases, an H-cluster geometry is preserved that features a bridging CO ligand. PCET levels the redox potential for two steps of sequential cofactor reduction. The concept of consecutive PCET at a geometrically inert cofactor with tight control of electron and proton localization may inspire the design of a novel generation of biomimetic catalysts for the production of H₂ as a fuel.

Electronic Structure of Two Catalytic States of the [FeFe] Hydrogenase H-Cluster As Probed by Pulse Electron Paramagnetic Resonance Spectroscopy

The active site of the [FeFe] hydrogenase (HydA1), the H-cluster, is a 6-Fe cofactor that contains CO and CN^- ligands. It undergoes several different oxidation and protonation state changes in its catalytic cycle to metabolize H₂. Among them, the well-known H_ox state and the recently identified H_hyd state are thought to be directly involved in H₂ activation and evolution, and they are both EPR active with net spin S = 1/2. Herein, we report the pulse electronic paramagnetic spectroscopic investigation of these two catalytic states in Chlamydomonas reinhardtii HydA1 ( CrHydA1). Using an in vitro biosynthetic maturation approach, we site-specifically installed ¹³C into the CO or CN^- ligands and ⁵⁷Fe into the [2Fe]_H subcluster of the H-cluster in order to measure the hyperfine couplings to these magnetic nuclei. For H_ox, we measured ¹³C hyperfine couplings (¹³CO a_iso of 25.5, 5.8, and 4.5 MHz) corresponding to all three CO ligands in the H-cluster. We also observed two ⁵⁷Fe hyperfine couplings (⁵⁷Fe a_iso of ∼17 and 5.7 MHz) arising from the two Fe atoms in the [2Fe]_H subcluster. For H_hyd, we only observed two distinct ¹³CO hyperfine interactions (¹³CO a_iso of 0.16 and 0.08 MHz) and only one for ¹³CN^- (¹³CN a_iso of 0.16 MHz); the couplings to the ¹³CO/¹³CN^- on the distal Fe of [2Fe]_H may be too small to detect. We also observed a very small (<0.3 MHz) ⁵⁷Fe HFI from the labeled [2Fe]_H subcluster and four ⁵⁷Fe HFI from the labeled [4Fe-4S]_H subcluster (⁵⁷Fe a_iso of 7.2, 16.6, 28.2, and 35.3 MHz). These hyperfine coupling constants are consistent with the previously proposed electronic structure of the H-cluster at both H_ox and H_hyd states and provide a basis for more detailed analysis.

Terminal Hydride Species in [FeFe]-Hydrogenases Are Vibrationally Coupled to the Active Site Environment

A combination of nuclear resonance vibrational spectroscopy (NRVS), FTIR spectroscopy, and DFT calculations was used to observe and characterize Fe-H/D bending modes in CrHydA1 [FeFe]-hydrogenase Cys-to-Ser variant C169S. Mutagenesis of cysteine to serine at position 169 changes the functional group adjacent to the H-cluster from a -SH to -OH, thus altering the proton transfer pathway. The catalytic activity of C169S is significantly reduced compared to that of native CrHydA1, presumably owing to less efficient proton transfer to the H-cluster. This mutation enabled effective capture of a hydride/deuteride intermediate and facilitated direct detection of the Fe-H/D normal modes. We observed a significant shift to higher frequency in an Fe-H bending mode of the C169S variant, as compared to previous findings with reconstituted native and oxadithiolate (ODT)-substituted CrHydA1. On the basis of DFT calculations, we propose that this shift is caused by the stronger interaction of the -OH group of C169S with the bridgehead -NH- moiety of the active site, as compared to that of the -SH group of C169 in the native enzyme.

Sulfide Protects [FeFe] Hydrogenases From O2

[FeFe] hydrogenases catalyze proton reduction and hydrogen oxidation with high rates and efficiency under physiological conditions, but are highly oxygen sensitive. The [FeFe] hydrogenase from Desulfovibrio desulfuricans ( DdHydAB) can be purified under air in an oxygen stable inactive state H_ox^air. The formation of the H_ox^air state in vitro allows the handling of hydrogenases in air, making their implementation in biotechnological applications more feasible. Here, we report a simple and robust protocol for the formation of the H_ox^air state in DdHydAB and the [FeFe] hydrogenase from Chlamydomonas reinhardtii, which is based on high potential inactivation in the presence of sulfide.

High-Frequency Fe-H Vibrations in a Bridging Hydride Complex Characterized by NRVS and DFT

High-spin iron species with bridging hydrides have been detected in species trapped during nitrogenase catalysis, but there are few general methods of evaluating Fe-H bonds in high-spin multinuclear iron systems. An ⁵⁷ Fe nuclear resonance vibrational spectroscopy (NRVS) study on an Fe(μ-H)₂ Fe model complex reveals Fe-H stretching vibrations for bridging hydrides at frequencies greater than 1200 cm^-1 . These isotope-sensitive vibrational bands are not evident in infrared (IR) spectra, showing the power of NRVS for identifying hydrides in this high-spin iron system. Complementary density functional theory (DFT) calculations elucidate the normal modes of the rhomboidal iron hydride core.

CO-Bridged H-Cluster Intermediates in the Catalytic Mechanism of [FeFe]-Hydrogenase CaI

The [FeFe]-hydrogenases ([FeFe] H₂ases) catalyze reversible H₂ activation at the H-cluster, which is composed of a [4Fe-4S]_H subsite linked by a cysteine thiolate to a bridged, organometallic [2Fe-2S] ([2Fe]_H) subsite. Profoundly different geometric models of the H-cluster redox states that orchestrate the electron/proton transfer steps of H₂ bond activation have been proposed. We have examined this question in the [FeFe] H₂ase I from Clostridium acetobutylicum (CaI) by Fourier-transform infrared (FTIR) spectroscopy with temperature annealing and H/D isotope exchange to identify the relevant redox states and define catalytic transitions. One-electron reduction of H_ox led to formation of H_redH⁺ ([4Fe-4S]_H²⁺-Fe^I-Fe^I) and H_red' ([4Fe-4S]_H¹⁺-Fe^II-Fe^I), with both states characterized by low frequency μ-CO IR modes consistent with a fully bridged [2Fe]_H. Similar μ-CO IR modes were also identified for H_redH⁺ of the [FeFe] H₂ase from Chlamydomonas reinhardtii (CrHydA1). The CaI proton-transfer variant C298S showed enrichment of an H/D isotope-sensitive μ-CO mode, a component of the hydride bound H-cluster IR signal, H_hyd. Equilibrating CaI with increasing amounts of NaDT, and probed at cryogenic temperatures, showed H_redH⁺ was converted to H_hyd. Over an increasing temperature range from 10 to 260 K catalytic turnover led to loss of H_hyd and appearance of H_ox, consistent with enzymatic turnover and H₂ formation. The results show for CaI that the μ-CO of [2Fe]_H remains bridging for all of the "H_red" states and that H_redH⁺ is on pathway to H_hyd and H₂ evolution in the catalytic mechanism. These results provide a blueprint for designing small molecule catalytic analogs.

Spectroscopic investigations of a semi-synthetic [FeFe] hydrogenase with propane di-selenol as bridging ligand in the binuclear subsite: comparison to the wild type and propane di-thiol variants

[FeFe] Hydrogenases catalyze the reversible conversion of H₂ into electrons and protons. Their catalytic site, the H-cluster, contains a generic [4Fe–4S]_H cluster coupled to a [2Fe]_H subsite [Fe₂(ADT)(CO)₃(CN)₂]²⁻, ADT = µ(SCH₂)₂NH. Heterologously expressed [FeFe] hydrogenases (apo-hydrogenase) lack the [2Fe]_H unit, but this can be incorporated through artificial maturation with a synthetic precursor [Fe₂(ADT)(CO)₄(CN)₂]²⁻. Maturation with a [2Fe] complex in which the essential ADT amine moiety has been replaced by CH₂ (PDT = propane-dithiolate) results in a low activity enzyme with structural and spectroscopic properties similar to those of the native enzyme, but with simplified redox behavior. Here, we study the effect of sulfur-to-selenium (S-to-Se) substitution in the bridging PDT ligand incorporated in the [FeFe] hydrogenase HydA1 from Chlamydomonas reinhardtii using magnetic resonance (EPR, NMR), FTIR and spectroelectrochemistry. The resulting HydA1-PDSe enzyme shows the same redox behavior as the parent HydA1-PDT. In addition, a state is observed in which extraneous CO is bound to the open coordination site of the [2Fe]_H unit. This state was previously observed only in the native enzyme HydA1-ADT and not in HydA1-PDT. The spectroscopic features and redox behavior of HydA1-PDSe, resulting from maturation with [Fe₂(PDSe)(CO)₄(CN)₂]²⁻, are discussed in terms of spin and charge density shifts and provide interesting insight into the electronic structure of the H-cluster. We also studied the effect of S-to-Se substitution in the [4Fe–4S] subcluster. The reduced form of HydA1 containing only the [4Fe–4Se]_H cluster shows a characteristic S = 7/2 spin state which converts back into the S = 1/2 spin state upon maturation with a [2Fe]–PDT/ADT complex.

A [RuRu] Analogue of an [FeFe]-Hydrogenase Traps the Key Hydride Intermediate of the Catalytic Cycle

The active site of the [FeFe]-hydrogenases features a binuclear [2Fe]_H sub-cluster that contains a unique bridging amine moiety close to an exposed iron center. Heterolytic splitting of H₂ results in the formation of a transient terminal hydride at this iron site, which, however is difficult to stabilize. We show that the hydride intermediate forms immediately when [2Fe]_H is replaced with [2Ru]_H analogues through artificial maturation. Outside the protein, the [2Ru]_H analogues form bridging hydrides, which rearrange to terminal hydrides after insertion into the apo-protein. H/D exchange of the hydride only occurs for [2Ru]_H analogues containing the bridging amine moiety.

Direct Detection of the Terminal Hydride Intermediate in [FeFe] Hydrogenase by NMR Spectroscopy

Hydride state intermediates are known to occur in various hydrogen conversion enzymes, including the highly efficient [FeFe] hydrogenases. The intermediate state involving a terminal iron-bound hydride has been recognized as crucial for the catalytic mechanism, but its occurrence has up to now eluded unequivocal proof under (near) physiological conditions. Here we show that the terminal hydride in the [FeFe] hydrogenase from Chlamydomonas reinhardtii can be directly detected using solution ¹H NMR spectroscopy at room temperature, opening new avenues for detailed in situ investigations under catalytic conditions.

Sterically Stabilized Terminal Hydride of a Diiron Dithiolate

The kinetically robust hydride [t-HFe₂(Me₂pdt)(CO)₂(dppv)₂]⁺ ([t-H1]⁺) (Me₂pdt^2- = Me₂C(CH₂S^-)₂; dppv = cis-1,2-C₂H₂(PPh₂)₂) and related derivatives were prepared with ⁵⁷Fe enrichment for characterization by NMR, FT-IR, and NRVS. The experimental results were rationalized using DFT molecular modeling and spectral simulations. The spectroscopic analysis was aimed at supporting assignments of Fe-H vibrational spectra as they relate to recent measurements on [FeFe]-hydrogenase enzymes. The combination of bulky Me₂pdt^2- and dppv ligands stabilizes the terminal hydride with respect to its isomerization to the 5-16 kcal/mol more stable bridging hydride ([μ-H1]⁺) with t_1/2(313.3 K) = 19.3 min. In agreement with the nOe experiments, the calculations predict that one methyl group in [t-H1]⁺ interacts with the hydride with a computed CH···HFe distance of 1.7 Å. Although [t-H⁵⁷1]⁺ exhibits multiple NRVS features in the 720-800 cm^-1 region containing the bending Fe-H modes, the deuterated [t-D⁵⁷1]⁺ sample exhibits a unique Fe-D/CO band at ∼600 cm^-1. In contrast, the NRVS spectra for [μ-H⁵⁷1]⁺ exhibit weaker bands near 670-700 cm^-1 produced by the Fe-H-Fe wagging modes coupled to Me₂pdt^2- and dppv motions.

1H NMR Spectroscopy of [FeFe] Hydrogenase: Insight into the Electronic Structure of the Active Site

The [FeFe] hydrogenase HydA1 from Chlamydomonas reinhardtii has been studied using ¹H NMR spectroscopy identifying the paramagnetically shifted ¹H resonances associated with both the [4Fe-4S]_H and the [2Fe]_H subclusters of the active site “H-cluster”. The signal pattern of the unmaturated HydA1 containing only [4Fe-4S]_H is reminiscent of bacterial-type ferredoxins. The spectra of maturated HydA1, with a complete H-cluster in the active H_ox and the CO-inhibited H_ox–CO state, reveal additional upfield and downfield shifted ¹H resonances originating from the four methylene protons of the azadithiolate ligand in the [2Fe]_H subsite. The two axial protons are affected by positive spin density, while the two equatorial protons experience negative spin density. These protons can be used as important probes sensing the effects of ligand-binding to the catalytic site of the H-cluster.

[FeFe]-Hydrogenases: recent developments and future perspectives

[FeFe]-Hydrogenases are the most efficient enzymes for catalytic hydrogen turnover.