Reversible or Irreversible Catalysis of H+/H2 Conversion by FeFe Hydrogenases

Indications for a universal hydrogen catalysis mechanism in [FeFe]-hydrogenases of different phylogenetic groups

[FeFe]-hydrogenases are metalloenzymes catalysing bidirectional hydrogen (H2) turnover. These enzymes are generally considered to be extremely efficient and fast catalysts. However, [FeFe]-hydrogenases constitute a very diverse enzyme family that can be divided into several distinct phylogenetic groups, denoted as groups A-G. Very little is known about the properties of [FeFe]-hydrogenases outside of the intensively studied group A, but recent studies on putatively sensory group C and D enzymes have revealed distinct differences in reactivity. The variation in structure, reactivity and physiological function observed between phylogenetic groups raises the question if all [FeFe]-hydrogenases follow the same mechanism for H2 turnover. Here, we provide the first detailed spectroscopic investigation of a slow-acting putatively sensory group D [FeFe]-hydrogenase from Thermoanaerobacter mathranii (TamHydS). Photo-reduction enabled us to characterize redox states in group D [FeFe]-hydrogenase via infrared spectroscopy under catalytic conditions. The sequential population of redox states similar to group A [FeFe]-hydrogenases supports the notion that group A and D [FeFe]-hydrogenases follow a universal catalytic mechanism. However, clear differences between enzymes from different phylogenetic groups become evident when comparing the relative stability and protonation state of suggested key catalytic intermediates. Moreover, the spectroscopic data collected on TamHydS provides new insight into the structure of the reduced active site, lending further support for the notion of a retained bridging CO ligand throughout the entire catalytic cycle.

Protein Dynamics Affect O2-Stability of Group B [FeFe]-Hydrogenase from Thermosediminibacter oceani

In the pursuit of sustainable "green" energy generation, [FeFe]-hydrogenases have attracted significant attention due to their ability to catalyze hydrogen production. However, the sensitivity of these enzymes to O2 is a major obstacle for their application as biocatalysts in energy conversion technologies. In the search for an O2-stable [FeFe]-hydrogenase, we identified the hydrogenase ToHydA from Thermosediminibacter oceani that belongs to the rarely characterized Group B (M2a) [FeFe]-hydrogenases. Our findings demonstrate that ToHydA exhibits remarkable O2-stability, even under prolonged O2 exposure. By characterizing site-directed mutagenesis variants, we found that the highly conserved proton-transporting active site cysteine residue protects the H-cluster from O2-induced degradation by forming the Hinact state. The additional cysteine residue in the TSCCCP motif of ToHydA, a feature unique to Group B (M2a) [FeFe]-hydrogenases, enhances the flexibility of that motif and facilitates the formation of the Hinact state. Moreover, ToHydA possesses unique features, including the formation of an unusual Hinact resting state that distinguishes the enzyme from other [FeFe]-hydrogenases. Our atomistic molecular dynamics simulations reveal a previously unrecognized cluster of hydrophobic residues centered around the proton-transporting cysteine-bearing loop. This structural feature appears to be a common molecular characteristic in hydrogenases that form the O2-protected Hinact state. By exploiting these molecular features of ToHydA, future research can aim to rationally design hydrogenases that combine high catalytic activity with enhanced O2-stability to develop more efficient and durable catalysts.

Probing the ferredoxin:hydrogenase electron transfer complex by infrared difference spectroscopy

Ferredoxins are small iron-sulfur proteins that engage in one-electron transfer with oxidoreductases across all domains of life. The catalyzed reactions often include multiple electrons, e.g., in the two-electron reduction of NADP+ during photosynthesis or the reduction of protons to H2 by the metalloenzyme hydrogenase. To date, the microscopic details of how ferredoxins facilitate multiple electron redox chemistry are unknown. Ferredoxins of the Allochromatium vinosum subfamily contain two [4Fe-4S] clusters, which allows for two one-electron transfer reactions. However, the iron-sulfur clusters of conventional 2[4Fe-4S]-type ferredoxins have very similar reduction potentials and conclusive evidence for the transfer of two electrons during a single protein-protein interaction (PPI) has not been reported. In this work, the electron transfer complexes between the clostridial 2[4Fe-4S] ferredoxin, CpFd, and [FeFe]-hydrogenases from both Clostridium pasteurianum (CpI) and Chlamydomonas reinhardtii (CrHydA), were investigated. Introducing a non-canonical amino acid near to one of the iron-sulfur clusters of CpFd permitted the quantification of electric field changes via the vibrational Stark effect by Fourier-transform infrared (FTIR) spectroscopy. Upon reduction, in situ FTIR difference spectroscopy reported on protein structural changes and microscale thermophoresis revealed that the affinity between ferredoxin and hydrogenase is modulated by redox-dependent PPIs. Prompted by these findings, we suggest a model how ferredoxin efficiently facilitates multiple electron redox chemistry based on individual one-electron transfer reactions.

Initial quality assessment and qualitative interpretation of protein film electrochemistry catalytic data

When a redox enzyme is wired to an electrode under conditions of direct electron transfer (DET), its activity can be simply detected as a current. This approach has been reviewed extensively, but here we address a gap in the literature by discussing the initial qualitative interpretation and assessment of catalytic DET electrochemical data. Topics addressed here include electroactive coverage, turnover frequencies, mass transport limitations, film loss, redox-driven (in)activation, signal corrections, distinction between steady-state and transient responses, and identification of non-ideal behaviors. Based on our group's expertise, we provide explanations, general advice, and prescriptive guidance to help readers understand experimental issues.

Probing the Influence of the Protein Scaffold on H-Cluster Reactivity via Gain-of-Function Studies─Improved H2 Evolution and O2 Tolerance through Rational Design of [FeFe] Hydrogenase

[FeFe] hydrogenases make up a structurally diverse family of metalloenzymes that catalyze proton/dihydrogen interconversion. They can be classified into phylogenetically distinct groups denoted A-G, which differ in structure and reactivity. Prototypical Group A hydrogenases have high turnover rates and remarkable energy efficiency. As compared to Group A enzymes, the putatively sensory Group D hydrogenase from Thermoanaerobacter mathranii (TamHydS) has a thousand-fold lower H2 evolution rate and a high overpotential requirement to drive catalysis (irreversible) but shows increased inhibitor tolerance. This divergence in structure and activity between hydrogenases makes them ideal models for studying second (active-site environment) and outer (e.g., substrate transport) coordination sphere effects on metal cofactors. Herein, we generated three TamHydS-based variants, each mimicking proposed key structural features of Group A hydrogenase: the "active site" (AS), "proton-transfer pathway" (PTP), and "combined" (CM = AS + PTP) variant. A fourth single-point variant, A137C, which introduces a proposed critical cysteine in the active site, was characterized as a reference. No change in isolation resulted in Group A-like behavior; i.e., no positive impact on catalytic performance was observed. The CM variant, however, showed increased H2 evolution activity but retained the overpotential requirement. Additionally, the CM variant improved the already relatively high stability of TamHydS against O2 and CO inhibition. These findings show that activity rates, (ir)reversibility, and susceptibility to gaseous inhibitors are decoupled. Moreover, the results highlight the importance of exploring hydrogenase diversity as a path toward understanding the structural factors that enable the outstanding catalytic properties of [FeFe] hydrogenases.

Proton Relays in Molecular Catalysis for Hydrogen Evolution and Oxidation: Lessons From the Mimicry of Hydrogenases and Electrochemical Kinetic Analyses

The active sites of metalloenzymes involved in small molecules activation often contain pendant bases that act as proton relay promoting proton-coupled electron-transfer processes. Here we focus on hydrogenases and on the reactions they catalyze, i. e. the hydrogen evolution and oxidation reactions. After a short description of these enzymes, we review some of the various biomimetic and bioinspired molecular systems that contain proton relays. We then provide the formal electrochemical framework required to decipher the key role of such proton relay to enhance catalysis in a single direction and discuss the few systems active for H2 evolution for which quantitative kinetic data are available. We finally highlight key parameters required to reach bidirectional catalysis (both hydrogen evolution and hydrogen oxidation catalyzed) and then transition to reversible catalysis (both reactions catalyzed in a narrow potential range) as well as illustrate these features on few systems from the literature.

The missing pieces in the catalytic cycle of [FeFe] hydrogenases

Hydrogen could provide a suitable means for storing energy from intermittent renewable sources for later use on demand. However, many challenges remain regarding the activity, specificity, stability and sustainability of current hydrogen production and consumption methods. The lack of efficient catalysts based on abundant and sustainable elements lies at the heart of this problem. Nature's solution led to the evolution of hydrogenase enzymes capable of reversible hydrogen conversion at high rates using iron- and nickel-based active sites. Through a detailed understanding of these enzymes, we can learn how to mimic them to engineer a new generation of highly active synthetic catalysts. Incredible progress has been made in our understanding of biological hydrogen activation over the last few years. In particular, detailed studies of the [FeFe] hydrogenase class have provided substantial insight into a sophisticated, optimised, molecular catalyst, the active site H-cluster. In this short perspective, we will summarise recent findings and highlight the missing pieces needed to complete the puzzle.

Oxygen sensitivity of [FeFe]-hydrogenase: a comparative study of active site mimics inside vs. outside the enzyme

[FeFe]-hydrogenase is nature's most efficient proton reducing and H2-oxidizing enzyme. However, biotechnological applications are hampered by the O2 sensitivity of this metalloenzyme, and the mechanism of aerobic deactivation is not well understood. Here, we explore the oxygen sensitivity of four mimics of the organometallic active site cofactor of [FeFe]-hydrogenase, [Fe2(adt)(CO)6-x(CN)x]x- and [Fe2(pdt)(CO)6-x(CN)x]x- (x = 1, 2) as well as the corresponding cofactor variants of the enzyme by means of infrared, Mössbauer, and NMR spectroscopy. Additionally, we describe a straightforward synthetic recipe for the active site precursor complex Fe2(adt)(CO)6. Our data indicate that the aminodithiolate (adt) complex, which is the synthetic precursor of the natural active site cofactor, is most oxygen sensitive. This observation highlights the significance of proton transfer in aerobic deactivation, and supported by DFT calculations facilitates an identification of the responsible reactive oxygen species (ROS). Moreover, we show that the ligand environment of the iron ions critically influences the reactivity with O2 and ROS like superoxide and H2O2 as the oxygen sensitivity increases with the exchange of ligands from CO to CN-. The trends in aerobic deactivation observed for the model complexes are in line with the respective enzyme variants. Based on experimental and computational data, a model for the initial reaction of [FeFe]-hydrogenase with O2 is developed. Our study underscores the relevance of model systems in understanding biocatalysis and validates their potential as important tools for elucidating the chemistry of oxygen-induced deactivation of [FeFe]-hydrogenase.

Superior electrocatalytic hydrogen evolution activity of a triply bridged diruthenium(II) complex on a carbon cloth support

This article describes the structural authentication of a unique triply bridged [1](ClO4)2 and monomeric [2]ClO4/[3]ClO4. Electrochemical HER on a carbon cloth support demonstrated the superior performance of [1](ClO4)2 with high TON (>105) and its long-term stability. The primary kinetic isotope effect of [1](ClO4)2 revealed the involvement of PCET in the rate-determining step.

Outer-sphere effects on the O2 sensitivity, catalytic bias and catalytic reversibility of hydrogenases

The comparison of homologous metalloenzymes, in which the same inorganic active site is surrounded by a variable protein matrix, has demonstrated that residues that are remote from the active site may have a great influence on catalytic properties. In this review, we summarise recent findings on the diverse molecular mechanisms by which the protein matrix may define the oxygen tolerance, catalytic directionality and catalytic reversibility of hydrogenases, enzymes that catalyse the oxidation and evolution of H2. These mechanisms involve residues in the second coordination sphere of the active site metal ion, more distant residues affecting protein flexibility through their side chains, residues lining the gas channel and even accessory subunits. Such long-distance effects, which contribute to making enzymes efficient, robust and different from one another, are a source of wonder for biochemists and a challenge for synthetic bioinorganic chemists.

Cable Bacteria Skeletons as Catalytically Active Electrodes

Cable bacteria are multicellular, filamentous bacteria that use internal conductive fibers to transfer electrons over centimeter distances from donors within anoxic sediment layers to oxygen at the surface. We extracted the fibers and used them as free-standing bio-based electrodes to investigate their electrocatalytic behavior. The fibers catalyzed the reversible interconversion of oxygen and water, and an electric current was running through the fibers even when the potential difference was generated solely by a gradient of oxygen concentration. Oxygen reduction as well as oxygen evolution were confirmed by optical measurements. Within living cable bacteria, oxygen reduction by direct electrocatalysis on the fibers and not by membrane-bound proteins readily explains exceptionally high cell-specific oxygen consumption rates observed in the oxic zone, while electrocatalytic water oxidation may provide oxygen to cells in the anoxic zone.

Kinetic modeling of 2e-/1H+ and 2e-/2H+ bidirectional catalytic cycles

When a redox enzyme or synthetic catalyst is interfaced with an electrode, the electrochemical response depends on the details of the catalytic cycle. Here we focus on the steady-state catalytic waveshape of enzymes such as formate dehydrogenase (2e-/1H+), hydrogenases (2e-/2H+) and other bidirectional molecular catalysts that can be adsorbed on, and undergo direct electron transfer with an electrode. We seek to examine the relations between the dependence on pH of the waveshape, the sequence of events in the catalytic cycle, and the properties of the catalytic intermediates (their reduction potentials and pKa's). Discussing the interpretation of the dependence on pH of the limiting currents and catalytic potentials in various simple situations leads us to introduce the concept of "catalytic pKa". The reasoning is general and could be used in relation to any bidirectional two-electron catalytic cycle. Understanding what defines and tunes the catalytic potentials will be crucial for the design of reversible catalysts, which operate at a fast rate in either direction in response to even a small overpotential.

The isomer-sensitive electrochemical HER of ruthenium(II)-hydrido complexes involving redox-active azoheteroaromatics

The article deals with the development of isomeric ruthenium(II)-hydrido complexes [RuII(H)(L1)(PPh3)2(CO)]ClO4 ([1a]ClO4-[1b]ClO4)/[RuII(H)(L2)(PPh3)2(CO)]ClO4 ([2a]ClO4-[2b]ClO4) involving azo coupled L1 [L1: (E)-1,2-bis(1-methyl-1H-pyrazol-3-yl)diazene]/L2 [L2: (E)-1,2-bis(4-iodo-1-methyl-1H-pyrazol-3-yl)diazene], respectively. Structural evaluation of the complexes affirmed the syn conformation of the coordinated/uncoordinated pyrazole groups of L and its unperturbed neutral azo (NN) state. Isomeric forms in [1a]ClO4/[1b]ClO4 or [2a]ClO4/[2b]ClO4 differed with respect to the cis and trans orientations of the coordinated CO and N(azo) donor of L, respectively. It also demonstrated the formation of intermolecular hydrogen-bonded dimeric or 1D-polymeric chains in [1a]ClO4/[2b]ClO4 or [1b]ClO4, respectively. Successive two-electron reductions of the complexes varied to an appreciable extent as a function of the heterocycles connected to L. The involvement of the azo function of L towards the reductions ([NN]0 → [NN]˙- → [NN]2-) was supported by the DFT calculated MOs and Mulliken spin density at the paramagnetic state, which was further validated by the radical EPR profile of the first reduced (S = 1/2) state. Isomeric [1a]ClO4/[1b]ClO4 or [2a]ClO4/[2b]ClO4 immobilised on the carbon cloth support underwent various electrochemical acidic HERs (hydrogen evolution reactions) with TOF/10-1 s-1: [1a]ClO4 (0.83) > [1b]ClO4 (0.68) > [2a]ClO4 (0.50) > [2b]ClO4 (0.37).

Kinetic Modeling of the Reversible or Irreversible Electrochemical Responses of FeFe-Hydrogenases

The enzyme FeFe-hydrogenase catalyzes H2 evolution and oxidation at an active site that consists of a [4Fe-4S] cluster bridged to a [Fe2(CO)3(CN)2(azadithiolate)] subsite. Previous investigations of its mechanism were mostly conducted on a few "prototypical" FeFe-hydrogenases, such as that from Chlamydomonas reinhardtii(Cr HydA1), but atypical hydrogenases have recently been characterized in an effort to explore the diversity of this class of enzymes. We aim at understanding why prototypical hydrogenases are active in either direction of the reaction in response to a small deviation from equilibrium, whereas the homologous enzyme from Thermoanaerobacter mathranii (Tam HydS) shows activity only under conditions of very high driving force, a behavior that was referred to as "irreversible catalysis". We follow up on previous spectroscopic studies and recent developments in the kinetic modeling of bidirectional reactions to investigate and compare the catalytic cycles of Cr HydA1 and Tam HydS under conditions of direct electron transfer with an electrode. We compare the hypothetical catalytic cycles described in the literature, and we show that the observed changes in catalytic activity as a function of potential, pH, and H2 concentration can be explained with the assumption that the same catalytic mechanism applies. This helps us identify which variations in properties of the catalytic intermediates give rise to the distinct "reversible" or "irreversible" catalytic behaviors.

A Chimeric NiFe Hydrogenase Heterodimer to Assess the Role of the Electron Transfer Chain in Tuning the Enzyme's Catalytic Bias and Oxygen Tolerance

The observation that some homologous enzymes have the same active site but very different catalytic properties demonstrates the importance of long-range effects in enzyme catalysis, but these effects are often difficult to rationalize. The NiFe hydrogenases 1 and 2 (Hyd 1 and Hyd 2) from E. coli both consist of a large catalytic subunit that embeds the same dinuclear active site and a small electron-transfer subunit with a chain of three FeS clusters. Hyd 1 is mostly active in H2 oxidation and resistant to inhibitors, whereas Hyd 2 also catalyzes H2 production and is strongly inhibited by O2 and CO. Based on structural and site-directed mutagenesis data, it is currently believed that the catalytic bias and tolerance to O2 of Hyd 1 are defined by the distal and proximal FeS clusters, respectively. To test these hypotheses, we produced and characterized a hybrid enzyme made of the catalytic subunit of Hyd 1 and the electron transfer subunit of Hyd 2. We conclude that catalytic bias and sensitivity to CO are set by the catalytic subunit rather than by the electron transfer chain. We confirm the importance of the proximal cluster in making the enzyme Hyd 1 resist long-term exposure to O2, but we show that other structural determinants, in both subunits, contribute to O2 tolerance. A similar strategy based on the design of chimeric heterodimers could be used in the future to elucidate various structure-function relationships in hydrogenases and other multimeric metalloenzymes and to engineer useful hydrogenases that combine the desirable properties of distinct, homologous enzymes.

Deciphering Reversible Homogeneous Catalysis of the Electrochemical H2 Evolution and Oxidation: Role of Proton Relays and Local Concentration Effects

Nickel bisdiphosphine complexes bearing pendant amines form a unique series of catalysts (so-called DuBois' catalysts) capable of bidirectional/reversible electrocatalytic oxidation and production of dihydrogen. This unique behaviour is directly linked to the presence of proton relays installed close to the metal center. We report here for the arginine derivative [Ni(P2 Cy N2 Arg )2 ]6+ on a mechanistic model and its kinetic treatment that may apply to all DuBois' catalysts and show that it allows for a good fit of experimental data measured at different pH values, catalyst concentrations and partial hydrogen pressures. The bidirectionality of catalysis results from balanced equilibria related to hydrogen uptake/evolution on one side and (metal)-hydride installation/capture on the other side, both controlled by concentration effects resulting from the presence of proton relays and connected by two square schemes corresponding to proton-coupled electron transfer processes. We show that the catalytic bias is controlled by the kinetic of the H2 uptake/evolution step. Reversibility does not require that the energy landscape be flat, with redox transitions occurring at potentials up to 250 mV away for the equilibrium potential, although such large deviations from a flat energy landscape can negatively impacts the rate of catalysis when coupled with slow interfacial electron transfer kinetics.

Probing Substrate Transport Effects on Enzymatic Hydrogen Catalysis: An Alternative Proton Transfer Pathway in Putatively Sensory [FeFe] Hydrogenase

[FeFe] hydrogenases, metalloenzymes catalyzing proton/dihydrogen interconversion, have attracted intense attention due to their remarkable catalytic properties and (bio-)technological potential for a future hydrogen economy. In order to unravel the factors enabling their efficient catalysis, both their unique organometallic cofactors and protein structural features, i.e., "outer-coordination sphere" effects have been intensively studied. These structurally diverse enzymes are divided into distinct phylogenetic groups, denoted as Group A-D. Prototypical Group A hydrogenases display high turnover rates (104-105 s-1). Conversely, the sole characterized Group D representative, Thermoanaerobacter mathranii HydS (TamHydS), shows relatively low catalytic activity (specific activity 10-1 μmol H2 mg-1 min-1) and has been proposed to serve a H2-sensory function. The various groups of [FeFe] hydrogenase share the same catalytic cofactor, the H-cluster, and the structural factors causing the diverging reactivities of Group A and D remain to be elucidated. In the case of the highly active Group A enzymes, a well-defined proton transfer pathway (PTP) has been identified, which shuttles H+ between the enzyme surface and the active site. In Group D hydrogenases, this conserved pathway is absent. Here, we report on the identification of highly conserved amino acid residues in Group D hydrogenases that constitute a possible alternative PTP. We varied two proposed key amino acid residues of this pathway (E252 and E289, TamHydS numbering) via site-directed mutagenesis and analyzed the resulting variants via biochemical and spectroscopic methods. All variants displayed significantly decreased H2-evolution and -oxidation activities. Additionally, the variants showed two redox states that were not characterized previously. These findings provide initial evidence that these amino acid residues are central to the putative PTP of Group D [FeFe] hydrogenase. Since the identified residues are highly conserved in Group D exclusively, our results support the notion that the PTP is not universal for different phylogenetic groups in [FeFe] hydrogenases.

From Protein Film Electrochemistry to Nanoconfined Enzyme Cascades and the Electrochemical Leaf

Protein film electrochemistry (PFE) has given unrivalled insight into the properties of redox proteins and many electron-transferring enzymes, allowing investigations of otherwise ill-defined or intractable topics such as unstable Fe-S centers and the catalytic bias of enzymes. Many enzymes have been established to be reversible electrocatalysts when attached to an electrode, and further investigations have revealed how unusual dependences of catalytic rates on electrode potential have stark similarities with electronics. A special case, the reversible electrochemistry of a photosynthetic enzyme, ferredoxin-NADP⁺ reductase (FNR), loaded at very high concentrations in the 3D nanopores of a conducting metal oxide layer, is leading to a new technology that brings PFE to myriad enzymes of other classes, the activities of which become controlled by the primary electron exchange. This extension is possible because FNR-based recycling of NADP(H) can be coupled to a dehydrogenase, and thence to other enzymes linked in tandem by the tight channelling of cofactors and intermediates within the nanopores of the material. The earlier interpretations of catalytic wave-shapes and various analogies with electronics are thus extended to initiate a field perhaps aptly named "cascade-tronics", in which the flow of reactions along an enzyme cascade is monitored and controlled through an electrochemical analyzer. Unlike in photosynthesis where FNR transduces electron transfer and hydride transfer through the unidirectional recycling of NADPH, the "electrochemical leaf" (e-Leaf) can be used to drive reactions in both oxidizing and reducing directions. The e-Leaf offers a natural way to study how enzymes are affected by nanoconfinement and crowding, mimicking the physical conditions under which enzyme cascades operate in living cells. The reactions of the trapped enzymes, often at very high local concentration, are thus studied electrochemically, exploiting the potential domain to control rates and direction and the current-rate analogy to derive kinetic data. Localized NADP(H) recycling is very efficient, resulting in very high cofactor turnover numbers and new opportunities for controlling and exploiting biocatalysis.

High Titer of (S)-Equol Synthesis from Daidzein in Escherichia coli

(S)-Equol is the terminal metabolite of daidzein and plays important roles in human health. However, due to anaerobic inefficiency, limited productivity in (S)-equol-producing strains often hinders (S)-equol mass production. Here, a multi-enzyme cascade system was designed to generate a higher (S)-equol titer. First, full reversibility of the (S)-equol synthesis pathway was found and a blocking reverse conversion strategy was established. As biosynthetic genes are present in the microbial genome, an effective daidzein reductase was chosen using evolutionary principles. And our analyses showed that NADPH was crucial for the pathway. In response to this, a novel NADPH pool was redesigned after analyzing a cofactor metabolism model. By adjusting synthesis pathway genes at the right expression level, the entire synthesis pathway can take place smoothly. Thus, the cascade system was optimized by regulating the gene expression intensity. Finally, after optimizing fermentation conditions, a 5 L bioreactor was used to generate a high (S)-equol production titer (3418.5 mg/L), with a conversion rate of approximately 85.9%. This study shows a feasible green process route for the production of (S)-equol.

The Contribution of Proton-Donor pKa on Reactivity Profiles of [FeFe]-hydrogenases

The [FeFe]-hydrogenases are enzymes that catalyze the reversible activation of H2 coupled to the reduction-oxidation of electron carriers. Members of the different taxonomic groups of [FeFe]-hydrogenases display a wide range of preference, or bias, for H2 oxidation or H2 production reactions, despite sharing a common catalytic cofactor, or H-cluster. Identifying the properties that control reactivity remains an active area of investigation, and models have emerged that include diversity in the catalytic site coordination environments and compositions of electron transfer chains. The kinetics of proton-coupled electron transfer at the H-cluster might be expected to be a point of control of reactivity. To test this hypothesis, systematic changes were made to the conserved cysteine residue that functions in proton exchange with the H-cluster in the three model enzymes: CaI, CpII, and CrHydA1. CaI and CpII both employ electron transfer accessory clusters but differ in bias, whereas CrHydA1 lacks accessory clusters having only the H-cluster. Changing from cysteine to either serine (more basic) or aspartate (more acidic) modifies the sidechain pKa and thus the barrier for the proton exchange step. The reaction rates for H2 oxidation or H2 evolution were surveyed and measured for model [FeFe]-hydrogenases, and the results show that the initial proton-transfer step in [FeFe]-hydrogenase is tightly coupled to the control of reactivity; a change from cysteine to more basic serine favored H2 oxidation in all enzymes, whereas a change to more acidic aspartate caused a shift in preference toward H2 evolution. Overall, the changes in reactivity profiles were profound, spanning 105 in ratio of the H2 oxidation-to-H2 evolution rates. The fact that the change in reactivity follows a common trend implies that the effect of changing the proton-transfer residue pKa may also be framed as an effect on the scaling relationship between the H-cluster di(thiolmethyl)amine (DTMA) ligand pKa and E m values of the H-cluster. Experimental observations that support this relationship, and how it relates to catalytic function in [FeFe]-hydrogenases, are discussed.

Investigating the role of the strong field ligands in [FeFe] hydrogenase: spectroscopic and functional characterization of a semi-synthetic mono-cyanide active site

Artificial maturation of hydrogenases provides a path towards generating new semi-synthetic enzymes with novel catalytic properties. Here enzymes featuring a synthetic asymmetric mono-cyanide cofactor have been prepared using two different hydrogenase scaffolds. Their structure and reactivity was investigated in order to elucidate the design rationale behind the native di-cyanide cofactor, and by extension the second coordination sphere of the active-site pocket. Surprisingly, the choice of host enzyme was found to have a dramatic impact on reactivity. Moreover, the study shows that synthetic manipulations of the active-site can significantly increase inhibitor tolerance, as compared to native [FeFe] hydrogenase, while retaining the enzyme's native capacity for reversible catalysis.

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Gases like H2, N2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N2, CO2, and CO and the production of H2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N2 fixation by nitrogenase and H2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

Hydride state accumulation in native [FeFe]-hydrogenase with the physiological reductant H2 supports its catalytic relevance

Small molecules in solution may interfere with mechanistic investigations, as they can affect the stability of catalytic states and produce off-cycle states that can be mistaken for catalytically relevant species. Here we show that the hydride state (H_hyd), a proposed central intermediate in the catalytic cycle of [FeFe]-hydrogenase, can be formed in wild-type [FeFe]-hydrogenases treated with H₂ in absence of other, non-biological, reductants. Moreover, we reveal a new state with unclear role in catalysis induced by common low pH buffers.

Studies of enzymatic catalysis often rely on non-biological reagents, which may affect catalytic intermediates and produce off-cycle states. Here the influence of buffer and reductant on key intermediates of [FeFe]-hydrogenase are explored.