A threonine stabilizes the NiC and NiR catalytic intermediates of [NiFe]-hydrogenase

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.

Proton Transfer Mechanisms in Bimetallic Hydrogenases

Hydrogenases are metalloenzymes that catalyze proton reduction and H₂ oxidation with outstanding efficiency. They are model systems for bioinorganic chemistry, including low-valent transition metals, hydride chemistry, and proton-coupled electron transfer. In this Account, we describe how photochemistry and infrared difference spectroscopy can be used to identify the dynamic hydrogen-bonding changes that facilitate proton transfer in [NiFe]- and [FeFe]-hydrogenase.[NiFe]-hydrogenase binds a heterobimetallic nickel/iron site embedded in the protein by four cysteine ligands. [FeFe]-hydrogenase carries a homobimetallic iron/iron site attached to the protein by only a single cysteine. Carbon monoxide and cyanide ligands in the active site facilitate detailed investigations of hydrogenase catalysis by infrared spectroscopy because of their strong signals and redox-dependent frequency shifts. We found that specific redox-state transitions in [NiFe]- and [FeFe]-hydrogenase can be triggered by visible light to record extremely sensitive "light-minus-dark" infrared difference spectra monitoring key amino acid residues. As these transitions are coupled to protonation changes, our data allowed investigation of dynamic hydrogen-bonding changes that go well beyond the resolution of protein crystallography.In [NiFe]-hydrogenase, photolysis of the bridging hydride ligand in the Ni-C state was followed by infrared difference spectroscopy. Our data clearly indicate the formation of a protonated cysteine residue as well as hydrogen-bonding changes involving a glutamic acid residue and a "dangling water" molecule. These findings are in excellent agreement with crystallographic analyses of [NiFe]-hydrogenase. In [FeFe]-hydrogenase, an external redox dye was used to accumulate the Hred state. Infrared difference spectra indicate hydrogen-bonding changes involving two glutamic acid residues and a conserved arginine residue. While crystallographic analyses of [FeFe]-hydrogenase in the oxidized state failed to explain the rapid proton transfer because of a breach in the succession of residues, our findings facilitated a precise molecular model of discontinued proton transfer.Comparing both systems, our data emphasize the role of the outer coordination sphere in bimetallic hydrogenases: we suggest that protonation of a nickel-ligating cysteine in [NiFe]-hydrogenase causes the notable preference toward H₂ oxidation. On the contrary, proton transfer in [FeFe]-hydrogenase involves an adjacent cysteine as a relay group, promoting both H₂ oxidation and proton reduction. These observations may guide the design of organometallic compounds that mimic the catalytic properties of hydrogenases.

Metal-ligand cooperativity in the soluble hydrogenase-1 from Pyrococcus furiosus

Metal–ligand cooperativity is an essential feature of bioinorganic catalysis. The design principles of such cooperativity in metalloenzymes are underexplored, but are critical to understand for developing efficient catalysts designed with earth abundant metals for small molecule activation. The simple substrate requirements of reversible proton reduction by the [NiFe]-hydrogenases make them a model bioinorganic system. A highly conserved arginine residue (R355) directly above the exogenous ligand binding position of the [NiFe]-catalytic core is known to be essential for optimal function because mutation to a lysine results in lower catalytic rates. To expand on our studies of soluble hydrogenase-1 from Pyrococcus furiosus (Pf SH1), we investigated the role of R355 by site-directed-mutagenesis to a lysine (R355K) using infrared and electron paramagnetic resonance spectroscopic probes sensitive to active site redox and protonation events. It was found the mutation resulted in an altered ligand binding environment at the [NiFe] centre. A key observation was destabilization of the Ni_a³⁺–C state, which contains a bridging hydride. Instead, the tautomeric Ni_a⁺–L states were observed. Overall, the results provided insight into complex metal–ligand cooperativity between the active site and protein scaffold that modulates the bridging hydride stability and the proton inventory, which should prove valuable to design principles for efficient bioinspired catalysts.

Metal–ligand cooperativity is an essential feature of bioinorganic catalysis.

X-ray Crystallography and Vibrational Spectroscopy Reveal the Key Determinants of Biocatalytic Dihydrogen Cycling by [NiFe] Hydrogenases

[NiFe] hydrogenases are complex model enzymes for the reversible cleavage of dihydrogen (H₂). However, structural determinants of efficient H₂ binding to their [NiFe] active site are not properly understood. Here, we present crystallographic and vibrational‐spectroscopic insights into the unexplored structure of the H₂‐binding [NiFe] intermediate. Using an F₄₂₀‐reducing [NiFe]‐hydrogenase from Methanosarcina barkeri as a model enzyme, we show that the protein backbone provides a strained chelating scaffold that tunes the [NiFe] active site for efficient H₂ binding and conversion. The protein matrix also directs H₂ diffusion to the [NiFe] site via two gas channels and allows the distribution of electrons between functional protomers through a subunit‐bridging FeS cluster. Our findings emphasize the relevance of an atypical Ni coordination, thereby providing a blueprint for the design of bio‐inspired H₂‐conversion catalysts.

Computational analyses, molecular dynamics, and mutagenesis studies of unprocessed form of [NiFe] hydrogenase reveal the role of disorder for efficient enzyme maturation

Biological production and oxidation of hydrogen is mediated by hydrogenases, key enzymes for these energy-relevant reactions. Synthesis of [NiFe] hydrogenases involves a complex series of biochemical reactions to assemble protein subunits and metallic cofactors required for enzyme function. A final step in this biosynthetic pathway is the processing of a C-terminal tail (CTT) from its large subunit, thus allowing proper insertion of nickel in the unique NiFe(CN)₂CO cofactor present in these enzymes. In silico modelling and Molecular Dynamics (MD) analyses of processed vs. unprocessed forms of Rhizobium leguminosarum bv. viciae (Rlv) hydrogenase large subunit HupL showed that its CTT (residues 582-596) is an intrinsically disordered region (IDR) that likely provides the required flexibility to the protein for the final steps of proteolytic maturation. Prediction of pKa values of ionizable side chains in both forms of the enzyme's large subunit also revealed that the presence of the CTT strongly modify the protonation state of some key residues around the active site. Furthermore, MD simulations and mutant analyses revealed that two glutamate residues (E27 in the N-terminal region and E589 inside the CTT) likely contribute to the process of nickel incorporation into the enzyme. Computational analysis also revealed structural details on the interaction of Rlv hydrogenase LSU with the endoprotease HupD responsible for the removal of CTT.

Reactivation of standard [NiFe]-hydrogenase and bioelectrochemical catalysis of proton reduction and hydrogen oxidation in a mediated-electron-transfer system

Standard [NiFe]-hydrogenase from Desulfovibrio vulgaris Miyazaki F (DvMF-H₂ase) catalyzes the uptake and production of hydrogen (H₂) and is a promising biocatalyst for future energy devices. However, DvMF-H₂ase experiences oxidative inactivation under oxidative stress to generate Ni-A and Ni-B states. It takes a long time to reactivate the Ni-A state by chemical reduction, whereas the Ni-B state is quickly reactivated under reducing conditions. Oxidative inhibition limits the application of DvMF-H₂ase in practical devices. In this research, we constructed a mediated-electron-transfer system by co-immobilizing DvMF-H₂ase and a viologen redox polymer (VP) on electrodes. The system can avoid oxidative inactivation into the Ni-B state at high electrode potentials and rapidly reactivate the Ni-A state by electrochemical reduction of VP. H₂ oxidation and H⁺ reduction were realized by adjusting the pH from a thermodynamic viewpoint. Using carbon felt as a working-electrode material, high current densities-up to (200 ± 70) and -(100 ± 9) mA cm^-3 for the H₂-oxidation and H⁺-reduction reactions, respectively-were attained.

Structural Characterization of Poised States in the Oxygen Sensitive Hydrogenases and Nitrogenases

The crystallization of FeS cluster-containing proteins has been challenging due to their oxygen sensitivity, and yet these enzymes are involved in many critical catalytic reactions. The last few years have seen a wealth of innovative experiments designed to elucidate not just structural but mechanistic insights into FeS cluster enzymes. Here, we focus on the crystallization of hydrogenases, which catalyze the reversible reduction of protons to hydrogen, and nitrogenases, which reduce dinitrogen to ammonia. A specific focus is given to the different experimental parameters and strategies that are used to trap distinct enzyme states, specifically, oxidants, reductants, and gas treatments. Other themes presented here include the recent use of Cryo-EM, and how coupling various spectroscopies to crystallization is opening up new approaches for structural and mechanistic analysis.

Proton Transfer in the Catalytic Cycle of [NiFe] Hydrogenases: Insight from Vibrational Spectroscopy

Catalysis of H₂ production and oxidation reactions is critical in renewable energy systems based around H₂ as a clean fuel, but the present reliance on platinum-based catalysts is not sustainable. In nature, H₂ is oxidized at minimal overpotential and high turnover frequencies at [NiFe] catalytic sites in hydrogenase enzymes. Although an outline mechanism has been established for the [NiFe] hydrogenases involving heterolytic cleavage of H₂ followed by a first and then second transfer of a proton and electron away from the active site, details remain vague concerning how the proton transfers are facilitated by the protein environment close to the active site. Furthermore, although [NiFe] hydrogenases from different organisms or cellular environments share a common active site, they exhibit a broad range of catalytic characteristics indicating the importance of subtle changes in the surrounding protein in controlling their behavior. Here we review recent time-resolved infrared (IR) spectroscopic studies and IR spectroelectrochemical studies carried out in situ during electrocatalytic turnover. Additionally, we re-evaluate the significant body of IR spectroscopic data on hydrogenase active site states determined through more conventional solution studies, in order to highlight mechanistic steps that seem to apply generally across the [NiFe] hydrogenases, as well as steps which so far seem limited to specific groups of these enzymes. This analysis is intended to help focus attention on the key open questions where further work is needed to assess important aspects of proton and electron transfer in the mechanism of [NiFe] hydrogenases.

Electrochemical insights into the mechanism of NiFe membrane-bound hydrogenases

Hydrogenases are enzymes of great biotechnological relevance because they catalyse the interconversion of H₂, water (protons) and electricity using non-precious metal catalytic active sites. Electrochemical studies into the reactivity of NiFe membrane-bound hydrogenases (MBH) have provided a particularly detailed insight into the reactivity and mechanism of this group of enzymes. Significantly, the control centre for enabling O₂ tolerance has been revealed as the electron-transfer relay of FeS clusters, rather than the NiFe bimetallic active site. The present review paper will discuss how electrochemistry results have complemented those obtained from structural and spectroscopic studies, to present a complete picture of our current understanding of NiFe MBH.

Structure and function of [NiFe] hydrogenases

Hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons via a heterolytic splitting mechanism. The active sites of [NiFe] hydrogenases comprise a dinuclear Ni-Fe center carrying CO and CN^- ligands. The catalytic activity of the standard (O₂-sensitive) [NiFe] hydrogenases vanishes under aerobic conditions. The O₂-tolerant [NiFe] hydrogenases can sustain H₂ oxidation activity under atmospheric conditions. These hydrogenases have very similar active site structures that change the ligand sphere during the activation/catalytic process. An important structural difference between these hydrogenases has been found for the proximal iron-sulphur cluster located in the vicinity of the active site. This unprecedented [4Fe-3S]-6Cys cluster can supply two electrons, which lead to rapid recovery of the O₂ inactivation, to the [NiFe] active site.

A Ni(i)Fe(ii) analogue of the Ni-L state of the active site of the [NiFe] hydrogenases

[Ni(L¹)Fe(^tBuNC)₄]⁺ is an unprecedented Ni(i)Fe(ii) species that reproduces the electronic configuration of the Ni-L state of the [NiFe] hydrogenases.