Going beyond Structure: Nickel-Substituted Rubredoxin as a Mechanistic Model for the [NiFe] Hydrogenases

Artificial Metalloenzymes with Two Catalytic Cofactors for Tandem Abiotic Transformations

Artificial metalloenzymes (ArMs) enable the integration of abiotic cofactors within a native protein scaffold, allowing for non-natural catalytic activities. Previous ArMs, however, have primarily relied on single cofactor systems, limiting them to only one catalytic function. Here we present an approach to construct ArMs embedding two catalytic cofactors based on the biotin-streptavidin technology. By incorporating multiple catalytic cofactors into the four binding sites of streptavidin, we engineered programmable ArMs for tandem abiotic transformations including an enantioselective formal C-H hydroxylation and a photooxidation-Michael addition. This work thus outlines a promising strategy for the development of ArMs embedding multiple cofactors.

A semisynthetic, multicofactor artificial metalloenzyme retains independent site activity

Native metalloenzymes are unparalleled in their ability to perform efficient small molecule activation reactions, converting simple substrates into complex products. Most of these natural systems possess multiple metallocofactors to facilitate electron transfer or cascade catalysis. While the field of artificial metalloenzymes is growing at a rapid rate, examples of artificial enzymes that leverage two distinct cofactors remain scarce. In this work, we describe a new class of artificial enzymes containing two different metallocofactors, incorporated through bioorthogonal strategies. Nickel-substituted rubredoxin (NiRd), which is a structural and functional mimic of [NiFe] hydrogenases, is used as a scaffold. Incorporation of a synthetic bimetallic inorganic complex based on a macrocyclic biquinazoline ligand (MMBQ) was accomplished using a novel chelating thioether linker. Neither the structure of the NiRd active site nor the MMBQ were altered upon attachment, and each site retained independent redox activity. Electrocatalysis was observed from each site, with the switchability of the system demonstrated through the use of catalytically inert metal centers. This MMBQ-NiRd platform offers a new avenue to create multicofactor artificial metalloenzymes in a robust system that can be easily tuned both through modifications to the protein scaffold and the synthetic moiety, with applications for redox catalysis and tandem reactivity.

Targeted Modulation of Photocatalytic Hydrogen Evolution Activity by Nickel-Substituted Rubredoxin through Functionalized Ruthenium Phototriggers

Light-driven hydrogen evolution is a promising means of sustainable energy production to meet global energy demand. This study investigates the photocatalytic hydrogen evolution activity of nickel-substituted rubredoxin (NiRd), an artificial hydrogenase mimic, covalently attached to a ruthenium phototrigger (RuNiRd). By systematically modifying the para-substituents on Ru(II) polypyridyl complexes, we sought to optimize the intramolecular electron transfer processes within the RuNiRd system. A series of electron-donating and electron-withdrawing groups were introduced to tune the photophysical, photochemical, and electrochemical properties of the ruthenium complexes. Our findings reveal that electron-donating substituents can increase the hydrogen evolution capabilities of the artificial enzyme to a point; however, the complexes with the most electron-donating substituents suffer from short lifetimes and inefficient reductive quenching, rendering them inactive. The present work highlights the intricate balance required between driving force, lifetime, and quenching efficiency for effective light-driven catalysis, providing valuable insights into the design of artificial enzyme-photosensitizer constructs.

Challenges and Future Perspectives in Photocatalysis: Conclusions from an Interdisciplinary Workshop

Photocatalysis is a versatile and rapidly developing field with applications spanning artificial photosynthesis, photo-biocatalysis, photoredox catalysis in solution or supramolecular structures, utilization of abundant metals and organocatalysts, sustainable synthesis, and plastic degradation. In this Perspective, we summarize conclusions from an interdisciplinary workshop of young principal investigators held at the Lorentz Center in Leiden in March 2023. We explore how diverse fields within photocatalysis can benefit from one another. We delve into the intricate interplay between these subdisciplines, by highlighting the unique challenges and opportunities presented by each field and how a multidisciplinary approach can drive innovation and lead to sustainable solutions for the future. Advanced collaboration and knowledge exchange across these domains can further enhance the potential of photocatalysis. Artificial photosynthesis has become a promising technology for solar fuel generation, for instance, via water splitting or CO2 reduction, while photocatalysis has revolutionized the way we think about assembling molecular building blocks. Merging such powerful disciplines may give rise to efficient and sustainable protocols across different technologies. While photocatalysis has matured and can be applied in industrial processes, a deeper understanding of complex mechanisms is of great importance to improve reaction quantum yields and to sustain continuous development. Photocatalysis is in the perfect position to play an important role in the synthesis, deconstruction, and reuse of molecules and materials impacting a sustainable future. To exploit the full potential of photocatalysis, a fundamental understanding of underlying processes within different subfields is necessary to close the cycle of use and reuse most efficiently. Following the initial interactions at the Lorentz Center Workshop in 2023, we aim to stimulate discussions and interdisciplinary approaches to tackle these challenges in diverse future teams.

Hydrogen production by a fully de novo enzyme

Molecular catalysts based on abundant elements that function in neutral water represent an essential component of sustainable hydrogen production. Artificial hydrogenases based on protein-inorganic hybrids have emerged as an intriguing class of catalysts for this purpose. We have prepared a novel artificial hydrogenase based on cobaloxime bound to a de novo three alpha-helical protein, α3C, via a pyridyl-based unnatural amino acid. The functionalized de novo protein was characterised by UV-visible, CD, and EPR spectroscopy, as well as MALDI spectrometry, which confirmed the presence and ligation of cobaloxime to the protein. The new de novo enzyme produced hydrogen under electrochemical, photochemical and reductive chemical conditions in neutral water solution. A change in hydrogen evolution capability of the de novo enzyme compared with native cobaloxime was observed, with turnover numbers around 80% of that of cobaloxime, and hydrogen evolution rates of 40% of that of cobaloxime. We discuss these findings in the context of existing literature, how our study contributes important information about the functionality of cobaloximes as hydrogen evolving catalysts in protein environments, and the feasibility of using de novo proteins for development into artificial metalloenzymes. Small de novo proteins as enzyme scaffolds have the potential to function as upscalable bioinspired catalysts thanks to their efficient atom economy, and the findings presented here show that these types of novel enzymes are a possible product.

Electronic isomerism in a heterometallic nickel-iron-sulfur cluster models substrate binding and cyanide inhibition of carbon monoxide dehydrogenase

The nickel-iron carbon monoxide dehydrogenase (CODH) enzyme uses a heterometallic nickel-iron-sulfur ([NiFe4S4]) cluster to catalyze the reversible interconversion of carbon dioxide (CO2) and carbon monoxide (CO). These reactions are essential for maintaining the global carbon cycle and offer a route towards sustainable greenhouse gas conversion but have not been successfully replicated in synthetic models, in part due to a poor understanding of the natural system. Though the general protein architecture of CODH is known, the electronic structure of the active site is not well-understood, and the mechanism of catalysis remains unresolved. To better understand the CODH enzyme, we have developed a protein-based model containing a heterometallic [NiFe3S4] cluster in the Pyrococcus furiosus (Pf) ferredoxin (Fd). This model binds small molecules such as carbon monoxide and cyanide, analogous to CODH. Multiple redox- and ligand-bound states of [NiFe3S4] Fd (NiFd) have been investigated using a suite of spectroscopic techniques, including resonance Raman, Ni and Fe K-edge X-ray absorption spectroscopy, and electron paramagnetic resonance, to resolve charge and spin delocalization across the cluster, site-specific electron density, and ligand activation. The facile movement of charge through the cluster highlights the fluidity of electron density within iron-sulfur clusters and suggests an electronic basis by which CN- inhibits the native system while the CO-bound state continues to elude isolation in CODH. The detailed characterization of isolable states that are accessible in our CODH model system provides valuable insight into unresolved enzymatic intermediates and offers design principles towards developing functional mimics of CODH.

Electrocatalytic Hydrogen Evolution using a Nickel-based Calixpyrrole Complex: Controlling the Secondary Coordination Sphere on an Electrode Surface

Incorporating design elements from homogeneous catalysts to construct well defined active sites on electrode surfaces is a promising approach for developing next generation electrocatalysts for energy conversion reactions. Furthermore, if functionalities that control the electrode microenvironment could be integrated into these active sites it would be particularly appealing. In this context, a square planar nickel calixpyrrole complex, Ni(DPMDA) (DPMDA=2,2'-((diphenylmethylene)bis(1H-pyrrole-5,2-diyl))bis(methaneylylidene))bis(azaneylylidene))dianiline) with pendant amine groups is reported that forms a heterogeneous hydrogen evolution catalyst using anilinium tetrafluoroborate as the proton source. The supported Ni(DPMDA) catalyst was surprisingly stable and displayed fast reaction kinetics with turnover frequencies (TOF) up to 25,900 s-1 or 366,000 s-1  cm-2 . Kinetic isotope effect (KIE) studies revealed a KIE of 5.7, and this data, combined with Tafel slope analysis, suggested that a proton-coupled electron transfer (PCET) process involving the pendant amine groups was rate-limiting. While evidence of an outer-sphere reduction of the Ni(DPMDA) catalyst was observed, it is hypothesized that the control over the secondary coordination sphere provided by the pendant amines facilitated such high TOFs and enabled the PCET mechanism. The results reported herein provide insight into heterogeneous catalyst design and approaches for controlling the secondary coordination sphere on electrode surfaces.

Rubredoxin Protein Scaffolds Sourced from Diverse Environmental Niches as an Artificial Hydrogenase Platform

Nickel-substituted rubredoxin (NiRd) from Desulfovibrio desulfuricans has previously been shown to act as both a structural and functional mimic of the [NiFe] hydrogenase. However, improvements both in turnover frequency and overpotential are needed to rival the native [NiFe] hydrogenase enzymes. Characterization of a library of NiRd mutants with variations in the secondary coordination sphere suggested that protein dynamics played a substantial role in modulating activity. In this work, rubredoxin scaffolds were selected from diverse organisms to study the effects of distal sequence variation on catalytic activity. It was found that though electrochemical catalytic activity was only slightly impacted across the series, the Rd sequence from a psychrophilic organism exhibited substantially higher levels of solution-phase hydrogen production. Additionally, Eyring analyses suggest that catalytic activation properties relate to the growth temperature of the parent organism, implying that the general correlation between the parent organism environment and catalytic activity often seen in naturally occurring enzymes may also be observed in artificial enzymes. Selecting protein scaffolds from hosts that inhabit diverse environments, particularly low-temperature environments, represents an alternative approach for engineering artificial metalloenzymes.

Comprehensive structural, infrared spectroscopic and kinetic investigations of the roles of the active-site arginine in bidirectional hydrogen activation by the [NiFe]-hydrogenase 'Hyd-2' from Escherichia coli

The active site of [NiFe]-hydrogenases contains a strictly-conserved pendant arginine, the guanidine head group of which is suspended immediately above the Ni and Fe atoms. Replacement of this arginine (R479) in hydrogenase-2 from E. coli results in an enzyme that is isolated with a very tightly-bound diatomic ligand attached end-on to the Ni and stabilised by hydrogen bonding to the Nζ atom of the pendant lysine and one of the three additional water molecules located in the active site of the variant. The diatomic ligand is bound under oxidising conditions and is removed only after a prolonged period of reduction with H2 and reduced methyl viologen. Once freed of the diatomic ligand, the R479K variant catalyses both H2 oxidation and evolution but with greatly decreased rates compared to the native enzyme. Key kinetic characteristics are revealed by protein film electrochemistry: most importantly, a very low activation energy for H2 oxidation that is not linked to an increased H/D isotope effect. Native electrocatalytic reversibility is retained. The results show that the sluggish kinetics observed for the lysine variant arise most obviously because the advantage of a more favourable low-energy pathway is massively offset by an extremely unfavourable activation entropy. Extensive efforts to establish the identity of the diatomic ligand, the tight binding of which is an unexpected further consequence of replacing the pendant arginine, prove inconclusive.

Artificial Small Molecules as Cofactors and Biomacromolecular Building Blocks in Synthetic Biology: Design, Synthesis, Applications, and Challenges

Enzymes are essential catalysts for various chemical reactions in biological systems and often rely on metal ions or cofactors to stabilize their structure or perform functions. Improving enzyme performance has always been an important direction of protein engineering. In recent years, various artificial small molecules have been successfully used in enzyme engineering. The types of enzymatic reactions and metabolic pathways in cells can be expanded by the incorporation of these artificial small molecules either as cofactors or as building blocks of proteins and nucleic acids, which greatly promotes the development and application of biotechnology. In this review, we summarized research on artificial small molecules including biological metal cluster mimics, coenzyme analogs (mNADs), designer cofactors, non-natural nucleotides (XNAs), and non-natural amino acids (nnAAs), focusing on their design, synthesis, and applications as well as the current challenges in synthetic biology.

Design of a minimal di-nickel hydrogenase peptide

Ancestral metabolic processes involve the reversible oxidation of molecular hydrogen by hydrogenase. Extant hydrogenase enzymes are complex, comprising hundreds of amino acids and multiple cofactors. We designed a 13-amino acid nickel-binding peptide capable of robustly producing molecular hydrogen from protons under a wide variety of conditions. The peptide forms a di-nickel cluster structurally analogous to a Ni-Fe cluster in [NiFe] hydrogenase and the Ni-Ni cluster in acetyl-CoA synthase, two ancient, extant proteins central to metabolism. These experimental results demonstrate that modern enzymes, despite their enormous complexity, likely evolved from simple peptide precursors on early Earth.

Photocatalytic Hydrogen Evolution by a De Novo Designed Metalloprotein that Undergoes Ni-Mediated Oligomerization Shift

De novo metalloprotein design involves the construction of proteins guided by specific repeat patterns of polar and apolar residues, which, upon self-assembly, provide a suitable environment to bind metals and produce artificial metalloenzymes. While a wide range of functionalities have been realized in de novo designed metalloproteins, the functional repertoire of such constructs towards alternative energy-relevant catalysis is currently limited. Here we show the application of de novo approach to design a functional H2 evolving protein. The design involved the assembly of an amphiphilic peptide featuring cysteines at tandem a/d sites of each helix. Intriguingly, upon NiII addition, the oligomers shift from a major trimeric assembly to a mix of dimers and trimers. The metalloprotein produced H2 photocatalytically with a bell-shape pH dependence, having a maximum activity at pH 5.5. Transient absorption spectroscopy is used to determine the timescales of electron transfer as a function of pH. Selective outer sphere mutations are made to probe how the local environment tunes activity. A preferential enhancement of activity is observed via steric modulation above the NiII site, towards the N-termini, compared to below the NiII site towards the C-termini.

Classifying metal-binding sites with neural networks

To advance our ability to predict impacts of the protein scaffold on catalysis, robust classification schemes to define features of proteins that will influence reactivity are needed. One of these features is a protein's metal-binding ability, as metals are critical to catalytic conversion by metalloenzymes. As a step toward realizing this goal, we used convolutional neural networks (CNNs) to enable the classification of a metal cofactor binding pocket within a protein scaffold. CNNs enable images to be classified based on multiple levels of detail in the image, from edges and corners to entire objects, and can provide rapid classification. First, six CNN models were fine-tuned to classify the 20 standard amino acids to choose a performant model for amino acid classification. This model was then trained in two parallel efforts: to classify a 2D image of the environment within a given radius of the central metal binding site, either an Fe ion or a [2Fe-2S] cofactor, with the metal visible (effort 1) or the metal hidden (effort 2). We further used two sub-classifications of the [2Fe-2S] cofactor: (1) a standard [2Fe-2S] cofactor and (2) a Rieske [2Fe-2S] cofactor. The accuracy for the model correctly identifying all three defined features was >95%, despite our perception of the increased challenge of the metalloenzyme identification. This demonstrates that machine learning methodology to classify and distinguish similar metal-binding sites, even in the absence of a visible cofactor, is indeed possible and offers an additional tool for metal-binding site identification in proteins.

Incorporation of a molybdenum atom in a Rubredoxin-type Centre of a de novo-designed α3DIV-L21C three-helical bundle peptide

The rational design and functionalization of small, simple, and stable peptides scaffolds is an attractive avenue to mimic catalytic metal-centres of complex proteins, relevant for the design of metalloenzymes with environmental, biotechnological and health impacts. The de novo designed α3DIV-L21C framework has a rubredoxin-like metal binding site and was used in this work to incorporate a Mo-atom. Thermostability studies using differential scanning calorimetry showed an increase of 4 °C in the melting temperature of the Mo-α3DIV-L21C when compared to the apo-α3DIV-L21C. Circular dichroism in the visible and far-UV regions corroborated these results showing that Mo incorporation provides stability to the peptide even though there were almost no differences observed in the secondary structure. A formal reduction potential of ∼ -408 mV vs. NHE, pH 7.6 was determined. Combining electrochemical results, EPR and UV-visible data we discuss the oxidation state of the molybdenum centre in Mo-α3DIV-L21C and propose that is mainly in a Mo (VI) oxidation state.

Improving the synthetic H2 production catalyst design strategy with the neurotransmitter dopamine

The strategic incorporation of the neurotransmitter dopamine around a cobaloxime core resulted in excellent electrocatalytic (rate 8400 s^-1) and photocatalytic H₂ production under neutral aqueous conditions. The influence of the synthetic outer coordination sphere features continues even with a phenylene-diimino-dioxime motif-coordinated cobalt core.

Bioinspired and biomolecular catalysts for energy conversion and storage

Metalloenzymes are remarkable for facilitating challenging redox transformations with high efficiency and selectivity. In the area of alternative energy, scientists aim to capture these properties in bioinspired and engineered biomolecular catalysts for the efficient and fast production of fuels from low-energy feedstocks such as water and carbon dioxide. In this short review, efforts to mimic biological catalysts for proton reduction and carbon dioxide reduction are highlighted. Two important recurring themes are the importance of the microenvironment of the catalyst active site and the key role of proton delivery to the active site in achieving desired reactivity. Perspectives on ongoing and future challenges are also provided.

Molecular-Modified Photocathodes for Applications in Artificial Photosynthesis and Solar-to-Fuel Technologies

Nature offers inspiration for developing technologies that integrate the capture, conversion, and storage of solar energy. In this review article, we highlight principles of natural photosynthesis and artificial photosynthesis, drawing comparisons between solar energy transduction in biology and emerging solar-to-fuel technologies. Key features of the biological approach include use of earth-abundant elements and molecular interfaces for driving photoinduced charge separation reactions that power chemical transformations at global scales. For the artificial systems described in this review, emphasis is placed on advancements involving hybrid photocathodes that power fuel-forming reactions using molecular catalysts interfaced with visible-light-absorbing semiconductors.

Thioester synthesis by a designed nickel enzyme models prebiotic energy conversion

The formation of carbon-carbon bonds from prebiotic precursors such as carbon dioxide represents the foundation of all primordial life processes. In extant organisms, this reaction is carried out by the carbon monoxide dehydrogenase (CODH)/acetyl coenzyme A synthase (ACS) enzyme, which performs the cornerstone reaction in the ancient Wood-Ljungdahl metabolic pathway to synthesize the key biological metabolite, acetyl-CoA. Despite its significance, a fundamental understanding of this transformation is lacking, hampering efforts to harness analogous chemistry. To address these knowledge gaps, we have designed an artificial metalloenzyme within the azurin protein scaffold as a structural, functional, and mechanistic model of ACS. We demonstrate the intermediacy of the Ni^I species and requirement for ordered substrate binding in the bioorganometallic carbon-carbon bond-forming reaction from the one-carbon ACS substrates. The electronic and geometric structures of the nickel-acetyl intermediate have been characterized using time-resolved optical, electron paramagnetic resonance, and X-ray absorption spectroscopy in conjunction with quantum chemical calculations. Moreover, we demonstrate that the nickel-acetyl species is chemically competent for selective acyl transfer upon thiol addition to biosynthesize an activated thioester. Drawing an analogy to the native enzyme, a mechanism for thioester generation by this ACS model has been proposed. The fundamental insight into the enzymatic process provided by this rudimentary ACS model has implications for the evolution of primitive ACS-like proteins. Ultimately, these findings offer strategies for development of highly active catalysts for sustainable generation of liquid fuels from one-carbon substrates, with potential for broad applications across diverse fields ranging from energy storage to environmental remediation.

Artificial Metalloproteins: At the Interface between Biology and Chemistry

Artificial metalloproteins (ArMs) have recently gained significant interest due to their potential to address issues in a broad scope of applications, including biocatalysis, biotechnology, protein assembly, and model chemistry. ArMs are assembled by the incorporation of a non-native metallocofactor into a protein scaffold. This can be achieved by a number of methods that apply tools of chemical biology, computational de novo design, and synthetic chemistry. In this Perspective, we highlight select systems in the hope of demonstrating the breadth of ArM design strategies and applications and emphasize how these systems address problems that are otherwise difficult to do so with strictly biochemical or synthetic approaches.

Promotion of Phenol Electro-oxidation by Oxygen Evolution Reaction on an Active Electrode for Efficient Pollution Control and Hydrogen Evolution

We report an electrolysis system using NiFe layered double hydroxide/CoMoO₄/nickel foam (NFLDH/CMO/NF) as the anode and CMO/NF as the cathode for simultaneous phenol electro-oxidation and water electrolysis. This system shows high performance for both phenol degradation and hydrogen evolution. We demonstrate that the degradation rate of phenol on the active anode is governed by the mass transfer rate at a low phenol concentration (0.5-2 mM) and by the electro-oxidation rate at a high phenol concentration (5 mM). The anodic oxygen evolution reaction (OER) can promote the phenol degradation through enhanced mass transfer efficiency. More importantly, the common deactivation issue of phenol electro-oxidation on the inert anode can be eliminated by the high OER activity of the active anode. The constructed full electrolytic cell only needs a low potential of 1.498 V to achieve 10 mA/cm² for water electrolysis. The reported promotion effect of phenol degradation by OER as well as the improved anode resistance to deactivation offer new insights into efficient and robust waste-to-resource electrolysis system for water treatment.

Protein-based models offer mechanistic insight into complex nickel metalloenzymes

There are ten nickel enzymes found across biological systems, each with a distinct active site and reactivity that spans reductive, oxidative, and redox-neutral processes. We focus on the reductive enzymes, which catalyze reactions that are highly germane to the modern-day climate crisis: [NiFe] hydrogenase, carbon monoxide dehydrogenase, acetyl coenzyme A synthase, and methyl coenzyme M reductase. The current mechanistic understanding of each enzyme system is reviewed along with existing knowledge gaps, which are addressed through the development of protein-derived models, as described here. This opinion is intended to highlight the advantages of using robust protein scaffolds for modeling multiscale contributions to reactivity and inspire the development of novel artificial metalloenzymes for other small molecule transformations.

Development of Nonheme {FeNO}7 Complexes Based on the Pyrococcus furiosus Rubredoxin for Red-Light-Controllable Nitric Oxide Release

Nitric oxide (NO) is an essential biological messenger, contributing a significant role in a diverse range of physiological processes. The light-controllable NO releasers are of great interest because of their potential as agents for NO-related research and therapeutics. Herein, we developed a pair of red-light-controllable NO releasers, pfRd-C9A-{FeNO}⁷ and pfRd-C42A-{FeNO}⁷ (pfRd = Pyrococcus furiosus rubredoxin), by constructing a nonheme {FeNO}⁷ center within the redesigned iron-sulfur protein scaffolds. While shown to be both air and thermally stable, these complexes are highly sensitive to red-light irradiation with temporal precision, which was confirmed by electron paramagnetic resonance spin trapping and Griess assay. The temporally controlled NO release from these complexes was also demonstrated in DNA cleavage assay. Overall, this study demonstrates that such a protein-based nonheme iron nitrosyl system could be a viable chemical tool for precise NO administration.

Reversible Electron Transfer and Substrate Binding Support [NiFe3S4] Ferredoxin as a Protein-Based Model for [NiFe] Carbon Monoxide Dehydrogenase

The nickel-iron carbon monoxide dehydrogenase (CODH) enzyme catalyzes the reversible and selective interconversion of carbon dioxide (CO₂) to carbon monoxide (CO) with high rates and negligible overpotential. Despite decades of research, many questions remain about this complex metalloenzyme system. A simplified model enzyme could provide substantial insight into biological carbon cycling. Here, we demonstrate reversible electron transfer and binding of both CO and cyanide, a substrate and an inhibitor of CODH, respectively, in a Pyrococcus furiosus (Pf) ferredoxin (Fd) protein that has been reconstituted with a nickel-iron sulfide cluster ([NiFe₃S₄] Fd). The [NiFe₃S₄] cluster mimics the core of the native CODH active site and thus serves as a protein-based structural model of the CODH subsite. Notably, despite binding cyanide, no CO binding is observed for the physiological [Fe₄S₄] clusters in Pf Fd, providing chemical rationale underlying the evolution of a site-differentiated cluster for substrate conversion in native CODH. The demonstration of a substrate-binding metalloprotein model of CODH sets the stage for high-resolution spectroscopic and mechanistic studies correlating the subsite structure and function, ultimately guiding the design of anthropogenic catalysts that harness the advantages of CODH for effective CO₂ reduction.

In Vivo Assembly of a Genetically Encoded Artificial Metalloenzyme for Hydrogen Production

The genetic encoding of artificial enzymes represents a substantial advantage relative to traditional molecular catalyst optimization, as laboratory-based directed evolution coupled with high-throughput screening methods can provide rapid development and functional characterization of enzyme libraries. However, these techniques have been of limited utility in the field of artificial metalloenzymes due to the need for in vitro cofactor metalation. Here, we report the development of methodology for in vivo production of nickel-substituted rubredoxin, an artificial metalloenzyme that is a structural, functional, and mechanistic mimic of the [NiFe] hydrogenases. Direct voltammetry on cell lysate establishes precedent for the development of an electrochemical screen. This technique will be broadly applicable to the in vivo generation of artificial metalloenzymes that require a non-native metal cofactor, offering a route for rapid enzyme optimization and setting the stage for integration of artificial metalloenzymes into biochemical pathways within diverse hosts.

A De Novo-Designed Artificial Metallopeptide Hydrogenase: Insights into Photochemical Processes and the Role of Protonated Cys

Hydrogenase enzymes produce H₂ gas, which can be a potential source of alternative energy. Inspired by the [NiFe] hydrogenases, we report the construction of a de novo-designed artificial hydrogenase (ArH). The ArH is a dimeric coiled coil where two cysteine (Cys) residues are introduced at tandem a/d positions of a heptad to create a tetrathiolato Ni binding site. Spectroscopic studies show that Ni binding significantly stabilizes the peptide producing electronic transitions characteristic of Ni-thiolate proteins. The ArH produces H₂ photocatalytically, demonstrating a bell-shaped pH-dependence on activity. Fluorescence lifetimes and transient absorption spectroscopic studies are undertaken to elucidate the nature of pH-dependence, and to monitor the reaction kinetics of the photochemical processes. pH titrations are employed to determine the role of protonated Cys on reactivity. Through combining these results, a fine balance is found between solution acidity and the electron transfer steps. This balance is critical to maximize the production of Ni^I -peptide and protonation of the Ni^II -H^- intermediate (Ni-R) by a Cys (pK_a ≈6.4) to produce H₂ .

Repurposing metalloproteins as mimics of natural metalloenzymes for small-molecule activation

Artificial metalloenzymes (ArMs) consist of an unnatural metal or cofactor embedded in a protein scaffold, and are an excellent platform for applying the concepts of protein engineering to catalysis. In this Focused Review, we describe the application of ArMs as simple, tunable artificial models of the active sites of complex natural metalloenzymes for small-molecule activation. In this sense, ArMs expand the strategies of synthetic model chemistry to protein-based supporting ligands with potential for participation from the second coordination sphere. We focus specifically on ArMs that are structural, spectroscopic, and functional models of enzymes for activation of small molecules like CO, CO₂, O₂, N₂, and NO, as well as production/consumption of H₂. These ArMs give insight into the identities and roles of metalloenzyme structural features within and near the cofactor. We give examples of ArM work relevant to hydrogenases, acetyl-coenzyme A synthase, superoxide dismutase, heme oxygenases, nitric oxide reductase, methyl-coenzyme M reductase, copper-O₂ enzymes, and nitrogenases.

A new twist of rubredoxin function in M. tuberculosis

Electron transfer mediated by metalloproteins drives many biological processes. Rubredoxins are a ubiquitous [1Fe-0S] class of electron carriers that play an important role in bacterial adaptation to changing environmental conditions. In Mycobacterium tuberculosis, oxidative and acidic stresses as well as iron starvation induce rubredoxins expression. However, their functions during M. tuberculosis infection are unknown. In the present work, we show that rubredoxin B (RubB) is able to efficiently shuttle electrons from cognate reductases, FprA and FdR to support catalytic activity of cytochrome P450s, CYP124, CYP125, and CYP142, which are important for bacterial viability and pathogenicity. We solved the crystal structure of RubB and characterized the interaction between RubB and CYPs using site-directed mutagenesis. Mutations that not only neutralize single charge but also change the specific residues on the surface of RubB did not dramatically decrease activity of studied CYPs. Together with isothermal calorimetry (ITC) experiments, the obtained results suggest that interactions are transient and not highly specific. The redox potential of RubB is -264 mV vs. Ag/AgCl and the measured extinction coefficients are 9931 M^-1cm^-1 and 8371 M^-1cm^-1 at 380 nm and 490 nm, respectively. Characteristic parameters of RubB along with the discovered function might be useful for biotechnological applications. Our findings suggest that a switch from ferredoxins to rubredoxins might be crucial for M. tuberculosis to support CYPs activity during the infection.

Streamlined purification and characterization of Pyrococcus furiosus rubredoxins with different N-terminal modifications by reversed-phase HPLC

Rubredoxins (Rds), like those from Pyrococcus furious (Pf), have largely been found to be expressed in Escherichia coli (E. coli) as a mixture of different N-terminal forms, which may affect the properties of the protein. The typical procedures for the purification of Rds are cumbersome and usually with low yield. We present herein a streamlined purification strategy based on the reversed-phase high performance liquid chromatography (RP-HPLC), which offers high yield and high resolution after simply one-step purification following pre-treatment. We also show that RP-HPLC can be a valuable tool to gain information related to the thermal decomposition pathway of Pf-Rds.

Ligand Field Inversion as a Mechanism to Gate Bioorganometallic Reactivity: Investigating a Biochemical Model of Acetyl CoA Synthase Using Spectroscopy and Computation

The biological global carbon cycle is largely regulated through microbial nickel enzymes, including carbon monoxide dehydrogenase (CODH), acetyl coenzyme A synthase (ACS), and methyl coenzyme M reductase (MCR). These systems are suggested to utilize organometallic intermediates during catalysis, though characterization of these species has remained challenging. We have established a mutant of nickel-substituted azurin as a scaffold upon which to develop protein-based models of enzymatic intermediates, including the organometallic states of ACS. In this work, we report the comprehensive investigation of the S = 1/2 Ni-CO and Ni-CH₃ states using pulsed EPR spectroscopy and computational techniques. While the Ni-CO state shows conventional metal-ligand interactions and a classical ligand field, the Ni-CH₃ hyperfine interactions between the methyl protons and the nickel indicate a closer distance than would be expected for an anionic methyl ligand. Structural analysis instead suggests a near-planar methyl ligand that can be best described as cationic. Consistent with this conclusion, the frontier molecular orbitals of the Ni-CH₃ species indicate a ligand-centered LUMO, with a d⁹ population on the metal center, rather than the d⁷ population expected for a typical metal-alkyl species generated by oxidative addition. Collectively, these data support the presence of an inverted ligand field configuration for the Ni-CH₃ Az species, in which the lowest unoccupied orbital is centered on the ligands rather than the more electropositive metal. These analyses provide the first evidence for an inverted ligand field within a biological system. The functional relevance of the electronic structures of both the Ni-CO and Ni-CH₃ species are discussed in the context of native ACS, and an inverted ligand field is proposed as a mechanism by which to gate reactivity both within ACS and in other thiolate-containing metalloenzymes.

Mononuclear Mn complexes featuring N,S-/N,N-donor and 1,3,5-triaza-7-phosphaadamantane ligands: synthesis and electrocatalytic properties

Mononuclear Mn(i) carbonyl complexes incorporating 2-mercaptobenzothiazole or 2-mercaptobenzimidazole and phosphaadamantane ligands were evaluated as electrocatalysts for the HER both in acetonitrile and acetonitrile/water.

Biosynthetic Approaches towards the Design of Artificial Hydrogen-Evolution Catalysts

Hydrogen is a clean and sustainable form of fuel that can minimize our heavy dependence on fossil fuels as the primary energy source. The need of finding greener ways to generate H₂ gas has ignited interest in the research community to synthesize catalysts that can produce H₂ by the reduction of H⁺ . The natural H₂ producing enzymes hydrogenases have served as an inspiration to produce catalytic metal centers akin to these native enzymes. In this article we describe recent advances in the design of a unique class of artificial hydrogen evolving catalysts that combine the features of the active site metal(s) surrounded by a polypeptide component. The examples of these biosynthetic catalysts discussed here include i) assemblies of synthetic cofactors with native proteins; ii) peptide-appended synthetic complexes; iii) substitution of native cofactors with non-native cofactors; iv) metal substitution from rubredoxin; and v) a reengineered Cu storage protein into a Ni binding protein. Aspects of key design considerations in the construction of these artificial biocatalysts and insights gained into their chemical reactivity are discussed.

Light-driven catalysis with engineered enzymes and biomimetic systems

Efforts to drive catalytic reactions with light, inspired by natural processes like photosynthesis, have a long history and have seen significant recent growth. Successfully engineering systems using biomolecular and bioinspired catalysts to carry out light-driven chemical reactions capitalizes on advantages offered from the fields of biocatalysis and photocatalysis. In particular, driving reactions under mild conditions and in water, in which enzymes are operative, using sunlight as a renewable energy source yield environmentally friendly systems. Furthermore, using enzymes and bioinspired systems can take advantage of the high efficiency and specificity of biocatalysts. There are many challenges to overcome to fully capitalize on the potential of light-driven biocatalysis. In this mini-review, we discuss examples of enzymes and engineered biomolecular catalysts that are activated via electron transfer from a photosensitizer in a photocatalytic system. We place an emphasis on selected forefront chemical reactions of high interest, including CH oxidation, proton reduction, water oxidation, CO2 reduction, and N2 reduction.

H2 Evolution from a Thiolate-Bound Ni(III) Hydride

Terminal Ni^III hydrides are proposed intermediates in proton reduction catalyzed by both molecular electrocatalysts and metalloenzymes, but well-defined examples of paramagnetic nickel hydride complexes are largely limited to bridging hydrides. Herein, we report the synthesis of an S = 1/2, terminally bound thiolate-Ni^III-H complex. This species and its terminal hydride ligand in particular have been thoroughly characterized by vibrational and EPR techniques, including pulse EPR studies. Corresponding DFT calculations suggest appreciable spin leakage onto the thiolate ligand. The hyperfine coupling to the terminal hydride ligand of the thiolate-Ni^III-H species is comparable to that of the hydride ligand proposed for the Ni-C hydrogenase intermediate (Ni^III-H-Fe^II). Upon warming, the featured thiolate-Ni^III-H species undergoes bimolecular reductive elimination of H₂. Associated kinetic studies are discussed and compared with a structurally related Fe^III-H species that has also recently been reported to undergo bimolecular H-H coupling.

The oxygen reactivity of an artificial hydrogenase designed in a reengineered copper storage protein

The O₂ reactivity of an artificial biomolecular hydrogenase, the nickel binding protein (NBP) is investigated.

Understanding and Modulating Metalloenzymes with Unnatural Amino Acids, Non-Native Metal Ions, and Non-Native Metallocofactors

Metalloproteins set the gold standard for performing important functions, including catalyzing demanding reactions under mild conditions. Designing artificial metalloenzymes (ArMs) to catalyze abiological reactions has been a major endeavor for many years, but most ArM activities are far below those of native enzymes, making them unsuitable for most pratical applications. A critical step to advance the field is to fundamentally understand what it takes to not only confer but also fine-tune ArM activities so they match those of native enzymes. Indeed, only once we can freely modulate ArM activity to rival (or surpass!) natural enzymes can the potential of ArMs be fully realized. A key to unlocking ArM potential is the observation that one metal primary coordination sphere can display a range of functions and levels of activity, leading to the realization that secondary coordination sphere (SCS) interactions are critically important. However, SCS interactions are numerous, long-range, and weak, making them very difficult to reproduce in ArMs. Furthermore, natural enzymes are tied to a small set of biologically available functional moieties from canonical amino acids and physiologically available metal ions and metallocofactors, severely limiting the chemical space available to probe and tune ArMs. In this Account, we summarize the use of unnatural amino acids (UAAs) and non-native metal ions and metallocofactors by our group and our collaborators to probe and modulate ArM functions. We incorporated isostructural UAAs in a type 1 copper (T1Cu) protein azurin to provide conclusive evidence that axial ligand hydrophobicity is a major determinant of T1Cu redunction potential ( E°'). Closely related work from other groups are also discussed. We also probed the role of protein backbone interactions that cannot be altered by standard mutagenesis by replacing the peptide bond with an ester linkage. We used insight gained from these studies to tune the E°' of azurin across the entire physiological range, the broadest range ever achieved in a single metalloprotein. Introducing UAA analogues of Tyr into ArM models of heme-copper oxidase (HCO) revealed a linear relationship between p K_a, E°', and activity. We also substituted non-native hemes and non-native metal ions for their native equivalents in these models to resolve several issues that were intractable in native HCOs and the closely related nitric oxide reductases, such as their roles in modulating substrate affinity, electron transfer rate, and activity. We incorporated abiological cofactors such as ferrocene and Mn(salen) into azurin and myoglobin, respectively, to stabilize these inorganic and organometallic compounds in water, confer abiological functions, tune their E°' and activity through SCS interactions, and show that the approach to metallocofactor anchoring and orientation can tune enantioselectivity and alter function. Replacing Cu in azurin with non-native Fe or Ni can impart novel activities, such as superoxide reduction and C-C bond formation. While progress was made, we have identified only a small fraction of the interactions that can be generally applied to ArMs to fine-tune their functions. Because SCS interactions are subtle and heavily interconnected, it has been difficult to characterize their effects quantitatively. It is vital to develop spectroscopic and computational techniques to detect and quantify their effects in both resting states and catalytic intermediates.

The Periodic Table's Impact on Bioinorganic Chemistry and Biology's Selective Use of Metal Ions

Despite the availability of a vast variety of metal ions in the periodic table, biology uses only a selective few metal ions. Most of the redox active metals used belong to the first row of transition metals in the periodic table and include Fe, Co, Ni, Mn and Cu. On the other hand, Ca, Zn and Mg are the most commonly used redox inactive metals in biology. In this chapter, we discuss the periodic table's impact on bio-inorganic chemistry, by exploring reasons behind this selective choice of metals biology. A special focus is placed on the chemical and functional reasons why one metal ion is preferred over another one. We discuss the implications of metal choice in various biological processes including catalysis, electron transfer, redox sensing and signaling. We find that bioavailability of metal ions along with their redox potentials, coordination flexibility, valency and ligand affinity determine the specificity of metals for biological processes. Understanding the implications underlying the selective choice of metals of the periodic table in these biological processes can help design more efficient catalysts, more precise biosensors and more effective drugs.