Reengineering cyt b562 for hydrogen production: A facile route to artificial hydrogenases

An artificial metalloenzyme that can oxidize water photocatalytically: design, synthesis, and characterization

In nature, light-driven water oxidation (WO) catalysis is performed by photosystem II via the delicate interplay of different cofactors positioned in its protein scaffold. Artificial systems for homogeneous photocatalytic WO are based on small molecules that often have limited solubility in aqueous solutions. In this work, we alleviated this issue and present a cobalt-based WO-catalyst containing artificial metalloenzyme (ArM) that is active in light-driven, homogeneous WO catalysis in neutral-pH aqueous solutions. A haem-containing electron transfer protein, cytochrome B5 (CB5), served to host a first-row transition-metal-based WO catalyst, CoSalen (CoIISalen, where H2Salen = N,N'-bis(salicylidene)ethylenediamine), thus producing an ArM capable of driving photocatalytic WO. The CoSalen ArM formed a water-soluble pre-catalyst in the presence of [Ru(bpy)3](ClO4)2 as photosensitizer and Na2S2O8 as the sacrificial electron acceptor, with photocatalytic activity similar to that of free CoSalen. During photocatalysis, the CoSalen-protein interactions were destabilized, and the protein partially unfolded. Rather than forming tens of nanometer sized CoOx nanoparticles as free CoSalen does under photocatalytic WO conditions, the CB5 : CoSalen ArM showed limited protein cross-linking and remained soluble. We conclude that a weak, dynamic interaction between a soluble cobalt species and apoCB5 was formed, which generated a catalytically active adduct during photocatalysis. A detailed analysis was performed on protein stability and decomposition processes during the harsh oxidizing reaction conditions of WO, which will serve for the future design of WO ArMs with improved activity and stability.

Hydrogen Evolution of a Unique DNAzyme Composed of Cobalt-Protoporphyrin IX and G-Quadruplex DNA

Molecular hydrogen (H2 ) is a clean and renewable fuel that has garnered significant interest in the search for alternatives to fossil fuels. Here, we constructed an artificial DNAzyme composed of cobalt-protoporphyrin IX (CoPP) and G-quadruplex DNA, possessing a unique H2 Oint ligand between the CoPP and G-quartet planes. We show for the first time that CoPP-DNAzyme catalyzes photo-induced H2 production under anaerobic conditions with a turnover number (TON) of 1229 ± 51 over 12 h at pH 6.05 and 10 °C. Compared with free-CoPP, complexation with G-quadruplex DNA resulted in a 4.7-fold increase in H2 production activity. The TON of the CoPP-DNAzyme revealed an optimal acid-base equilibrium with a pKa value of 7.60 ± 0.05, apparently originating from the equilibrium between Co(III)-H- and Co(I) states. Our results demonstrate that the H2 Oint ligand can augment and modulate the intrinsic catalytic activity of H2 production catalysts. These systems pave the way to using DNAzymes for H2 evolution in the direct conversion of solar energy to H2 from water.

Enzymatic and Bioinspired Systems for Hydrogen Production

The extraordinary potential of hydrogen as a clean and sustainable fuel has sparked the interest of the scientific community to find environmentally friendly methods for its production. Biological catalysts are the most attractive solution, as they usually operate under mild conditions and do not produce carbon-containing byproducts. Hydrogenases promote reversible proton reduction to hydrogen in a variety of anoxic bacteria and algae, displaying unparallel catalytic performances. Attempts to use these sophisticated enzymes in scalable hydrogen production have been hampered by limitations associated with their production and stability. Inspired by nature, significant efforts have been made in the development of artificial systems able to promote the hydrogen evolution reaction, via either electrochemical or light-driven catalysis. Starting from small-molecule coordination compounds, peptide- and protein-based architectures have been constructed around the catalytic center with the aim of reproducing hydrogenase function into robust, efficient, and cost-effective catalysts. In this review, we first provide an overview of the structural and functional properties of hydrogenases, along with their integration in devices for hydrogen and energy production. Then, we describe the most recent advances in the development of homogeneous hydrogen evolution catalysts envisioned to mimic hydrogenases.

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.

Rational design of photosynthetic reaction center protein maquettes

New technologies for efficient solar-to-fuel energy conversion will help facilitate a global shift from dependence on fossil fuels to renewable energy. Nature uses photosynthetic reaction centers to convert photon energy into a cascade of electron-transfer reactions that eventually produce chemical fuel. The design of new reaction centers de novo deepens our understanding of photosynthetic charge separation and may one day allow production of biofuels with higher thermodynamic efficiency than natural photosystems. Recently, we described the multi-step electron-transfer activity of a designed reaction center maquette protein (the RC maquette), which can assemble metal ions, tyrosine, a Zn tetrapyrrole, and heme into an electron-transport chain. Here, we detail our modular strategy for rational protein design and show that the intended RC maquette design agrees with crystal structures in various states of assembly. A flexible, dynamic apo-state collapses by design into a more ordered holo-state upon cofactor binding. Crystal structures illustrate the structural transitions upon binding of different cofactors. Spectroscopic assays demonstrate that the RC maquette binds various electron donors, pigments, and electron acceptors with high affinity. We close with a critique of the present RC maquette design and use electron-tunneling theory to envision a path toward a designed RC with a substantially higher thermodynamic efficiency than natural photosystems.

De novo protein design of photochemical reaction centers

Natural photosynthetic protein complexes capture sunlight to power the energetic catalysis that supports life on Earth. Yet these natural protein structures carry an evolutionary legacy of complexity and fragility that encumbers protein reengineering efforts and obfuscates the underlying design rules for light-driven charge separation. De novo development of a simplified photosynthetic reaction center protein can clarify practical engineering principles needed to build new enzymes for efficient solar-to-fuel energy conversion. Here, we report the rational design, X-ray crystal structure, and electron transfer activity of a multi-cofactor protein that incorporates essential elements of photosynthetic reaction centers. This highly stable, modular artificial protein framework can be reconstituted in vitro with interchangeable redox centers for nanometer-scale photochemical charge separation. Transient absorption spectroscopy demonstrates Photosystem II-like tyrosine and metal cluster oxidation, and we measure charge separation lifetimes exceeding 100 ms, ideal for light-activated catalysis. This de novo-designed reaction center builds upon engineering guidelines established for charge separation in earlier synthetic photochemical triads and modified natural proteins, and it shows how synthetic biology may lead to a new generation of genetically encoded, light-powered catalysts for solar fuel production.

A cobalt mimochrome for photochemical hydrogen evolution from neutral water

A system for visible light-driven hydrogen production from water is reported. This system makes use of a synthetic mini-enzyme known as a mimochrome (CoMC6*a) consisting of a cobalt deuteroporphyrin and two attached peptides as a catalyst, [Ru(bpy)₃]²⁺ (bpy = 2,2'-bipyridine) as a photosensitizer, and ascorbic acid as a sacrificial electron donor. The system achieves turnover numbers (TONs) up to 10,000 with respect to catalyst and optimal activity at pH 7. Comparison with related systems shows that CoMC6*a maintains the advantages of biomolecular catalysts, while exceeding other cobalt porphyrins in terms of total TON and longevity of catalysis. Herein, we lay groundwork for future study, where the synthetic nature of CoMC6*a will provide a unique opportunity to tailor proton reduction chemistry and expand to new reactivity.

Light-Driven CO2 Reduction by Co-Cytochrome b 562

The current trend in atmospheric carbon dioxide concentrations is causing increasing concerns for its environmental impacts, and spurring the developments of sustainable methods to reduce CO2 to usable molecules. We report the light-driven CO2 reduction in water in mild conditions by artificial protein catalysts based on cytochrome b 562 and incorporating cobalt protoporphyrin IX as cofactor. Incorporation into the protein scaffolds enhances the intrinsic reactivity of the cobalt porphyrin toward proton reduction and CO generation. Mutations around the binding site modulate the activity of the enzyme, pointing to the possibility of further improving catalytic activity through rational design or directed evolution.

De novo biosynthesis of a nonnatural cobalt porphyrin cofactor in E. coli and incorporation into hemoproteins

Enzymes that bear a nonnative or artificially introduced metal center can engender novel reactivity and enable new spectroscopic and structural studies. In the case of metal-organic cofactors, such as metalloporphyrins, no general methods exist to build and incorporate new-to-nature cofactor analogs in vivo. We report here that a common laboratory strain, Escherichia coli BL21(DE3), biosynthesizes cobalt protoporphyrin IX (CoPPIX) under iron-limited, cobalt-rich growth conditions. In supplemented minimal media containing CoCl₂, the metabolically produced CoPPIX is directly incorporated into multiple hemoproteins in place of native heme b (FePPIX). Five cobalt-substituted proteins were successfully expressed with this new-to-nature cobalt porphyrin cofactor: myoglobin H64V V68A, dye decolorizing peroxidase, aldoxime dehydratase, cytochrome P450 119, and catalase. We show conclusively that these proteins incorporate CoPPIX, with the CoPPIX making up at least 95% of the total porphyrin content. In cases in which the native metal ligand is a sulfur or nitrogen, spectroscopic parameters are consistent with retention of native metal ligands. This method is an improvement on previous approaches with respect to both yield and ease-of-implementation. Significantly, this method overcomes a long-standing challenge to incorporate nonnatural cofactors through de novo biosynthesis. By utilizing a ubiquitous laboratory strain, this process will facilitate spectroscopic studies and the development of enzymes for CoPPIX-mediated biocatalysis.

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.

Engineering a solid-state metalloprotein hydrogen evolution catalyst

Hydrogen has the potential to play an important role in decarbonising our energy systems. Crucial to achieving this is the ability to produce clean sources of hydrogen using renewable energy sources. Currently platinum is commonly used as a hydrogen evolution catalyst, however, the scarcity and expense of platinum is driving the need to develop non-platinum-based catalysts. Here we report a protein-based hydrogen evolution catalyst based on a recombinant silk protein from honeybees and a metal macrocycle, cobalt protoporphyrin (CoPPIX). We enhanced the hydrogen evolution activity three fold compared to the unmodified silk protein by varying the coordinating ligands to the metal centre. Finally, to demonstrate the use of our biological catalyst, we built a proton exchange membrane (PEM) water electrolysis cell using CoPPIX-silk as the hydrogen evolution catalyst that is able to produce hydrogen with a 98% Faradaic efficiency. This represents an exciting advance towards allowing protein-based catalysts to be used in electrolysis cells.

CfbA promotes insertion of cobalt and nickel into ruffled tetrapyrroles in vitro

The nickel chelatase CfbA is the smallest member of the chelatase family, but the mechanism by which this enzyme inserts nickel into sirohydrochlorin is unknown. In order to gain mechanistic insight, metal binding, tetrapyrrole binding, and enzyme activity were characterized for a variety of substrates using several spectroscopic and computational approaches. Mass spectrometery and magnetic circular dichroism experiments revealed that CfbA binds an octahedral, high-spin metal substrate. UV/Vis absorption spectroscopy demonstrated that the enzyme binds a wide range of tetrapyrrole substrates and perturbs their electronic structures. Based upon activity assays, CfbA promotes insertion of cobalt and nickel into several tetrapyrroles, including cobalt insertion into protopophyrin IX. Finally, density functional theory models were developed which strongly suggest that observed spectral changes upon binding to the enzyme can be explained by tetrapyrrole ruffling, but not deprotonation or saddling. The observation of an octahedral, high-spin metal bound to CfbA leads to a generalization for all class II chelatases: these enzymes bind labile metal substrates and metal desolvation is not a rate-limiting step. The conclusion that CfbA ruffles its tetrapyrrole substrate reveals that the CfbA mechanism is different from that currently proposed for ferrochelatase, and identifies an intriguing correlation between metal substrate specificity and tetrapyrrole distortion mode in chelatases.

Hydrogen evolution from water catalyzed by cobalt-mimochrome VI*a, a synthetic mini-protein

The folding of a synthetic mini-hydrogenase is shown to enhance catalyst efficiency and longevity.

A synthetic enzyme is reported that electrocatalytically reduces protons to hydrogen (H₂) in water near neutral pH under aerobic conditions. Cobalt mimochrome VI*a (CoMC6*a) is a mini-protein with a cobalt deuteroporphyrin active site within a scaffold of two synthetic peptides covalently bound to the porphyrin. Comparison of the activity of CoMC6*a to that of cobalt microperoxidase-11 (CoMP11-Ac), a cobalt porphyrin catalyst with a single “proximal” peptide and no organized secondary structure, reveals that CoMC6*a has significantly enhanced longevity, yielding a turnover number exceeding 230 000, in comparison to 25 000 for CoMP11-Ac. Furthermore, comparison of cyclic voltammograms of CoMC6*a and CoMP11-Ac indicates that the trifluoroethanol-induced folding of CoMC6*a lowers the overpotential for catalytic H₂ evolution by up to 100 mV. These results demonstrate that even a minimal polypeptide matrix can enhance longevity and efficiency of a H₂-evolution catalyst.

From protein engineering to artificial enzymes - biological and biomimetic approaches towards sustainable hydrogen production

Hydrogen gas is used extensively in industry today and is often put forward as a suitable energy carrier due its high energy density. Currently, the main source of molecular hydrogen is fossil fuels via steam reforming. Consequently, novel production methods are required to improve the sustainability of hydrogen gas for industrial processes, as well as paving the way for its implementation as a future solar fuel. Nature has already developed an elaborate hydrogen economy, where the production and consumption of hydrogen gas is catalysed by hydrogenase enzymes. In this review we summarize efforts on engineering and optimizing these enzymes for biological hydrogen gas production, with an emphasis on their inorganic cofactors. Moreover, we will describe how our understanding of these enzymes has been applied for the preparation of bio-inspired/-mimetic systems for efficient and sustainable hydrogen production.

Reaction mechanism of hydrogen evolution catalysed by Co and Fe complexes containing a tetra-dentate phosphine ligand - a DFT study

The reaction mechanism of the electro-catalytic proton reduction in neutral phosphate buffer enabled by mononuclear cobalt and iron complexes containing a tetra-dentate phosphine ligand (MP₄N₂, M = Fe, Co) has been elucidated by density functional calculations. The phosphate from the buffer was found to play a crucial role by coordinating to the metal and delivering a proton to the metal hydride in the H-H bond formation. For the more efficient cobalt catalyst, the starting species is a Co^II complex with a hydrogen phosphate and a water molecule ligated at the two vacant coordination sites. Two sequential proton-coupled electron transfer reductions lead to the formation of a Co^II-H intermediate with a dihydrogen phosphate ligand, and the reduction potentials for these two steps were calculated to be -0.58 V and -0.72 V, respectively. Subsequently, the H-H bond formation takes place via coupling of the Co^II-H and the proton from the dihydrogen phosphate ligand. The total barrier was calculated to be 18.2 kcal mol^-1 with an applied potential of -0.5 V, which can further decrease to only 11.2 kcal mol^-1 with an applied potential of -0.8 V. When the phosphate is displaced by a water molecule, the total barrier for the dihydrogen formation increases by 7.3 kcal mol^-1. For the iron catalyst, the overall mechanism is essentially the same; however, the first reduction (Fe^II/Fe^I, potential of -1.13 V) is likely the rate-limiting step. The calculated results are in good agreement with the experimental data, which showed an onset potential of -0.50 V for the cobalt complex and -1.03 V for the iron complex.

Artificial Metalloenzymes: Reaction Scope and Optimization Strategies

The incorporation of a synthetic, catalytically competent metallocofactor into a protein scaffold to generate an artificial metalloenzyme (ArM) has been explored since the late 1970's. Progress in the ensuing years was limited by the tools available for both organometallic synthesis and protein engineering. Advances in both of these areas, combined with increased appreciation of the potential benefits of combining attractive features of both homogeneous catalysis and enzymatic catalysis, led to a resurgence of interest in ArMs starting in the early 2000's. Perhaps the most intriguing of potential ArM properties is their ability to endow homogeneous catalysts with a genetic memory. Indeed, incorporating a homogeneous catalyst into a genetically encoded scaffold offers the opportunity to improve ArM performance by directed evolution. This capability could, in turn, lead to improvements in ArM efficiency similar to those obtained for natural enzymes, providing systems suitable for practical applications and greater insight into the role of second coordination sphere interactions in organometallic catalysis. Since its renaissance in the early 2000's, different aspects of artificial metalloenzymes have been extensively reviewed and highlighted. Our intent is to provide a comprehensive overview of all work in the field up to December 2016, organized according to reaction class. Because of the wide range of non-natural reactions catalyzed by ArMs, this was done using a functional-group transformation classification. The review begins with a summary of the proteins and the anchoring strategies used to date for the creation of ArMs, followed by a historical perspective. Then follows a summary of the reactions catalyzed by ArMs and a concluding critical outlook. This analysis allows for comparison of similar reactions catalyzed by ArMs constructed using different metallocofactor anchoring strategies, cofactors, protein scaffolds, and mutagenesis strategies. These data will be used to construct a searchable Web site on ArMs that will be updated regularly by the authors.

Ru-protein-Co biohybrids designed for solar hydrogen production: understanding electron transfer pathways related to photocatalytic function

Two ruthenium-protein-cobaloxime biohybrids produce photocatalytic hydrogen through different catalytic pathways characterized by EPR and transient optical spectroscopies.

A series of Ru–protein–Co biohybrids have been prepared using the electron transfer proteins ferredoxin (Fd) and flavodoxin (Fld) as scaffolds for photocatalytic hydrogen production. The light-generated charge separation within these hybrids has been monitored by transient optical and electron paramagnetic resonance spectroscopies. Two distinct electron transfer pathways are observed. The Ru–Fd–Co biohybrid produces up to 650 turnovers of H₂ utilizing an oxidative quenching mechanism for Ru(ii)* and a sequential electron transfer pathway via the native [2Fe–2S] cluster to generate a Ru(iii)–Fd–Co(i) charge separated state that lasts for ∼6 ms. In contrast, a direct electron transfer pathway occurs for the Ru–ApoFld–Co biohybrid, which lacks an internal electron relay, generating Ru(i)–ApoFld–Co(i) charge separated state that persists for ∼800 μs and produces 85 turnovers of H₂ by a reductive quenching mechanism for Ru(ii)*. This work demonstrates the utility of protein architectures for linking donor and catalytic function via direct or sequential electron transfer pathways to enable stabilized charge separation which facilitates photocatalysis for solar fuel production.

Design Strategies for Redox Active Metalloenzymes: Applications in Hydrogen Production

The last decades have seen an increased interest in finding alternative means to produce renewable fuels in order to satisfy the growing energy demands and to minimize environmental impact. Nature can serve as an inspiration for development of these methodologies, as enzymes are able to carry out a wide variety of redox processes at high efficiency, employing a wide array of earth-abundant transition metals to do so. While it is well recognized that the protein environment plays an important role in tuning the properties of the different metal centers, the structure/function relationships between amino acids and catalytic centers are not well resolved. One specific approach to study the role of proteins in both electron and proton transfer is the biomimetic design of redox active peptides, binding organometallic clusters in well-understood protein environments. Here we discuss different strategies for the design of peptides incorporating redox active FeS clusters, [FeFe]-hydrogenase organometallic mimics, and porphyrin centers into different peptide and protein environments in order to understand natural redox enzymes.

DFT study of the mechanism of hydrogen evolution catalysed by molecular Ni, Co and Fe catalysts containing a diamine–tripyridine ligand

Electrolysis of water to obtain hydrogen is a practical way to transform surplus electrical power into clean and sustainable hydrogen fuels.