Artificial hydrogenase: biomimetic approaches controlling active molecular catalysts

Site-Selective Incorporation of a Functional Group into Lys175 in the Vicinity of the Active Site of Chymotrypsin by Using Peptidyl α-Aminoalkylphosphonate Diphenyl Ester-Derivatives

We previously reported that Lys175 in the region of the active site of chymotrypsin (Csin) could be site-selectively modified by using an N-hydroxy succinimide (NHS) ester of the peptidyl derivative containing 1-amino-2-ethylphenylphosphonate diphenyl ester [NHS-Suc-Ala-Ala-PheP(OPh)2]. In this study, the Lys175-selective modification method was expanded to incorporate functional groups into Lys 175 in Csin. Two types of peptidyl phosphonate derivatives with the dansyl group (Dan) as a functional molecule, Dan-β-Ala-[Asp(NHS) or Glu(NHS)]-Ala-Ala-(R)-PheP(OPh)2 (DanD and DanE, respectively), were synthesized, and their action was evaluated when modifying Lys175 in Csin. Ion-exchange chromatography (IEC), fluorescence spectroscopy, and LC-MS/MS were used to analyze the products from the reaction of Csin with DanD or DanE. By IEC and LC-MS/MS, the results showed that DanE reacted with Csin more effectively than DanD to produce the modified Csin (DanMCsin) bearing Dan at Lys175. DanMCsin exhibited an enzymatic activity corresponding to 1/120 of Csin against Suc-Ala-Ala-Phe-pNA. In addition, an effect of Lys175 modification on the access of the proteinaceous Bowman–Birk inhibitor to the active site of DanMCsin was investigated. In conclusion, by using a peptidyl derivative containing 1-amino-2-ethylphenylphosphonate diphenyl ester, we demonstrated that a functional group could be incorporated into Lys175 in Csin.

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.

Photocatalytic Hydrogen Production and Carbon Dioxide Reduction Catalyzed by an Artificial Cobalt Hemoprotein

The covalent insertion of a cobalt heme into the cavity of an artificial protein named alpha Rep (αRep) leads to an artificial cobalt hemoprotein that is active as a catalyst not only for the photo-induced production of H₂, but also for the reduction of CO₂ in a neutral aqueous solution. This new artificial metalloenzyme has been purified and characterized by Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS), circular dichroism, and UltraViolet-Visible spectroscopy. Using theoretical experiments, the structure of this biohybrid and the positioning of the residues near the metal complex were examined, which made it possible to complete the coordination of the cobalt ion by an axial glutamine Gln283 ligand. While the Co(III)-porphyrin catalyst alone showed weak catalytic activity for both reactions, 10 times more H₂ and four times more CO₂ were produced when the Co(III)-porphyrin complex was buried in the hydrophobic cavity of the protein. This study thus provides a solid basis for further improvement of these biohybrids using well-designed modifications of the second and outer coordination sphere by site-directed mutagenesis of the host protein.

Mononuclear manganese complexes as hydrogen evolving catalysts

Molecular hydrogen (H₂) is one of the pillars of future non-fossil energy supply. In the quest for alternative, non-precious metal catalysts for hydrogen generation to replace platinum, biological systems such as the enzyme hydrogenase serve as a blueprint. By taking inspiration from the bio-system, mostly nickel- or iron-based catalysts were explored so far. Manganese is a known oxygen-reducing catalyst but has received much less attention for its ability to reduce protons in acidic media. Here, the synthesis, characterization, and reaction mechanisms of a series of four mono-nuclear Mn(I) complexes in terms of their catalytic performance are reported. The effect of the variation of equatorial and axial ligands in their first and second coordination spheres was assessed pertaining to their control of the turnover frequencies and overpotentials. All four complexes show reactivity and reduce protons in acidic media to release molecular hydrogen H₂. Quantum chemical studies were able to assign and interpret spectral characterizations from UV–Vis and electrochemistry and rationalize the reaction mechanism. Two feasible reaction mechanisms of electrochemical (E) and protonation (C) steps were compared. Quantum chemical studies can assign peaks in the cyclic voltammetry to structural changes of the complex during the reaction. The first one-electron reduction is essential to generate an open ligand-based site for protonation. The distorted octahedral Mn complexes possess an inverted second one-electron redox potential which is a pre-requisite for a swift and facile release of molecular hydrogen. This series on manganese catalysts extends the range of elements of the periodic table which are able to catalyze the hydrogen evolution reaction and will be explored further.

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 .

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.

Catalytic Metallopolymers from [2Fe-2S] Clusters: Artificial Metalloenzymes for Hydrogen Production

Reviewed herein is the development of novel polymer-supported [2Fe-2S] catalyst systems for electrocatalytic and photocatalytic hydrogen evolution reactions. [FeFe] hydrogenases are the best known naturally occurring metalloenzymes for hydrogen generation, and small-molecule, [2Fe-2S]-containing mimetics of the active site (H-cluster) of these metalloenzymes have been synthesized for years. These small [2Fe-2S] complexes have not yet reached the same capacity as that of enzymes for hydrogen production. Recently, modern polymer chemistry has been utilized to construct an outer coordination sphere around the [2Fe-2S] clusters to provide site isolation, water solubility, and improved catalytic activity. In this review, the various macromolecular motifs and the catalytic properties of these polymer-supported [2Fe-2S] materials are surveyed. The most recent catalysts that incorporate a single [2Fe-2S] complex, termed single-site [2Fe-2S] metallopolymers, exhibit superior activity for H₂ production.

Differential Protonation at the Catalytic Six-Iron Cofactor of [FeFe]-Hydrogenases Revealed by 57Fe Nuclear Resonance X-ray Scattering and Quantum Mechanics/Molecular Mechanics Analyses

[FeFe]-hydrogenases are efficient biological hydrogen conversion catalysts and blueprints for technological fuel production. The relations between substrate interactions and electron/proton transfer events at their unique six-iron cofactor (H-cluster) need to be elucidated. The H-cluster comprises a four-iron cluster, [4Fe4S], linked to a diiron complex, [FeFe]. We combined ⁵⁷Fe-specific X-ray nuclear resonance scattering experiments (NFS, nuclear forward scattering; NRVS, nuclear resonance vibrational spectroscopy) with quantum-mechanics/molecular-mechanics computations to study the [FeFe]-hydrogenase HYDA1 from a green alga. Selective ⁵⁷Fe labeling at only [4Fe4S] or [FeFe], or at both subcomplexes was achieved by protein expression with a ⁵⁷Fe salt and in vitro maturation with a synthetic diiron site precursor containing ⁵⁷Fe. H-cluster states were populated under infrared spectroscopy control. NRVS spectral analyses facilitated assignment of the vibrational modes of the cofactor species. This approach revealed the H-cluster structure of the oxidized state (Hox) with a bridging carbon monoxide at [FeFe] and ligand rearrangement in the CO-inhibited state (Hox-CO). Protonation at a cysteine ligand of [4Fe4S] in the oxidized state occurring at low pH (HoxH) was indicated, in contrast to bridging hydride binding at [FeFe] in a one-electron reduced state (Hred). These findings are direct evidence for differential protonation either at the four-iron or diiron subcomplex of the H-cluster. NFS time-traces provided Mössbauer parameters such as the quadrupole splitting energy, which differ among cofactor states, thereby supporting selective protonation at either subcomplex. In combination with data for reduced states showing similar [4Fe4S] protonation as HoxH without (Hred') or with (Hhyd) a terminal hydride at [FeFe], our results imply that coordination geometry dynamics at the diiron site and proton-coupled electron transfer to either the four-iron or the diiron subcomplex discriminate catalytic and regulatory functions of [FeFe]-hydrogenases. We support a reaction cycle avoiding diiron site geometry changes during rapid H₂ turnover.

Bioinspired approach toward molecular electrets: synthetic proteome for materials

Molecular-level control of charge transfer (CT) is essential for both, organic electronics and solar-energy conversion, as well as for a wide range of biological processes. This article provides an overview of the utility of local electric fields originating from molecular dipoles for directing CT processes. Systems with ordered dipoles, i.e. molecular electrets, are the centerpiece of the discussion. The conceptual evolution from biomimicry to biomimesis, and then to biological inspiration, paves the roads leading from testing the understanding of how natural living systems function to implementing these lessons into optimal paradigms for specific applications. This progression of the evolving structure-function relationships allows for the development of bioinspired electrets composed of non-native aromatic amino acids. A set of such non-native residues that are electron-rich can be viewed as a synthetic proteome for hole-transfer electrets. Detailed considerations of the electronic structure of an individual residue prove of key importance for designating the points for optimal injection of holes (i.e. extraction of electrons) in electret oligomers. This multifaceted bioinspired approach for the design of CT molecular systems provides unexplored paradigms for electronic and energy science and engineering.

Streptavidin as a Scaffold for Light-Induced Long-Lived Charge Separation

Long-lived photo-driven charge separation is demonstrated by assembling a triad on a protein scaffold. For this purpose, a biotinylated triarylamine was added to a Ru^II -streptavidin conjugate bearing a methyl viologen electron acceptor covalently linked to the N-terminus of streptavidin. To improve the rate and lifetime of the electron transfer, a negative patch consisting of up to three additional negatively charged amino acids was engineered through mutagenesis close to the biotin-binding pocket of streptavidin. Time-resolved laser spectroscopy revealed that the covalent attachment and the negative patch were beneficial for charge separation within the streptavidin hosted triad; the charge separated state was generated within the duration of the excitation laser pulse, and lifetimes up to 3120 ns could be achieved with the optimized supramolecular triad.

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.

Photosensitized H2 Production Using a Zinc Porphyrin-Substituted Protein, Platinum Nanoparticles, and Ascorbate with No Electron Relay: Participation of Good's Buffers

Development of efficient light-driven splitting of water, 2H₂O → 2H₂ + O₂, often attempts to optimize photosensitization of the reductive and oxidative half-reactions individually. Numerous homogeneous and heterogeneous systems have been developed for photochemical stimulation of the reductive half reaction, 2H⁺ + 2e^- → H₂. These systems generally consist of various combinations of a H⁺ reduction catalyst, a photosensitizer (PS), and a "sacrificial" electron donor. Zinc(II)-porphyrins (ZnPs) have frequently been used as PSs for H₂ generation, but they are subject to various self-quenching processes in aqueous solutions. Colloidal platinum in nanoparticle form (Pt NP) is a classical H⁺ reduction catalyst using ZnP photosensitizers, but efficient photosensitized H₂ generation requires an electron relay molecule between ZnP and Pt NP. The present report describes an aqueous system for visible (white) light-sensitized generation of H₂ using a protein-embedded Zn(II)-protoporphyrin IX as PS and Pt NP as H⁺ reduction catalyst without an added electron relay. This system operated efficiently in piperazino- and morpholino-alkylsulfonic acid (Good's buffers), which served as sacrificial electron donors. The system also required ascorbate at relatively modest concentrations, which stabilized the Zn(II)-protoporphyrin IX against photodegradation. In the absence of an electron relay molecule, the photosensitized H₂ generation must involve formation of at least a transient complex between a protein-embedded Zn(II)-protoporphyrin IX species and Pt NP.

Experimental and DFT Investigations Reveal the Influence of the Outer Coordination Sphere on the Vibrational Spectra of Nickel-Substituted Rubredoxin, a Model Hydrogenase Enzyme

Nickel-substituted rubredoxin (NiRd) is a functional enzyme mimic of hydrogenase, highly active for electrocatalytic and solution-phase hydrogen generation. Spectroscopic methods can provide valuable insight into the catalytic mechanism, provided the appropriate technique is used. In this study, we have employed multiwavelength resonance Raman spectroscopy coupled with DFT calculations on an extended active-site model of NiRd to probe the electronic and geometric structures of the resting state of this system. Excellent agreement between experiment and theory is observed, allowing normal mode assignments to be made on the basis of frequency and intensity analyses. Both metal-ligand and ligand-centered vibrational modes are enhanced in the resonance Raman spectra. The latter provide information about the hydrogen bonding network and structural distortions due to perturbations in the secondary coordination sphere. To reproduce the resonance enhancement patterns seen for high-frequency vibrational modes, the secondary coordination sphere must be included in the computational model. The structure and reduction potential of the Ni^IIIRd state have also been investigated both experimentally and computationally. This work begins to establish a foundation for computational resonance Raman spectroscopy to serve in a predictive fashion for investigating catalytic intermediates of NiRd.

Dynamic Flexibility of Hydrogenase Active Site Models Studied with 2D-IR Spectroscopy

Hydrogenase enzymes enable organisms to use H₂ as an energy source, having evolved extremely efficient biological catalysts for the reversible oxidation of molecular hydrogen. Small-molecule mimics of these enzymes provide both simplified models of the catalysis reactions and potential artificial catalysts that might be used to facilitate a hydrogen economy. We have studied two diiron hydrogenase mimics, μ-pdt-[Fe(CO)₃]₂ and μ-edt-[Fe(CO)₃]₂ (pdt = propanedithiolate, edt = ethanedithiolate), in a series of alkane solvents and have observed significant ultrafast spectral dynamics using two-dimensional infrared (2D-IR) spectroscopy. Since solvent fluctuations in nonpolar alkanes do not lead to substantial electrostatic modulations in a solute's vibrational mode frequencies, we attribute the spectral diffusion dynamics to intramolecular flexibility. The intramolecular origin is supported by the absence of any measurable solvent viscosity dependence, indicating that the frequency fluctuations are not coupled to the solvent motional dynamics. Quantum chemical calculations reveal a pronounced coupling between the low-frequency torsional rotation of the carbonyl ligands and the terminal CO stretching vibrations. The flexibility of the CO ligands has been proposed to play a central role in the catalytic reaction mechanism, and our results highlight that the CO ligands are highly flexible on a picosecond time scale.

Photosensitized H2 generation from "one-pot" and "two-pot" assemblies of a zinc-porphyrin/platinum nanoparticle/protein scaffold

We report photosensitized H2 generation using a protein scaffold that nucleates formation of platinum nanoparticles (Pt NPs) and contains "built-in" photosensitizers. The photosensitizers, zinc-protoporphyrin IX or zinc-mesoporphyrin IX (ZnP) were incorporated in place of the naturally occurring heme in the 24-subunit iron storage protein bacterioferritin (Bfr) when the ZnPs were added to the E. coli expression medium. We engineered a stable dimeric Bfr variant with two protein subunits sandwiching a ZnP. Ten glycines were also substituted in place of residues surrounding the vinyl side of the porphyrin in order increase access of solvent and/or redox agents. An optimized "one-pot" reaction of this glycine-substituted ZnMP-Bfr dimer with a Pt(iv) salt and borohydride resulted in a ∼50 : 50 mixture of protein in the form of Pt-free glycine-substituted ZnP-Bfr dimers and re-assembled 24-mers surrounding Pt NPs formed in situ. H2 production occurred upon visible light irradiation of this "one-pot" product when combined with triethanolamine as sacrificial electron donor and methyl viologen as electron relay. An analogous "two-pot" system containing mixtures of separately prepared Pt-free glycine-substituted ZnP-Bfr dimer and porphyrin-free Pt NP@Bfr 24-mer also showed robust photosensitized H2 generation. The glycine-substituted-ZnP-Bfr dimer thus served as photosensitizer for catalytic reduction of methyl viologen by triethanolamine, and the reduced methyl viologen was able to transfer electrons across the Bfr 24-mer protein shell to generate H2 at the enclosed Pt NP in a "dark" reaction. Our results demonstrate that Bfr is a readily manipulatable and versatile scaffold for photosensitized redox chemistry.

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.