[NiFe] hydrogenases are microbial metalloenzymes that catalyse the reversible interconversion between molecular hydrogen and protons with high selectivity and efficiency. The catalytic properties of different [NiFe] hydrogenases vary according to the physiological roles they each play, yet all seem to be based upon an almost identical catalytic site architecture. Through efforts to understand the structural and mechanistic basis for the differing properties of [NiFe] hydrogenases, it has become increasingly evident that electron transfer to and from the active site, mediated by a set of Iron-Sulphur clusters, influences to a significant extent the observed catalytic properties of different hydrogenases. Here we present a comprehensive study of E. coli Hyd-1, an O₂-tolerant hydrogenase, by PFE with a focus on the properties that are characteristic of O₂-tolerant enzymes: overpotential requirement, lack of H₂ production, low K^H₂<sub style='position: relative; left: -1.2em;'>M</sub>, and high E_switch. We show that Hyd-1 catalysis can be made reversible by increasing the equilibrium potential for the reaction through changes in substrate concentration, and that electron transfer into and out of the enzyme molecule, rather than active site properties, is responsible for the characteristics of overpotential and bias in Hyd-1. We present a set of experiments with Hyd-2 from E. coli in which surface-exposed cysteine residues are specifically introduced near the distal and medial Iron-Sulphur clusters to act as points of attachment for photosensitizer molecules, and a study of the kinetics of electron injection from photoexcited molecules to the enzyme and subsequent absorbance changes attributed to transient redox changes at the active site. We are able to show lightdependent H2 production from a Hyd-2 + photosensitizer system. Finally, we present the first purification of the formate-hydrogen lyase (FHL) complex from E. coli, the complex responsible for H2-production by this organism during fermentation, and we provide a characterisation of the complex by EPR and PFE. The properties of Hyd-3, the hydrogenase subunit of the FHL, seem to differ from those observed previously for other [NiFe] hydrogenases.

Metallocofactors are ubiquitous in nature, serving multiple purposes in proteins. These metallocofactors typically act as the site of catalysis or as an electron relay to move electrons within the protein, or within the cell, and are very energetically costly to manufacture. Yet, in nature it can appear that supernumerary, or ‘auxiliary’ cofactors are apparent, with no clear function. In this thesis, I address the question of what roles additional cofactors play, and why they are retained. The radical S-adenosylmethionine (AdoMet) enzyme superfamily has displayed great diversity in the cofactor requirements for its members. Some members of this family contain only the canonical [4Fe-4S] cluster, which reductively cleaves AdoMet to initiate chemistry, while others have additional [2Fe-2S] or [4Fe-4S] clusters. Even greater cofactor complexity is seen with the B12-dependent subclass, featuring a cobalamin-binding domain in addition to the canonical FeS cluster. The majority of this thesis has focused on using the technique of protein film electrochemistry (PFE) to study members of various subclasses of this superfamily: a dehydrogenase: BtrN, two methylthiotransferases: MiaB and RimO, as well as OxsB and TsrM, two B12-dependent enzymes. By evaluating the redox properties of members of different subclasses, we have been able to shed light on the redox properties of this superfamily, in general, and observed that the redox properties of auxiliary clusters can differ widely between subclasses (e.g. BtrN versus MiaB). PFE has also been used to evaluate five ferredoxins that are possible electron donors for MiaB from Thermotoga maritima. Additionally, bacterial cytochrome c peroxidases (bCCPs) are diheme enzymes catalyzing the detoxification of hydrogen peroxide; however, a novel subclass of bCCPs containing a third heme-binding motif has been identified in enteric pathogens. Protein film electrochemistry has been used to study the redox properties of Escherichia coli YhjA, a member of this subgroup. Further characterization of this novel bCCP was achieved with electron paramagnetic resonance, optical spectroscopy, and steady-state kinetics. Through characterizing YhjA and members of the AdoMet radical enzyme superfamily, we have shed light on the role these additional cofactors play in the mechanism and how these enzymes are tuned for their specific chemistries. / 2018-08-11T00:00:00Z

Hydrogenases are a class of metalloenzymes which catalyse H₂ oxidation and its reverse reaction, H⁺ reduction. There is interest in investigating how H₂ as an energy carrier is cycled in biology. Hydrogenases have also been studied extensively because there are potential applications for them as catalysts for H₂ oxidation in fuel cells or H₂ production via light-driven water splitting. For these applications, the ability for the hydrogenase to work in the presence of O₂ is an important issue. The microorganism Ralstonia eutropha is a well-studied model aerobic H₂ oxidiser: it can adopt H₂ as the sole energy source to grow cells in the presence of O₂. It produces at least three distinct O₂-tolerant NiFe hydrogenases: the membrane-bound hydrogenase (MBH), the NAD⁺-reducing soluble hydrogenase (SH) and the regulatory hydrogenase (RH). This Thesis employs protein film electrochemistry (PFE) to study the SH and RH. It is found that the SH is able to work in both direction (H₂ oxidation and H⁺ reduction) with minimum overpotential, which is critical in coupling 2H⁺/H₂ cycling with the closely spaced NAD⁺/NADH potential. Reactions of the SH with O₂ have been investigated, revealing at least two distinct O₂-inactivated states, but consistent with the requirement for the SH to function in air, it can be reactivated in the presence of O₂ at low potentials which could be provided by the NAD⁺/NADH pool in vivo. The affinity of the RH for H₂ was determined by PFE and found to be slightly higher than that of the SH and MBH. This may provide a way for the microbe to regulate hydrogenase expression in response to the H₂ availability. Carbon monoxide and O₂-inactivated states of the RH have been identified for the first time, confirming that a constricted gas channel is not sufficient to explain its O₂ tolerance. Observation of potential dependent reactions in hydrogenases means that it is important to have spectroscopic methods for characterising states triggered by inhibitors and potential. An Infrared spectroelectrochemical approach suitable for studying metalloenzymes has been developed and preliminary spectra on RH recorded. This method should provide many opportunities for future studies of redox states of hydrogenases.

Hydrogenases catalyse the interconversion of H₂ and H⁺. Protein Film Electrochemistry (PFE), a technique in which a redox enzyme is adsorbed directly onto an electrode, enables a detailed description of the catalytic function of these metalloenzymes to be obtained. Unlike small-molecule electrocatalysts, the hydrogenase active site is surrounded by a protein structure ensuring that it is relatively unperturbed by the electrode surface. In this thesis, PFE is used alongside mathematical modelling to explain differences between [NiFe]- and [FeFe]-hydrogenases, highlighting some important considerations for efficient, reversible electrocatalysis. This thesis probes the unusual reaction between [NiFe]-hydrogenases and cyanide. Through a detailed study utilising PFE, Electron Paramagnetic Resonance (EPR) and Attenuated Total Reflection Infrared spectroelectrochemistry (ATR-IR), it is demonstrated that cyanide promotes the formation of the inactive Ni-B state. Preferred formation of the Ni-B state over more slowly reactivating Unready states is considered an important characteristic of the O₂-tolerant class of [NiFe]-hydrogenases. The nature of the Ni-L state, commonly thought to be an artefact formed when a [NiFe]-hydrogenase is exposed to visible light, is probed via EPR and ATR-IR. In this thesis, the Ni-L state is shown to occur in samples of Hydrogenase-1 from Escherichia coli that have not been exposed to visible light, calling into question the true nature of this state. Finally, this thesis details the first study in which PFE is used to investigate the spontaneous incorporation of a synthetic active site mimic complex into apo-hydrogenase. Incorporation into apo-hydrogenase from Chlamydomonas reinhardtii and Clostridium pasteurianum is discussed, in both cases resulting in fully functional [FeFe]-hydrogenase, electrochemically indistinguishable from the native enzyme.

Nicotinamide cofactors in their reduced and oxidised forms are important redox agents in biology. Of about 3000 dehydrogenases available to date, many require these cofactors for their activity. Dehydrogenases are of interest to chemists as they offer asymmetric catalysis to yield chiral products. The requirement of dehydrogenases for nicotinamide cofactors necessitates research into finding the best way of recycling the oxidised or reduced forms of these cofactors. Electrocatalytic NAD(P)H oxidation and NAD(P)⁺ reduction on standard electrodes is problematic due to unwanted side reactions and high overpotential requirements, but in Nature efficient enzyme catalysts are available to facilitate these reactions. The focus of this Thesis, the Soluble Hydrogenase of R. eutropha (SH) is a multimeric bidirectional hydrogenase that couples H2 oxidation to the reduction of NAD⁺ to NADH. Protein Film Electrochemistry (PFE) has been employed to study NAD⁺-reducing catalytic moieties of the SH for the first time. It is shown that SH subunits on an electrode are able to catalyse NADH oxidation and NAD⁺ reduction efficiently with minimal overpotential, which is significant because in vivo, NAD(H) cycling is coupled to 2H⁺/H₂ cycling and these reactions are closely spaced in potential. Substrate affinities and inhibition constants for the SH, determined using PFE are discussed in the context of the SH function and the related catalytic domains of respiratory Complex I. A range of molecules that are known to inhibit the related Complex I have been investigated for their ability to inhibit the SH moieties: the similarity between inhibition constants is consistent with structural and functional similarity between the SH and Complex I. The ability of the SH moieties to sustain NAD(H) catalysis in the presence of O₂ is also demonstrated and is consistent with the requirement for the SH to function under aerobic conditions and to reactivate the inactivated hydrogenase moiety by supplying low potential electrons from NADH. Engineered variants of the SH, designed to enhance the affinity towards NADP⁺, were investigated for the first time, using PFE. Electrochemical characterisation of the variants is presented and results are discussed alongside findings on the wild type SH. The variants are shown to exhibit NADP⁺ reduction, and to have higher affinity towards NADP⁺ than the wild type SH. The first efficient NADP⁺ reduction and NADPH oxidation is observed for one of the variants on a graphite electrode and the best variant showed a K_M of 1.7 mM for NADP⁺. This Thesis also provides evidence for the ability of moieties of the SH to be used in cofactor regeneration systems. Two novel systems are demonstrated. The first involves H₂ driven NADH recycling based on the NAD⁺-reducing moiety of the SH immobilised on graphite particles together with a hydrogenase or platinum, with electrons from H₂ passed from the hydrogenase through the graphite to the NAD⁺-reducing moiety. The second involves an electrode modified with the NAD⁺-reducing moiety of the SH, and is demonstrated as an electrochemical NADH recycling system coupled with NADH-dependent pyruvate reduction to lactate by lactate dehydrogenase. The ability of variants of the SH to catalyse NADP⁺ reduction suggests that it may also be possible to use these systems for recycling NADPH for catalysis of important biotransformation reactions by NADPH-dependent dehydrogenases.

No description available.

The use of H2 as an energy carrier has in recent years been identified as a promising future solution to the current energy crisis. Hydrogenases are metalloenzymes found in many microorganisms and are used to catalyse the reversible inter-conversion of protons and H2. These enzymes and their synthetic analogues have been recognised as a way to facilitate the use of H2 as a fuel. A major challenge to the future use of these catalysts is their reactions with small molecule inhibitors, such as oxygen and carbon monoxide. Detailed understanding of the structure and catalytic mechanism of these highly efficient catalysts is vital for the design of bio-inspired functional analogues for use in technological applications. In this thesis electrochemical studies of three [FeFe]-hydrogenases are presented, performed using the technique of protein film electrochemistry. The strong potential dependence of the reaction of these hydrogenases with carbon monoxide and formaldehyde is characterised and rationalised. These studies provide compelling evidence for the formation of a previously ambiguous super-reduced state of [FeFe]-hydrogenase at low potential. This state is shown to be active and stable, and it is proposed that this state is involved in catalytic H2 production. This super-reduced state is shown to have a high affinity for the reversible binding of formaldehyde, but a very low affinity for both carbon monoxide and oxygen. Activation of carbon monoxide inhibited [FeFe]-hydrogenase can be very rapidly induced by the application of a sufficiently reducing potential. These enzymes, considered to be oxygen sensitive, are shown to be extremely tolerant to irreversible oxygen damage at very reducing potentials where the super-reduced state is formed.

Hydrogenases are a family of enzyme that catalyses the bidirectional interconversion of H⁺ and H₂. There are two major classes of hydrogenases: the [NiFe(Se)]- and [FeFe]-hydrogenases. Both of these benefit from characteristics which would be advantageous to their use in technological devices for H₂ evolution and the generation of energy. These features are explored in detail in this thesis, with a particular emphasis placed on defining the conditions that limit the activity of hydrogenases when reducing H⁺ to produce H₂. Electrochemistry can be used as a direct measure of enzymatic activity; thus, Protein Film Electrochemistry, in which the protein is adsorbed directly onto the electrode, has been employed to probe catalysis by hydrogenases. Various characteristics of hydrogenases were probed. The catalytic bias for H₂ production was interrogated and the inhibition of H₂ evolution by H₂ itself (a major drawback to the use of some hydrogenases in technological devices to produce H₂) was quantified for a number of different hydrogenase. Aerobic inactivation of hydrogenases is also a substantial technological limitation; thus, inactivation of both H₂ production and H₂ oxidation by O₂ was studied in detail. This was compared to inhibition of hydrogenases by CO so as to elucidate the mechanism of binding of diatomic molecules and determine the factors limiting inactivation. This allows for a preliminary proposal for the genetic redesigning of hydrogenases for biotechnological purposes to be made. Finally, preliminary investigation of the binding of formaldehyde, potentially at a site integral to proton transfer, opens the field for further research into proton transfer pathways, the structural implications thereof and their importance in catalysis.

abstract: Redox reactions are crucial to energy transduction in biology. Protein film electrochemistry (PFE) is a technique for studying redox proteins in which the protein is immobilized at an electrode surface so as to allow direct exchange of electrons. Establishing a direct electronic connection eliminates the need for redox­active mediators, thus allowing for interrogation of the redox protein of interest. PFE has proven a versatile tool that has been used to elucidate the properties of many technologically relevant redox proteins including hydrogenases, laccases, and glucose oxidase. This dissertation is comprised of two parts: extension of PFE to a novel electrode material and application of PFE to the investigation of a new type of hydrogenase. In the first part, mesoporous antimony-doped tin oxide (ATO) is employed for the first time as an electrode material for protein film electrochemistry. Taking advantage of the excellent optical transparency of ATO, spectroelectrochemistry of cytochrome c is demonstrated. The electrochemical and spectroscopic properties of the protein are analogous to those measured for the native protein in solution, and the immobilized protein is stable for weeks at high loadings. In the second part, PFE is used to characterize the catalytic properties of the soluble hydrogenase I from <italic>Pyrococcus furiosus</italic> (<italic>Pf</italic>SHI). Since this protein is highly thermostable, the temperature dependence of catalytic properties was investigated. I show that the preference of the enzyme for reduction of protons (as opposed to oxidation of hydrogen) and the reactions with oxygen are highly dependent on temperature, and the enzyme is tolerant to oxygen during both oxidative and reductive catalysis. / Dissertation/Thesis / Doctoral Dissertation Biochemistry 2014