Roles of multiple-proton transfer pathways and proton-coupled electron transfer in the reactivity of the bis-FeIV state of MauG

Protein-Derived Cofactors Revisited: Empowering Amino Acid Residues with New Functions

A protein-derived cofactor is a catalytic or redox-active site in a protein that is formed by post-translational modification of one or more amino acid residues. These post-translational modifications are irreversible and endow the modified amino acid residues with new functional properties. This Perspective focuses on the following advances in this area that have occurred during recent years. The biosynthesis of the tryptophan tryptophylquinone cofactor is catalyzed by a diheme enzyme, MauG. A bis-Fe^IV redox state of the hemes performs three two-electron oxidations of specific Trp residues via long-range electron transfer. In contrast, a flavoenzyme catalyzes the biosynthesis of the cysteine tryptophylquinone (CTQ) cofactor present in a newly discovered family of CTQ-dependent oxidases. Another carbonyl cofactor, the pyruvoyl cofactor found in classes of decarboxylases and reductases, is formed during an apparently autocatalytic cleavage of a precursor protein at the N-terminus of the cleavage product. It has been shown that in at least some cases, the cleavage is facilitated by binding to an accessory protein. Tyrosylquinonine cofactors, topaquinone and lysine tyrosylquinone, are found in copper-containing amine oxidases and lysyl oxidases, respectively. The physiological roles of different families of these enzymes in humans have been more clearly defined and shown to have significant implications with respect to human health. There has also been continued characterization of the roles of covalently cross-linked amino acid side chains that influence the reactivity of redox-active metal centers in proteins. These include Cys-Tyr species in galactose oxidase and cysteine dioxygenase and the Met-Tyr-Trp species in the catalase-peroxidase KatG.

The Nature and Reactivity of Ferryl Heme in Compounds I and II

Aerobic organisms have evolved to activate oxygen from the atmosphere, which allows them to catalyze the oxidation of different kinds of substrates. This activation of oxygen is achieved by a metal center (usually iron or copper) buried within a metalloprotein. In the case of iron-containing heme enzymes, the activation of oxygen is achieved by formation of transient iron-oxo (ferryl) intermediates; these intermediates are called Compound I and Compound II. The Compound I and II intermediates were first discovered in the 1930s in horseradish peroxidase, and it is now known that these same species are used across the family of heme enzymes, which include all of the peroxidases, the heme catalases, the P450s, cytochrome c oxidase, and NO synthase. Many years have passed since the first observations, but establishing the chemical nature of these transient ferryl species remains a fundamental question that is relevant to the reactivity, and therefore the usefulness, of these species in biology. This Account summarizes experiments that were conceived and conducted at Leicester and presents our ideas on the chemical nature, stability, and reactivity of these ferryl heme species. We begin by briefly summarizing the early milestones in the field, from the 1940s and 1950s. We present comparisons between the nature and reactivity of the ferryl species in horseradish peroxidase, cytochrome c peroxidase, and ascorbate peroxidase; and we consider different modes of electron delivery to ferryl heme, from different substrates in different peroxidases. We address the question of whether the ferryl heme is best formulated as an (unprotonated) Fe^IV═O or as a (protonated) Fe^IV-OH species. A range of spectroscopic approaches (EXAFS, resonance Raman, Mossbauer, and EPR) have been used over many decades to examine this question, and in the last ten years, X-ray crystallography has also been employed. We describe how information from all of these studies has blended together to create an overall picture, and how the recent application of neutron crystallography has directly identified protonation states and has helped to clarify the precise nature of the ferryl heme in cytochrome c peroxidase and ascorbate peroxidase. We draw comparisons between the Compound I and Compound II species that we have observed in peroxidases with those found in other heme systems, notably the P450s, highlighting possible commonality across these heme ferryl systems. The identification of proton locations from neutron structures of these ferryl species opens the door for understanding the proton translocations that need to occur during O-O bond cleavage.

A study of the competitive multiple hydrogen bonding effect and its associated excited-state proton transfer tautomerism

1,8-Dihydroxynaphthalene-2,7-dicarbaldehyde (DHDA) has been strategically designed and synthesized with the aim to study the competitive multiple hydrogen bonding (H-bonding) effect and the associated excited-state intramolecular proton transfer reaction (ESIPT). In nonpolar solvents such as cyclohexane, equilibrium exists between the two H-bonding isomers DHDA-23_OO and DHDA-23_OI, both of which possess double intramolecular H-bonds. In polar, aprotic solvents such as CH₂Cl₂, DHDA-23_OO becomes the predominant species. Due to various degrees of H-bond induced changes of electronic configuration each isomer reveals a distinct absorption feature and excited-state behavior, in which DHDA-23_OI in cyclohexane undergoes double ESIPT in a stepwise manner, giving the first and second proton-transfer tautomer emissions maximized at ∼500 nm and 660 nm, respectively. As for DHDA-23_OO both single and double ESIPT are prohibited, resulting in an intense normal 450 nm emission band. In a single crystal DHDA-23_OI is the dominant species, which undergoes excited state double proton transfer, giving intense emission bands at 530 nm and 650 nm. The mechanism associated with competitive multiple H-bonding energetics and ESIPT was underpinned by detailed spectroscopy/dynamics and computational approaches.

Radical Trapping Study of the Relaxation of bis-Fe(IV) MauG

The di-heme enzyme, MauG, utilizes a high-valent, charge-resonance stabilized bis-Fe(IV) state to perform protein radical-based catalytic chemistry. Though the bis-Fe(IV) species is able to oxidize remote tryptophan residues on its substrate protein, it does not rapidly oxidize its own residues in the absence of substrate. The slow return of bis-Fe(IV) MauG to its resting di-ferric state occurs via up to two intermediates, one of which has been previously proposed by Ma et al. (Biochem J 2016; 473:1769) to be a methionine-based radical in a recent study. In this work, we pursue intermediates involved in the return of high-valent MauG to its resting state in the absence of the substrate by EPR spectroscopy and radical trapping. The bis-Fe(IV) MauG is shown by EPR, HPLC, UV-Vis, and high-resolution mass spectrometry to oxidize the trapping agent, 5,5-dimethyl-1-pyrroline N-oxide (DMPO) to a radical species directly. Nitrosobenzene was also employed as a trapping agent and was shown to form an adduct with high-valent MauG species. The effects of DMPO and nitrosobenzene on the kinetics of the return to di-ferric MauG were both investigated. This work eliminates the possibility that a MauG-based methionine radical species accumulates during the self-reduction of bis-Fe(IV) MauG.

Ascorbate protects the diheme enzyme, MauG, against self-inflicted oxidative damage by an unusual antioxidant mechanism

Ascorbate protects MauG from self-inactivation that occurs during the autoreduction of the reactive bis-FeIV state of its diheme cofactor. The mechanism of protection does not involve direct reaction with reactive oxygen species in solution. Instead, it binds to MauG and mitigates oxidative damage that occurs via internal transfer of electrons from amino acid residues within the protein to the high-valent hemes. The presence of ascorbate does not inhibit the natural catalytic reaction of MauG, which catalyzes oxidative post-translational modifications of a substrate protein that binds to the surface of MauG and is oxidized by the high-valent hemes via long-range electron transfer. Ascorbate was also shown to prolong the activity of a P107V MauG variant that is more prone to inactivation. A previously unknown ascorbate peroxidase activity of MauG was characterized with a kcat of 0.24 s−1 and a Km of 2.2 µM for ascorbate. A putative binding site for ascorbate was inferred from inspection of the crystal structure of MauG and comparison with the structure of soybean ascorbate peroxidase with bound ascorbate. The ascorbate bound to MauG was shown to accelerate the rates of both electron transfers to the hemes and proton transfers to hemes which occur during the multistep autoreduction to the diferric state which is accompanied by oxidative damage. A structural basis for these effects is inferred from the putative ascorbate-binding site. This could be a previously unrecognized mechanism by which ascorbate mitigates oxidative damage to heme-dependent enzymes and redox proteins in nature.

Properties of the high-spin heme of MauG are altered by binding of preMADH at the protein surface 40 Å away

The diheme enzyme MauG catalyzes oxidative post-translational modifications of a protein substrate, precursor protein of methylamine dehydrogenase (preMADH), that binds to the surface of MauG. The high-spin heme iron of MauG is located 40 Å from preMADH. The ferric heme is an equilibrium of five- and six-coordinate states. PreMADH binding increases the proportion of five-coordinate heme three-fold. On reaction of MauG with H₂ O₂ both hemes become Fe^IV . In the absence of preMADH the hemes autoreduce to ferric in a multistep process involving multiple electron and proton transfers. Binding of preMADH in the absence of catalysis alters the mechanism of autoreduction of the ferryl heme. Thus, substrate binding alters the environment in the distal heme pocket of the high-spin heme over very long distance.

Reactivity of the copper(iii)-hydroxide unit with phenols

Kinetic studies of the reactions of two previously characterized copper(iii)-hydroxide complexes (LCuOH and NO2 LCuOH, where L = N,N'-bis(2,6-diisopropylphenyl)-2,6-pyridine-dicarboxamide and NO2 L = N,N'-bis(2,6-diisopropyl-4-nitrophenyl)pyridine-2,6-dicarboxamide) with a series of para substituted phenols (XArOH where X = NMe2, OMe, Me, H, Cl, NO2, or CF3) were performed using low temperature stopped-flow UV-vis spectroscopy. Second-order rate constants (k) were determined from pseudo first-order and stoichiometric experiments, and follow the trends CF3 < NO2 < Cl < H < Me < OMe < NMe2 and LCuOH < NO2 LCuOH. The data support a concerted proton-electron transfer (CPET) mechanism for all but the most acidic phenols (X = NO2 and CF3), for which a more complicated mechanism is proposed. For the case of the reactions between NO2 ArOH and LCuOH in particular, competition between a CPET pathway and one involving initial proton transfer followed by electron transfer (PT/ET) is supported by multiwavelength global analysis of the kinetic data, formation of the phenoxide NO2 ArO- as a reaction product, observation of an intermediate [LCu(OH2)]+ species derived from proton transfer from NO2 ArOH to LCuOH, and thermodynamic arguments indicating that initial PT should be competitive with CPET.

Spectroscopic Investigations of Catalase Compound II: Characterization of an Iron(IV) Hydroxide Intermediate in a Non-thiolate-Ligated Heme Enzyme

We report on the protonation state of Helicobacter pylori catalase compound II. UV/visible, Mössbauer, and X-ray absorption spectroscopies have been used to examine the intermediate from pH 5 to 14. We have determined that HPC-II exists in an iron(IV) hydroxide state up to pH 11. Above this pH, the iron(IV) hydroxide complex transitions to a new species (pKa = 13.1) with Mössbauer parameters that are indicative of an iron(IV)-oxo intermediate. Recently, we discussed a role for an elevated compound II pKa in diminishing the compound I reduction potential. This has the effect of shifting the thermodynamic landscape toward the two-electron chemistry that is critical for catalase function. In catalase, a diminished potential would increase the selectivity for peroxide disproportionation over off-pathway one-electron chemistry, reducing the buildup of the inactive compound II state and reducing the need for energetically expensive electron donor molecules.

Direct visualization of a Fe(IV)-OH intermediate in a heme enzyme

Catalytic heme enzymes carry out a wide range of oxidations in biology. They have in common a mechanism that requires formation of highly oxidized ferryl intermediates. It is these ferryl intermediates that provide the catalytic engine to drive the biological activity. Unravelling the nature of the ferryl species is of fundamental and widespread importance. The essential question is whether the ferryl is best described as a Fe(IV)=O or a Fe(IV)–OH species, but previous spectroscopic and X-ray crystallographic studies have not been able to unambiguously differentiate between the two species. Here we use a different approach. We report a neutron crystal structure of the ferryl intermediate in Compound II of a heme peroxidase; the structure allows the protonation states of the ferryl heme to be directly observed. This, together with pre-steady state kinetic analyses, electron paramagnetic resonance spectroscopy and single crystal X-ray fluorescence, identifies a Fe(IV)–OH species as the reactive intermediate. The structure establishes a precedent for the formation of Fe(IV)–OH in a peroxidase.

The nature of the ferryl intermediate generated in reactions catalysed by heme-containing enzymes is uncertain, due to the ambiguity of X-ray crystallography data. Here, the authors apply neutron diffraction, kinetics and other spectroscopy to directly observe a protonated ferryl intermediate in a heme peroxidase.

A Suicide Mutation Affecting Proton Transfers to High-Valent Hemes Causes Inactivation of MauG during Catalysis

In the absence of its substrate, the autoreduction of the high-valent bis-Fe^IV state of the hemes of MauG to the diferric state proceeds via a Compound I-like and then a Compound II-like intermediate. This process is coupled to oxidative damage to specific methionine residues and inactivation of MauG. The autoreduction of a P107V MauG variant, which is more prone to oxidative damage, proceeds directly from the bis-Fe^IV to the Compound II-like state with no detectable Compound I intermediate. Comparison of the crystal structures of native and P107V MauG reveals that this mutation alters the positions of amino acid residues in the heme site as well as the water network that delivers protons from the solvent to the hemes during their reduction. Kinetic, spectroscopic, and solvent kinetic isotope effect studies demonstrate that these changes in the heme site affect the protonation state of the ferryl heme and the relative efficiencies of two alternative pathways for the transfer of protons from solvent to the hemes. These changes enhance the rate of autoreduction of P107V MauG such that it competes with the catalytic reaction with substrate and causes the enzyme to inactivate itself during the steady-state reaction with H₂O₂ and its substrate. Thus, while this mutation has negligible effects on the initial steady-state kinetic parameters of MauG, it is a fatal mutation as it causes inactivation during catalysis.

Mechanism of protein oxidative damage that is coupled to long-range electron transfer to high-valent haems

In the absence of its substrate, the auto-reduction of the high-valent bis-Fe(IV) state of the dihaem enzyme MauG is coupled to oxidative damage of a methionine residue. Transient kinetic and solvent isotope effect studies reveal that this process occurs via two sequential long-range electron transfer (ET) reactions from methionine to the haems. The first ET is coupled to proton transfer (PT) to the haems from solvent via an ordered water network. The second ET is coupled to PT at the methionine site and occurs during the oxidation of the methionine to a sulfoxide. This process proceeds via Compound I- and Compound II-like haem intermediates. It is proposed that the methionine radical is stabilized by a two-centre three-electron (2c3e) bond. This provides insight into how oxidative damage to proteins may occur without direct contact with a reactive oxygen species, and how that damage can be propagated through the protein.

Converting the bis-FeIV state of the diheme enzyme MauG to Compound I decreases the reorganization energy for electron transfer

The electron transfer (ET) properties of two types of high-valent hemes were studied within the same protein matrix; the bis-Fe(IV) state of MauG and the Compound I state of Y294H MauG. The latter is formed as a consequence of mutation of the tyrosine which forms the distal axial ligand of the six-coordinate heme that allows it to stabilize Fe(IV) in the absence of an external ligand. The rates of the ET reaction of each high-valent species with the type I copper protein, amicyanin, were determined at different temperatures and analysed by ET theory. The reaction with bis-Fe(IV) wild-type (WT) MauG exhibited a reorganization energy (λ) that was 0.39 eV greater than that for the reaction of Compound I Y295H MauG. It is concluded that the delocalization of charge over the two hemes in the bis-Fe(IV) state is responsible for the larger λ, relative to the Compound I state in which the Fe(V) equivalent is isolated on one heme. Although the increase in λ decreases the rate of ET, the delocalization of charge decreases the ET distance to its natural substrate protein, thus increasing the ET rate. This describes how proteins can balance different ET properties of complex redox cofactors to optimize each system for its particular ET or catalytic reaction.