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

Identification of Fe(iii)–OH species as a catalytic intermediate in plant peroxidases at high H2O2 concentration

The structure for compound III formed after exposure of plant heme peroxidases to excess H2O2 seems to be a hydroxylated form, providing new evidence for understanding the structural basis of the substrate-induced suicidal behavior of these enzymes.

Functional and protective hole hopping in metalloenzymes

Electrons can tunnel through proteins in microseconds with a modest release of free energy over distances in the 15 to 20 Å range. To span greater distances, or to move faster, multiple charge transfers (hops) are required. When one of the reactants is a strong oxidant, it is convenient to consider the movement of a positively charged "hole" in a direction opposite to that of the electron. Hole hopping along chains of tryptophan (Trp) and tyrosine (Tyr) residues is a critical function in several metalloenzymes that generate high-potential intermediates by reactions with O2 or H2O2, or by activation with visible light. Examination of the protein structural database revealed that Tyr/Trp chains are common protein structural elements, particularly among enzymes that react with O2 and H2O2. In many cases these chains may serve a protective role in metalloenzymes by deactivating high-potential reactive intermediates formed in uncoupled catalytic turnover.

Understanding the Logistics for the Distribution of Heme in Cells

Heme is essential for the survival of virtually all living systems-from bacteria, fungi, and yeast, through plants to animals. No eukaryote has been identified that can survive without heme. There are thousands of different proteins that require heme in order to function properly, and these are responsible for processes such as oxygen transport, electron transfer, oxidative stress response, respiration, and catalysis. Further to this, in the past few years, heme has been shown to have an important regulatory role in cells, in processes such as transcription, regulation of the circadian clock, and the gating of ion channels. To act in a regulatory capacity, heme needs to move from its place of synthesis (in mitochondria) to other locations in cells. But while there is detailed information on how the heme lifecycle begins (heme synthesis), and how it ends (heme degradation), what happens in between is largely a mystery. Here we summarize recent information on the quantification of heme in cells, and we present a discussion of a mechanistic framework that could meet the logistical challenge of heme distribution.

Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography

Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.

A Mononuclear Non-heme Iron(III)-Peroxo Complex with an Unprecedented High O-O Stretch and Electrophilic Reactivity

A mononuclear non-heme iron(III)-peroxo complex, [Fe(III)(O₂)(13-TMC)]⁺ (1), was synthesized and characterized spectroscopically; the characterization with electron paramagnetic resonance, Mössbauer, X-ray absorption, and resonance Raman spectroscopies and mass spectrometry supported a high-spin S = ⁵/₂ Fe(III) species binding an O₂ unit. A notable observation was an unusually high ν_O-O at ∼1000 cm^-1 for the peroxo ligand. With regard to reactivity, 1 showed electrophilic reactivity in H atom abstraction (HAA) and O atom transfer (OAT) reactions. In the HAT reaction, a kinetic isotope effect (KIE) value of 5.8 was obtained in the oxidation of 9,10-dihydroanthracene. In the OAT reaction, a negative ρ value of -0.61 in the Hammett plot was determined in the oxidation of p-X-substituted thioanisoles. Another interesting observation was the electrophilic reactivity of 1 in the oxidation of benzaldehyde derivatives, such as a negative ρ value of -0.77 in the Hammett plot and a KIE value of 2.2. To the best of our knowledge, the present study reports the first example of a mononuclear non-heme iron(III)-peroxo complex with an unusually high ν_O-O value and unprecedented electrophilic reactivity in oxidation reactions.

Some fundamental insights into biological redox catalysis from the electrochemical characteristics of enzymes attached directly to electrodes

This article outlines examples of where electrochemical investigations of electrocatalysis by proteins immobilised on an electrode reveal fundamental information about electron-proton coupling in catalysis and provide a new way to energise, control and observe multi-enzyme cascades.

Aspartate or arginine? Validated redox state X-ray structures elucidate mechanistic subtleties of FeIV = O formation in bacterial dye-decolorizing peroxidases

Structure determination of proteins and enzymes by X-ray crystallography remains the most widely used approach to complement functional and mechanistic studies. Capturing the structures of intact redox states in metalloenzymes is critical for assigning the chemistry carried out by the metal in the catalytic cycle. Unfortunately, X-rays interact with protein crystals to generate solvated photoelectrons that can reduce redox active metals and hence change the coordination geometry and the coupled protein structure. Approaches to mitigate such site-specific radiation damage continue to be developed, but nevertheless application of such approaches to metalloenzymes in combination with mechanistic studies are often overlooked. In this review, we summarize our recent structural and kinetic studies on a set of three heme peroxidases found in the bacterium Streptomyces lividans that each belong to the dye decolourizing peroxidase (DyP) superfamily. Kinetically, each of these DyPs has a distinct reactivity with hydrogen peroxide. Through a combination of low dose synchrotron X-ray crystallography and zero dose serial femtosecond X-ray crystallography using an X-ray free electron laser (XFEL), high-resolution structures with unambiguous redox state assignment of the ferric and ferryl (Fe^IV = O) heme species have been obtained. Experiments using stopped-flow kinetics, solvent-isotope exchange and site-directed mutagenesis with this set of redox state validated DyP structures have provided the first comprehensive kinetic and structural framework for how DyPs can modulate their distal heme pocket Asp/Arg dyad to use either the Asp or the Arg to facilitate proton transfer and rate enhancement of peroxide heterolysis.

Serial synchrotron and XFEL crystallography for studies of metalloprotein catalysis

An estimated half of all proteins contain a metal, with these being essential for a tremendous variety of biological functions. X-ray crystallography is the major method for obtaining structures at high resolution of these metalloproteins, but there are considerable challenges to obtain intact structures due to the effects of radiation damage. Serial crystallography offers the prospect of determining low-dose synchrotron or effectively damage free XFEL structures at room temperature and enables time-resolved or dose-resolved approaches. Complementary spectroscopic data can validate redox and or ligand states within metalloprotein crystals. In this opinion, we discuss developments in the application of serial crystallographic approaches to metalloproteins and comment on future directions.

A Noncanonical Tryptophan Analogue Reveals an Active Site Hydrogen Bond Controlling Ferryl Reactivity in a Heme Peroxidase

Nature employs high-energy metal-oxo intermediates embedded within enzyme active sites to perform challenging oxidative transformations with remarkable selectivity. Understanding how different local metal-oxo coordination environments control intermediate reactivity and catalytic function is a long-standing objective. However, conducting structure-activity relationships directly in active sites has proven challenging due to the limited range of amino acid substitutions achievable within the constraints of the genetic code. Here, we use an expanded genetic code to examine the impact of hydrogen bonding interactions on ferryl heme structure and reactivity, by replacing the N-H group of the active site Trp51 of cytochrome c peroxidase by an S atom. Removal of a single hydrogen bond stabilizes the porphyrin π-cation radical state of CcP W191F compound I. In contrast, this modification leads to more basic and reactive neutral ferryl heme states, as found in CcP W191F compound II and the wild-type ferryl heme-Trp191 radical pair of compound I. This increased reactivity manifests in a >60-fold activity increase toward phenolic substrates but remarkably has negligible effects on oxidation of the biological redox partner cytc. Our data highlight how Trp51 tunes the lifetimes of key ferryl intermediates and works in synergy with the redox active Trp191 and a well-defined substrate binding site to regulate catalytic function. More broadly, this work shows how noncanonical substitutions can advance our understanding of active site features governing metal-oxo structure and reactivity.

Single Nucleotide Polymorphism Induces Divergent Dynamic Patterns in CYP3A5: A Microsecond Scale Biomolecular Simulation of Variants Identified in Sub-Saharan African Populations

Pharmacogenomics aims to reveal variants associated with drug response phenotypes. Genes whose roles involve the absorption, distribution, metabolism, and excretion of drugs, are highly polymorphic between populations. High coverage whole genome sequencing showed that a large proportion of the variants for these genes are rare in African populations. This study investigated the impact of such variants on protein structure to assess their functional importance. We used genetic data of CYP3A5 from 458 individuals from sub-Saharan Africa to conduct a structural bioinformatics analysis. Five missense variants were modeled and microsecond scale molecular dynamics simulations were conducted for each, as well as for the CYP3A5 wildtype and the Y53C variant, which has a known deleterious impact on enzyme activity. The binding of ritonavir and artemether to CYP3A5 variant structures was also evaluated. Our results showed different conformational characteristics between all the variants. No significant structural changes were noticed. However, the genetic variability seemed to act on the plasticity of the protein. The impact on drug binding might be drug dependant. We concluded that rare variants hold relevance in determining the pharmacogenomics properties of populations. This could have a significant impact on precision medicine applications in sub-Saharan Africa.

XFEL Crystal Structures of Peroxidase Compound II

Oxygen activation in all heme enzymes requires the formation of high oxidation states of iron, usually referred to as ferryl heme. There are two known intermediates: Compound I and Compound II. The nature of the ferryl heme-and whether it is an FeIV =O or FeIV -OH species-is important for controlling reactivity across groups of heme enzymes. The most recent evidence for Compound I indicates that the ferryl heme is an unprotonated FeIV =O species. For Compound II, the nature of the ferryl heme is not unambiguously established. Here, we report 1.06 Å and 1.50 Å crystal structures for Compound II intermediates in cytochrome c peroxidase (CcP) and ascorbate peroxidase (APX), collected using the X-ray free electron laser at SACLA. The structures reveal differences between the two peroxidases. The iron-oxygen bond length in CcP (1.76 Å) is notably shorter than in APX (1.87 Å). The results indicate that the ferryl species is finely tuned across Compound I and Compound II species in closely related peroxidase enzymes. We propose that this fine-tuning is linked to the functional need for proton delivery to the heme.

XFEL Crystal Structures of Peroxidase Compound II

Oxygen activation in all heme enzymes requires the formation of high oxidation states of iron, usually referred to as ferryl heme. There are two known intermediates: Compound I and Compound II. The nature of the ferryl heme-and whether it is an FeIV=O or FeIV-OH species-is important for controlling reactivity across groups of heme enzymes. The most recent evidence for Compound I indicates that the ferryl heme is an unprotonated FeIV=O species. For Compound II, the nature of the ferryl heme is not unambiguously established. Here, we report 1.06 Å and 1.50 Å crystal structures for Compound II intermediates in cytochrome c peroxidase (CcP) and ascorbate peroxidase (APX), collected using the X-ray free electron laser at SACLA. The structures reveal differences between the two peroxidases. The iron-oxygen bond length in CcP (1.76 Å) is notably shorter than in APX (1.87 Å). The results indicate that the ferryl species is finely tuned across Compound I and Compound II species in closely related peroxidase enzymes. We propose that this fine-tuning is linked to the functional need for proton delivery to the heme.

Local Electric Fields as a Natural Switch of Heme-Iron Protein Reactivity

Heme-iron oxidoreductases operating through the high-valent Fe^IVO intermediates perform crucial and complicated transformations, such as oxidations of unreactive saturated hydrocarbons. These enzymes share the same Fe coordination, only differing by the axial ligation, e.g., Cys in P450 oxygenases, Tyr in catalases, and His in peroxidases. By examining ~200 heme-iron proteins, we show that the protein hosts exert highly specific intramolecular electric fields on the active sites, and there is a strong correlation between the direction and magnitude of this field and the protein function. In all heme proteins, the field is preferentially aligned with the Fe-O bond ( F_z ). The Cys-ligated P450 oxygenases have the highest average F_z of 28.5 MV cm^-1, i.e., most enhancing the oxyl-radical character of the oxo group, and consistent with the ability of these proteins to activate strong C-H bonds. In contrast, in Tyr-ligated proteins, the average F_z is only 3.0 MV cm^-1, apparently suppressing single-electron off-pathway oxidations, and in His-ligated proteins, F_z is -8.7 MV cm^-1. The operational field range is given by the trade-off between the low reactivity of the Fe^IVO Compound I at the more negative F_z , and the low selectivity at the more positive F_z . Consequently, a heme-iron site placed in the field characteristic of another heme-iron protein class loses its canonical function, and gains an adverse one. Thus, electric fields produced by the protein scaffolds, together with the nature of the axial ligand, control all heme-iron chemistry.

New-to-nature chemistry from old protein machinery: carbene and nitrene transferases

Hemoprotein-catalyzed carbene and nitrene transformations have emerged as powerful tools for constructing complex molecules; they also nicely illustrate how new protein catalysts can emerge, evolve and diversify. These laboratory-invented enzymes exploit the ability of proteins to tame highly reactive carbene and nitrene species and direct their fates with high selectivity. New-to-nature carbene and nitrene transferases catalyze many useful reactions, including some that have no precedent using chemical methods. Here we cover recent advances in this field, including alkyne cyclopropenation, arene cyclopropanation, carbene CH insertion, intramolecular nitrene CH insertion, alkene aminohydroxylation, and primary amination. For such transformations, biocatalysts have exceeded the performance of reported small-molecule catalysts in terms of selectivity and catalyst turnovers. Finally, we offer our thoughts on using these new enzymatic reactions in chemical synthesis, integrating them into biological pathways and chemo-enzymatic cascades, and on their current limitations.

Abiological catalysis by myoglobin mutant with a genetically incorporated unnatural amino acid

To inculcate biocatalytic activity in the oxygen-storage protein myoglobin (Mb), a genetically engineered myoglobin mutant H64DOPA (DOPA = L-3,4-dihydroxyphenylalanine) has been created. Incorporation of unnatural amino acids has already demonstrated their ability to accomplish many non-natural functions in proteins efficiently. Herein, the presence of redox-active DOPA residue in the active site of mutant Mb presumably stabilizes the compound I in the catalytic oxidation process by participating in an additional hydrogen bonding (H-bonding) as compared to the WT Mb. Specifically, a general acid-base catalytic pathway was achieved due to the availability of the hydroxyl moieties of DOPA. The reduction potential values of WT (E° = -260 mV) and mutant Mb (E° = -300 mV), w.r.t. Ag/AgCl reference electrode, in the presence of hydrogen peroxide, indicated an additional H-bonding in the mutant protein, which is responsible for the peroxidase activity of the mutant Mb. We observed that in the presence of 5 mM H2O2, H64DOPA Mb oxidizes thioanisole and benzaldehyde with a 10 and 54 folds higher rate, respectively, as opposed to WT Mb. Based on spectroscopic, kinetic, and electrochemical studies, we deduce that DOPA residue, when present within the distal pocket of mutant Mb, alone serves the role of His/Arg-pair of peroxidases.

Ligand Architecture Perturbation Influences the Reactivity of Nonheme Iron(V)-Oxo Tetraamido Macrocyclic Ligand Complexes: A Combined Experimental and Theoretical Study

Iron(V)-oxo complexes bearing negatively charged tetraamido macrocyclic ligands (TAMLs) have provided excellent opportunities to investigate the chemical properties and the mechanisms of oxidation reactions of mononuclear nonheme iron(V)-oxo intermediates. Herein, we report the differences in chemical properties and reactivities of two iron(V)-oxo TAML complexes differing by modification on the "Head" part of the TAML framework; one has a phenyl group at the "Head" part (1), whereas the other has four methyl groups replacing the phenyl ring (2). The reactivities of 1 and 2 in both C-H bond activation reactions, such as hydrogen atom transfer (HAT) of 1,4-cyclohexadiene, and oxygen atom transfer (OAT) reactions, such as the oxidation of thioanisole and its derivatives, were compared experimentally. Under identical reaction conditions, 1 showed much greater reactivity than 2, such as a 10²-fold decrease in HAT and a 10⁵-fold decrease in OAT by replacing the phenyl group (i.e., 1) with four methyl groups (i.e., 2). Then, density functional theory calculations were performed to rationalize the reactivity differences between 1 and 2. Computations reproduced the experimental findings well and revealed that the replacement of the phenyl group in 1 with four methyl groups in 2 not only increased the steric hindrance but also enlarged the energy gap between the electron-donating orbital and the electron-accepting orbital. These two factors, steric hindrance and the orbital energy gap, resulted in differences in the reduction potentials of 1 and 2 and their reactivities in oxidation reactions.

Reactive Oxygen Species and Their Involvement in Red Blood Cell Damage in Chronic Kidney Disease

Reactive oxygen species (ROS) released in cells are signaling molecules but can also modify signaling proteins. Red blood cells perform a major role in maintaining the balance of the redox in the blood. The main cytosolic protein of RBC is hemoglobin (Hb), which accounts for 95-97%. Most other proteins are involved in protecting the blood cell from oxidative stress. Hemoglobin is a major factor in initiating oxidative stress within the erythrocyte. RBCs can also be damaged by exogenous oxidants. Hb autoxidation leads to the generation of a superoxide radical, of which the catalyzed or spontaneous dismutation produces hydrogen peroxide. Both oxidants induce hemichrome formation, heme degradation, and release of free iron which is a catalyst for free radical reactions. To maintain the redox balance, appropriate antioxidants are present in the cytosol, such as superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), and peroxiredoxin 2 (PRDX2), as well as low molecular weight antioxidants: glutathione, ascorbic acid, lipoic acid, α-tocopherol, β-carotene, and others. Redox imbalance leads to oxidative stress and may be associated with overproduction of ROS and/or insufficient capacity of the antioxidant system. Oxidative stress performs a key role in CKD as evidenced by the high level of markers associated with oxidative damage to proteins, lipids, and DNA in vivo. In addition to the overproduction of ROS, a reduced antioxidant capacity is observed, associated with a decrease in the activity of SOD, GPx, PRDX2, and low molecular weight antioxidants. In addition, hemodialysis is accompanied by oxidative stress in which low-biocompatibility dialysis membranes activate phagocytic cells, especially neutrophils and monocytes, leading to a respiratory burst. This review shows the production of ROS under normal conditions and CKD and its impact on disease progression. Oxidative damage to red blood cells (RBCs) in CKD and their contribution to cardiovascular disease are also discussed.

Conversion of Human Neuroglobin into a Multifunctional Peroxidase by Rational Design

Protein design has received much attention in the last decades. With an additional disulfide bond to enhance the protein stability, human A15C neuroglobin (Ngb) is an ideal protein scaffold for heme enzyme design. In this study, we rationally converted A15C Ngb into a multifunctional peroxidase by replacing the heme axial His64 with an Asp residue, where Asp64 and the native Lys67 at the heme distal site were proposed to act as an acid-base catalytic couple for H₂O₂ activation. Kinetic studies showed that the catalytic efficiency of A15C/H64D Ngb was much higher (∼50-80-fold) than that of native dehaloperoxidase, which even exceeds (∼3-fold) that of the most efficient native horseradish peroxidase. Moreover, the dye-decolorizing peroxidase activity was also comparable to that of some native enzymes. Electron paramagnetic resonance, molecular docking, and isothermal titration calorimetry studies provided valuable information for the substrate-protein interactions. Therefore, this study presents the rational design of an efficient multifunctional peroxidase based on Ngb with potential applications such as in bioremediation for environmental sustainability.

Bioinspired design of an artificial peroxidase: introducing key residues of native peroxidases into F43Y myoglobin with a Tyr-heme cross-link

Inspired by the structural features of native peroxidases, an artificial peroxidase was rationally designed using F43Y myoglobin with a Tyr-heme cross-link by further introduction of key residues, including both a distal Arg and a Trp close to the heme group, which exhibits an enhanced peroxidase activity similar to the most efficient native horseradish peroxidase. This study provides a simple approach for design of artificial heme enzymes by the combination of catalytic elements of native enzymes with the post-translational modifications of heme proteins.

Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in FeIV =O Formation

Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (FeIV =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the FeIII and FeIV =O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.

Unprecedented Reactivities of Highly Reactive Manganese(III)-Iodosylarene Porphyrins in Oxidation Reactions

We report that Mn(III)-iodosylarene porphyrins, [Mn^III(Porp)(^sArIO)]⁺, are capable of activating the C-H bonds of hydrocarbons, including unactivated alkanes such as cyclohexane, with unprecedented reactivities, such as a low kinetic isotope effect, a saturation behavior of reaction rates, and no electronic effect of porphyrin ligands on the reactivities of [Mn^III(Porp)(^sArIO)]⁺. In oxygen atom transfer (OAT) reactions, the sulfoxidation of para-X-substituted thioanisoles by [Mn^III(Porp)(^sArIO)]⁺ affords a very unusual behavior in the Hammett plot with the saturation behavior of reaction rates and no electronic effect of porphyrin ligands on reactivities. The reactivities and mechanisms of [Mn^III(Porp)(^sArIO)]⁺ are then compared with those of the corresponding Mn^IV(Porp)(O) complex. The present study reports the first example of highly reactive Mn(III)-iodosylarene porphyrins with unprecedented reactivities in C-H bond activation and OAT reactions.

Ascorbate Peroxidase Compound II Is an Iron(IV) Oxo Species

The protonation state of the iron(IV) oxo (or ferryl) form of ascorbate peroxidase compound II (APX-II) is a subject of debate. It has been reported that this intermediate is best described as an iron(IV) hydroxide species. Neutron diffraction data obtained from putative APX-II crystals indicate a protonated oxygenic ligand at 1.88 Å from the heme iron. This finding, if correct, would be unprecedented. A basic iron(IV) oxo species has yet to be spectroscopically observed in a histidine-ligated heme enzyme. The importance of ferryl basicity lies in its connection to our fundamental understanding of C-H bond activation. Basic ferryl species have been proposed to facilitate the oxidation of inert C-H bonds, reactions that are unknown for histidine-ligated hemes enzymes. To provide further insight into the protonation status of APX-II, we examined the intermediate using a combination of Mössbauer and X-ray absorption spectroscopies. Our data indicate that APX-II is an iron(IV) oxo species with an Fe-O bond distance of 1.68 Å, a K-edge pre-edge absorption of 18 units, and Mössbauer parameters of ΔEq = 1.65 mm/s and δ = 0.03 mm/s.

A Stable Homoleptic Organometallic Iron(IV) Complex

A homoleptic organometallic Fe^IV complex that is stable in both solution and in the solid state at ambient conditions has been synthesized and isolated as [Fe(phtmeimb)₂ ](PF₆ )₂ (phtmeimb=[phenyl(tris(3-methylimidazolin-2-ylidene))borate]^- ). This Fe^IV N-heterocyclic carbene (NHC) complex was characterized by ¹ H NMR, HR-MS, elemental analysis, scXRD analysis, electrochemistry, Mößbauer spectroscopy, and magnetic susceptibility. The two latter techniques unequivocally demonstrate that [Fe(phtmeimb)₂ ](PF₆ )₂ is a triplet Fe^IV low-spin S=1 complex in the ground state, in agreement with quantum chemical calculations. The electronic absorption spectrum of [Fe(phtmeimb)₂ ](PF₆ )₂ in acetonitrile shows an intense absorption band in the red and near IR, due to LMCT (ligand-to-metal charge transfer) excitation. For the first time the excited state dynamics of a Fe^IV complex was studied and revealed a ≈0.8 ps lifetime of the ³ LMCT excited state of [Fe(phtmeimb)₂ ](PF₆ )₂ in acetonitrile.

Effects of Noncovalent Interactions on High-Spin Fe(IV)-Oxido Complexes

High-valent nonheme Fe^IV-oxido species are key intermediates in biological oxidation, and their properties are proposed to be influenced by the unique microenvironments present in protein active sites. Microenvironments are regulated by noncovalent interactions, such as hydrogen bonds (H-bonds) and electrostatic interactions; however, there is little quantitative information about how these interactions affect crucial properties of high valent metal-oxido complexes. To address this knowledge gap, we introduced a series of Fe^IV-oxido complexes that have the same S = 2 spin ground state as those found in nature and then systematically probed the effects of noncovalent interactions on their electronic, structural, and vibrational properties. The key design feature that provides access to these complexes is the new tripodal ligand [poat]^3-, which contains phosphinic amido groups. An important structural aspect of [Fe^IVpoat(O)]^- is the inclusion of an auxiliary site capable of binding a Lewis acid (LA^II); we used this unique feature to further modulate the electrostatic environment around the Fe-oxido unit. Experimentally, studies confirmed that H-bonds and LA^II s can interact directly with the oxido ligand in Fe^IV-oxido complexes, which weakens the Fe═O bond and has an impact on the electronic structure. We found that relatively large vibrational changes in the Fe-oxido unit correlate with small structural changes that could be difficult to measure, especially within a protein active site. Our work demonstrates the important role of noncovalent interactions on the properties of metal complexes, and that these interactions need to be considered when developing effective oxidants.

Expression of recombinant apopholasin using a baculovirus-silkworm multigene expression system and activation via dehydrocoelenterazine

Pholasin is a photoprotein derived from the glowing bivalve mollusk, Pholas dactylus. Even though the chemical structure of the prosthetic group (chromophore) responsible for the light emission character of the mollusk remains unknown, research has shown that the presence of dehydrocoelenterazine (DCL) increased light emission and that the dithiothreitol adduct of DCL was isolated from Pholasin®. To date, our research has been focused on activating apopholasin, the naturally occurring apoprotein of Pholasin®, using DCL. In the current study, the expression of recombinant apopholasin via a baculovirus-silkworm multigene expression system is reported. Additionally, the purification of apopholasin using a Flag®-affinity column, the activation of apopholasin using DCL, and the initiation of its luminescent character through the addition of a peroxidase-hydrogen peroxide mixture are reported. The peroxidase-H₂O₂-dependent luminescence was observed from the recombinant apopholasin activated with DCL.

Visualizing the protons in a metalloenzyme electron proton transfer pathway

In redox metalloenzymes, the process of electron transfer often involves the concerted movement of a proton. These processes are referred to as proton-coupled electron transfer, and they underpin a wide variety of biological processes, including respiration, energy conversion, photosynthesis, and metalloenzyme catalysis. The mechanisms of proton delivery are incompletely understood, in part due to an absence of information on exact proton locations and hydrogen bonding structures in a bona fide metalloenzyme proton pathway. Here, we present a 2.1-Å neutron crystal structure of the complex formed between a redox metalloenzyme (ascorbate peroxidase) and its reducing substrate (ascorbate). In the neutron structure of the complex, the protonation states of the electron/proton donor (ascorbate) and all of the residues involved in the electron/proton transfer pathway are directly observed. This information sheds light on possible proton movements during heme-catalyzed oxygen activation, as well as on ascorbate oxidation.

Rewiring the "Push-Pull" Catalytic Machinery of a Heme Enzyme Using an Expanded Genetic Code

Nature employs a limited number of genetically encoded axial ligands to control diverse heme enzyme activities. Deciphering the functional significance of these ligands requires a quantitative understanding of how their electron-donating capabilities modulate the structures and reactivities of the iconic ferryl intermediates compounds I and II. However, probing these relationships experimentally has proven to be challenging as ligand substitutions accessible via conventional mutagenesis do not allow fine tuning of electron donation and typically abolish catalytic function. Here, we exploit engineered translation components to replace the histidine ligand of cytochrome c peroxidase (CcP) by a less electron-donating N_δ-methyl histidine (Me-His) with little effect on the enzyme structure. The rate of formation (k₁) and the reactivity (k₂) of compound I are unaffected by ligand substitution. In contrast, proton-coupled electron transfer to compound II (k₃) is 10-fold slower in CcP Me-His, providing a direct link between electron donation and compound II reactivity, which can be explained by weaker electron donation from the Me-His ligand (“the push”) affording an electron-deficient ferryl oxygen with reduced proton affinity (“the pull”). The deleterious effects of the Me-His ligand can be fully compensated by introducing a W51F mutation designed to increase “the pull” by removing a hydrogen bond to the ferryl oxygen. Analogous substitutions in ascorbate peroxidase lead to similar activity trends to those observed in CcP, suggesting that a common mechanistic strategy is employed by enzymes using distinct electron transfer pathways. Our study highlights how noncanonical active site substitutions can be used to directly probe and deconstruct highly evolved bioinorganic mechanisms.

Heme peroxidase-Trapping intermediates by cryo neutron crystallography

By combining the normal practice for X-ray crystallography of collecting diffraction data at 100K with neutron crystallography the structures of cryo-trapped enzyme intermediates have been determined, revealing the positions of the previously hidden hydrogens that are essential to a better understanding of the involved mechanism.

Recent advances in the field of artificial hemoproteins: New efficient eco-compatible biocatalysts for nitrene-, oxene- and carbene-transfer reactions

In the last few years, the field of artificial hemoproteins has been expanding through two main strategies involving either the incorporation of synthetic metalloporphyrin derivatives into the chiral cavity of a protein or the directed evolution of natural hemoproteins such as myoglobin and cytochromes P450. First, various synthetic water-soluble porphyrins including ions of transition metals such as iron and manganese have been inserted covalently or by supramolecular anchoring into non-specifically designed native proteins or into proteins modified by a minimum number of mutations. The obtained artificial hemoproteins were able to catalyze oxene transfer reactions such as epoxidation of alkenes or sulfoxidation of sulfides and cyclopropanation reactions with good activities and moderate enantioselectivities. Recently, a second approach, based on the design of the active site of already existing native hemoproteins such as myoglobin and cytochromes P450 by directed evolution, has led to new artificial hemoproteins that are able to catalyze oxene transfer reactions with improved activities as well as with abiological reactions. This approach thus provided promising tools for the catalysis of reactions such as intramolecular or intermolecular carbene and nitrene transfer reactions with high efficiencies. In addition, in all cases, after a few rounds of mutagenesis, mutants that were able to catalyze those reactions with a high enantioselectivity could be obtained. Finally, several groups showed that these new artificial metalloenzymes could also be used for the preparative scale-production of compounds with an excellent enantioselectivity, opening new pathways for the industrial synthesis of compounds of pharmaceutical interest.

A subtle structural change in the distal haem pocket has a remarkable effect on tuning hydrogen peroxide reactivity in dye decolourising peroxidases fromStreptomyces lividans

A subtle positional shift of the distal haem pocket aspartate in two dye decolourising peroxidase homologs has a remarkable effect on their reactivity with H₂O₂.

Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA

BACKGROUND

The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach.

SCOPE OF REVIEW

Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described.

MAJOR CONCLUSIONS

XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data.

GENERAL SIGNIFICANCE

XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.

Photocatalytic Oxygenation Reactions Using Water and Dioxygen

Water (H₂ O) is the most environmentally benign reductant and is oxidized to evolve dioxygen (O₂ )-the greenest oxidant-in photosystem II. This Minireview focuses on photocatalytic oxygenation of substrates with H₂ O as an oxygen source and O₂ as an oxidant. Metal complexes can be oxidized by two molecules of one-electron oxidants with H₂ O to produce high-valent metal-oxo complexes, which act as active oxidants for oxygenating organic substrates. When an appropriate oxidant is employed for the substrate oxidation, the reduced oxidant can be oxidized by dioxygen to regenerate the oxidant when water and dioxygen are used as an oxygen source and an oxidant, respectively. Photoinduced electron transfer from a substrate (S) to the excited state of complex [(L)M^III ]⁺ produces a substrate radical cation (S^.+ ), accompanied by the regeneration of [(L)M^II ]. S^.+ then reacts with H₂ O to produce an OH adduct radical that is oxidized by [(L)M^III ]⁺ to yield an oxygenated product (SO), in which the oxygen atom originates from H₂ O, accompanied by regeneration of [(L)M^II ]. Photocatalytic oxidation of H₂ O by O₂ to produce H₂ O₂ is combined with the catalytic oxygenation of substrates with H₂ O₂ to produce the oxygenated products, in which the oxygen atom originates from O₂ at the beginning but later from water. This Minireview provides a promising strategy for oxygenation of substrates by using H₂ O as an oxygen source and O₂ as the greenest oxidant.

Enhanced Rates of C-H Bond Cleavage by a Hydrogen-Bonded Synthetic Heme High-Valent Iron(IV) Oxo Complex

Secondary coordination sphere interactions are critical in facilitating the formation, stabilization, and enhanced reactivity of high-valent oxidants required for essential biochemical processes. Herein, we compare the C-H bond oxidizing capabilities of spectroscopically characterized synthetic heme iron(IV) oxo complexes, F8Cmpd-II (F8 = tetrakis(2,6-difluorophenyl)porphyrinate), and a 2,6-lutidinium triflate (LutH+) Lewis acid adduct involving ferryl O-atom hydrogen-bonding, F8Cmpd-II(LutH+). Second-order rate constants utilizing C-H and C-D substrates were obtained by UV-vis spectroscopic monitoring, while products were characterized and quantified by EPR spectroscopy and gas chromatography (GC). With xanthene, F8Cmpd-II(LutH+) reacts 40 times faster (k2 = 14.2 M-1 s-1; -90 °C) than does F8Cmpd-II, giving bixanthene plus xanthone and the heme product [F8FeIIIOH2]+. For substrates with greater C-H bond dissociation energies (BDEs) F8Cmpd-II(LutH+) reacts with the second order rate constants k2(9,10-dihydroanthracene; DHA) = 0.485 M-1 s-1 and k2(fluorene) = 0.102 M-1 s-1 (-90 °C); by contrast, F8Cmpd-II is unreactive toward these substrates. For xanthene vs xanthene-(d2), large, nonclassical deuterium kinetic isotope effects are roughly estimated for both F8Cmpd-II and F8Cmpd-II(LutH+). The deuterated H-bonded analog, F8Cmpd-II(LutD+), was also prepared; for the reaction with DHA, an inverse KIE (compared to F8Cmpd-II(LutH+)) was observed. This work originates/inaugurates experimental investigation of the reactivity of authentic H-bonded heme-based FeIV═O compounds, critically establishing the importance of oxo H-bonding (or protonation) in heme complexes and enzyme active sites.

Dose-resolved serial synchrotron and XFEL structures of radiation-sensitive metalloproteins

An approach is demonstrated to obtain, in a sample- and time-efficient manner, multiple dose-resolved crystal structures from room-temperature protein microcrystals using identical fixed-target supports at both synchrotrons and X-ray free-electron lasers (XFELs). This approach allows direct comparison of dose-resolved serial synchrotron and damage-free XFEL serial femtosecond crystallography structures of radiation-sensitive proteins. Specifically, serial synchrotron structures of a heme peroxidase enzyme reveal that X-ray induced changes occur at far lower doses than those at which diffraction quality is compromised (the Garman limit), consistent with previous studies on the reduction of heme proteins by low X-ray doses. In these structures, a functionally relevant bond length is shown to vary rapidly as a function of absorbed dose, with all room-temperature synchrotron structures exhibiting linear deformation of the active site compared with the XFEL structure. It is demonstrated that extrapolation of dose-dependent synchrotron structures to zero dose can closely approximate the damage-free XFEL structure. This approach is widely applicable to any protein where the crystal structure is altered by the synchrotron X-ray beam and provides a solution to the urgent requirement to determine intact structures of such proteins in a high-throughput and accessible manner.

Specific heme binding to heme regulatory motifs in iron regulatory proteins and its functional significance

Iron regulatory proteins (IRPs) control iron metabolism in mammalian cells by binding to the iron-responsive element (IRE) in the target mRNA. Heme regulatory motifs (HRMs) are conserved in the two IRP homologues IRP1 and IRP2 that specifically bind to two and three heme equivalents, respectively; however, only the heme binding to the iron-dependent degradation (IDD) domain of IRP2 causes heme-mediated oxidation, which does not occur in IRP1. Therefore, the functional significance of conserved HRMs outside the IDD domain is yet unclear. In this study, spectroscopic heme titration with IRP mutants confirmed heme binding to each HRM in IRPs, and the effect of heme binding to HRMs on IRE binding was examined. Native polyacrylamide gel electrophoresis analysis revealed that heme binding to HRMs near the IRE binding site inhibits complex formation between IRPs and IRE without oxidative modification, indicating that the function of HRMs varies outside and within the IDD domain. However, the formation of a typical reactive oxygen species (ROS), hydrogen peroxide, was spectroscopically detected in both heme-bound IRPs. Comparing the heme environmental structures surrounding HRMs, the flexible conformation and many amino acid residues sensitive to ROS of the IDD domain were suggested to promote specific oxidation by the generated hydrogen peroxide. Thus, heme binding to HRM near the IRE binding site sterically interferes with IRE binding, while HRM in the IDD domain facilitates specific heme-mediated oxidation of the protein moiety and the protein degradation via the ubiquitin-proteasome system, resulting in the inhibition of IRE binding.

Unique Tyr-heme double cross-links in F43Y/T67R myoglobin: an artificial enzyme with a peroxidase activity comparable to that of native peroxidases

The X-ray crystal structure of F43Y/T67R myoglobin revealed unique Tyr-heme double cross-links between Tyr43 and the heme 4-vinyl group, which represents a novel post-translational modification of heme proteins. Moreover, with the feature of a distal His-Arg pair, the designed artificial enzyme exhibited a peroxidase activity comparable to that of native peroxidases, such as the most efficient horseradish peroxidase.

Tuning the Geometric and Electronic Structure of Synthetic High-Valent Heme Iron(IV)-Oxo Models in the Presence of a Lewis Acid and Various Axial Ligands

High-valent ferryl species (e.g., (Por)FeIV═O, Cmpd-II) are observed or proposed key oxidizing intermediates in the catalytic cycles of heme-containing enzymes (P-450s, peroxidases, catalases, and cytochrome c oxidase) involved in biological respiration and oxidative metabolism. Herein, various axially ligated iron(IV)-oxo complexes were prepared to examine the influence of the identity of the base. These were generated by addition of various axial ligands (1,5-dicyclohexylimidazole (DCHIm), a tethered-imidazole system, and sodium derivatives of 3,5-dimethoxyphenolate and imidazolate). Characterization was carried out via UV-vis, electron paramagnetic resonance (EPR), 57Fe Mössbauer, Fe X-ray absorption (XAS), and 54/57Fe resonance Raman (rR) spectroscopies to confirm their formation and compare the axial ligand perturbation on the electronic and geometric structures of these heme iron(IV)-oxo species. Mössbauer studies confirmed that the axially ligated derivatives were iron(IV) and six-coordinate complexes. XAS and 54/57Fe rR data correlated with slight elongation of the iron-oxo bond with increasing donation from the axial ligands. The first reported synthetic H-bonded iron(IV)-oxo heme systems were made in the presence of the protic Lewis acid, 2,6-lutidinium triflate (LutH+), with (or without) DCHIm. Mössbauer, rR, and XAS spectroscopic data indicated the formation of molecular Lewis acid ferryl adducts (rather than full protonation). The reduction potentials of these novel Lewis acid adducts were bracketed through addition of outer-sphere reductants. The oxidizing capabilities of the ferryl species with or without Lewis acid vary drastically; addition of LutH+ to F8Cmpd-II (F8 = tetrakis(2,6-difluorophenyl)porphyrinate) increased its reduction potential by more than 890 mV, experimentally confirming that H-bonding interactions can increase the reactivity of ferryl species.

An Aromatic Dyad Motif in Dye Decolourising Peroxidases Has Implications for Free Radical Formation and Catalysis

Dye decolouring peroxidases (DyPs) are the most recent class of heme peroxidase to be discovered. On reacting with H₂ O₂ , DyPs form a high-valent iron(IV)-oxo species and a porphyrin radical (Compound I) followed by stepwise oxidation of an organic substrate. In the absence of substrate, the ferryl species decays to form transient protein-bound radicals on redox active amino acids. Identification of radical sites in DyPs has implications for their oxidative mechanism with substrate. Using a DyP from Streptomyces lividans, referred to as DtpA, which displays low reactivity towards synthetic dyes, activation with H₂ O₂ was explored. A Compound I EPR spectrum was detected, which in the absence of substrate decays to a protein-bound radical EPR signal. Using a newly developed version of the Tyrosyl Radical Spectra Simulation Algorithm, the radical EPR signal was shown to arise from a pristine tyrosyl radical and not a mixed Trp/Tyr radical that has been widely reported in DyP members exhibiting high activity with synthetic dyes. The radical site was identified as Tyr374, with kinetic studies inferring that although Tyr374 is not on the electron-transfer pathway from the dye RB19, its replacement with a Phe does severely compromise activity with other organic substrates. These findings hint at the possibility that alternative electron-transfer pathways for substrate oxidation are operative within the DyP family. In this context, a role for a highly conserved aromatic dyad motif is discussed.

Recent advances in metalloporphyrins for environmental and energy applications

Porphyrin-based chemistry has reached an unprecedented period of rapid development after decades of study. Due to attractive multifunctional properties, porphyrins and their analogues have emerged as multifunctional organometals for environmental and energy purposes. In particular, pioneer works have been conducted to explore their application in pollution abatement, energy conversion and storage and molecule recognition. This review summarizes recent advances of porphyrins chemistry, focusing on elucidating the nature of catalytic process. The Fenton-like redox chemistry and photo-excitability of porphyrins and their analogues are discussed, highlighting the generation of high-valent iron oxo porphyrin species. Finally, challenges in current research are identified and perspectives for future development in this area are presented.

Enhancement of protein stability by an additional disulfide bond designed in human neuroglobin

Human neuroglobin (Ngb) forms an intramolecular disulfide bond between Cys46 and Cys55, with a third Cys120 near the protein surface, which is a promising protein model for heme protein design. In order to protect the free Cys120 and to enhance the protein stability, we herein developed a strategy by designing an additional disulfide bond between Cys120 and Cys15 via A15C mutation. The design was supported by molecular modeling, and the formation of Cys15–Cys120 disulfide bond was confirmed experimentally by ESI-MS analysis. Molecular modeling, UV-Vis and CD spectroscopy showed that the additional disulfide bond caused minimal structural alterations of Ngb. Meanwhile, the disulfide bond of Cys15–Cys120 was found to enhance both Gdn·HCl-induced unfolding stability (increased by ∼0.64 M) and pH-induced unfolding stability (decreased by ∼0.69 pH unit), as compared to those of WT Ngb with a single native disulfide bond of Cys46–Cys55. Moreover, the half denaturation temperature (T_m) of A15C Ngb was determined to be higher than 100 °C. In addition, the disulfide bond of Cys15–Cys120 has slight effects on protein function, such as an increase in the rate of O₂ release by ∼1.4-fold. This study not only suggests a crucial role of the artificial disulfide in protein stabilization, but also lays the groundwork for further investigation of the structure and function of Ngb, as well as for the design of other functional heme proteins, based on the scaffold of A15C Ngb with an enhanced stability.

A disulfide bond of Cys120 and Cys15 was rationally designed in human neuroglobin (Ngb) by A15C mutation, which caused minimal structural alterations, whereas enhanced both chemical and pH stability, with a thermal stability higher than 100 °C.

Neuroglobin is capable of self-oxidation of methionine64 introduced at the heme axial position

Neuroglobin (Ngb), with its physiological role not fully understood, was found to be capable of self-oxidation of methionine64 introduced at the heme axial position (H64M Ngb), adopting a high-spin heme state and producing both methionine sulfoxide (SO-Met) and sulfone (SO2-Met), which represents the structure and function of cytochrome c in a non-native state.

Mn-Mimochrome VI*a: An Artificial Metalloenzyme With Peroxygenase Activity

Manganese-porphyrins are important tools in catalysis, due to their capability to promote a wide variety of synthetically valuable transformations. Despite their great reactivity, the difficulties to control the reaction selectivity and to protect the catalyst from self-degradation hamper their practical application. Compared to small-molecule porphyrin complexes, metalloenzymes display remarkable features, because the reactivity of the metal center is finely modulated by a complex interplay of interactions within the protein matrix. In the effort to combine the catalytic potential of manganese porphyrins with the unique properties of biological catalysts, artificial metalloenzymes have been reported, mainly by incorporation of manganese-porphyrins into native protein scaffolds. Here we describe the spectroscopic and catalytic properties of Mn-Mimochrome VI*a (Mn-MC6*a), a mini-protein with a manganese deuteroporphyrin active site within a scaffold of two synthetic peptides covalently bound to the porphyrin. Mn-MC6*a is an efficient catalyst endowed with peroxygenase activity. The UV-vis absorption spectrum of Mn-MC6*a resembles that of Mn-reconstituted horseradish peroxidase (Mn-HRP), both in the resting and high-valent oxidized states. Remarkably, Mn-MC6*a shows a higher reactivity compared to Mn-HRP, because higher yields and chemoselectivity were observed in thioether oxidation. Experimental evidences also provided indications on the nature of the high-valent reactive intermediate and on the sulfoxidation mechanism.