Nature of the ferryl heme in compounds I and II

Unusually Stable Synthetic Diheme Bis-Fe(IV)oxo: An Intermediate in Diheme Enzymes MauG and BthA

Widespread diheme enzymes MauG and BthA of the bacterial cytochrome c peroxidase (bCCP) superfamily produce an unusually stable bis-Fe(IV) intermediate upon 2e¯-oxidation. Herein, we report, for the first time, the synthesis and characterization of the unusually stable bis-Fe(IV)═O intermediate, as a synthetic mimic of the bis-Fe(IV) species generated in the catalytic cycle of the native diheme enzymes that display similar stability at room temperature. Various spectroscopic techniques, including UV-vis, ESI-MS, EPR, resonance Raman, and Mössbauer, were utilized to thoroughly characterize this fairly stable intermediate. The reaction of a diiron(III) porphyrin dimer with soluble iodosylbenzene (sPhIO) at -80 °C produces a red-colored solution of a hitherto unknown six-coordinate bis-Fe(III)porphyrin-sPhIO adduct which quickly undergoes O-I bond cleavage to yield the green bis-Fe(IV)═O intermediate. The reactivities of such a bis-Fe(IV)═O intermediate have also been demonstrated in the oxygen atom transfer (OAT) and C-H bond activation reactions. Computational studies revealed that the local electric field (LEF) of one heme exerted on the other heme unit is most likely the root cause of the unusual stability of the bis-Fe(IV)═O complex reported here. Indeed, the bis-Fe(IV)═O intermediate has been found to be stabilized significantly relative to its monomeric unit, and the stability of the dimeric system is maximized when the two porphyrin planes are relatively oriented by 20°, at which the LEF reaches its maximum value. The present work provides an excellent opportunity for the mechanistic investigation of the highly challenging and unexplored diheme enzymatic processes and will therefore have widespread practical applicability.

The interplay between the myeloperoxidase-hypochlorous acid system, heme oxygenase, and free iron in inflammatory diseases

Accumulated unbound free iron (Fe(II or III)) is a redox engine generating reactive oxygen species (ROS) that promote oxidative stress and inflammation. Iron is implicated in diseases with free radical pathology including cardiovascular, neurodegenerative, reproductive disorders, and some types of cancer. While many studies focus on iron overload disorders, few explore the potential link between the myeloperoxidase-hypochlorous acid (MPO-HOCl) system and localized iron accumulation through heme and iron‑sulfur (FeS) cluster protein destruction. Although inducible heme oxygenase (HO-1), the rate-limiting enzyme in heme catabolism, is frequently associated with these diseases, we hypothesize that HOCl also contributes to the generation of free iron and heme degradation products. Furthermore, HO-1 and HOCl may play a dual role in free iron accumulation by regulating the activity of key iron metabolism proteins. Enzymatic and non-enzymatic modulators, as well as scavengers of HOCl, can help prevent heme destruction and reduce the accumulation of free iron. Given iron's role in disease progression and severity, identifying the primary sources, mechanisms, and mediators involved in free iron generation is crucial for developing effective pharmacological treatments. Further investigation focusing on the specific contributions of the MPO-HOCl system and free iron is necessary to explore novel strategies to mitigate its harmful effects in biological systems.

Stabilization of the Ferryl═Oxoheme Form of Staphylococcus aureus IsdG by Electron Transfer from a Second-Sphere Tryptophan

The ferryl heme forms of Staphylococcus aureus IsdG and IsdI have novel UV/vis absorption spectra that are distinct from those of the three forms of ferryl heme typically found in biological systems: compound I, compound II, and compound ES. In this work, the ferryl heme form of IsdG was characterized because it is an analogue for the immediate product of enzyme-catalyzed heme hydroxylation. The ferryl heme form of IsdG generated following the addition of meta-chloroperoxybenzoic acid to the ferric heme form of IsdG has a half-life of 4.0 ± 0.2 min, which is more than 100 times longer than the half-life for the ferryl heme form of human heme oxygenase (hHO). Magnetic circular dichroism characterization of the IsdG species yielded spectral data and zero-field splitting parameters consistent with either a compound II- or compound ES-like ferryl heme. Further characterization of isotopically enriched samples with electron paramagnetic resonance spectroscopy revealed the presence of a protein-based organic radical, as would be expected for compound ES. Finally, multiscale quantum mechanics/molecular mechanics and time-dependent density functional theory strongly suggest that the ferryl heme form of IsdG has a ruffled porphyrin ligand and an oxo ligand. Thus, the ferryl heme form of IsdG is assigned to a compound ES-like species with a Trp67-based radical. Electron transfer from Trp67 to porphyrin will stabilize the immediate product of heme hydroxylation and provide a thermodynamic driving force for the reaction. Furthermore, the ability to transfer an electron between Trp67 and the substrate may explain the differential reactivity of meso-hydroxyheme in IsdG and hHO.

Exploring the Ascorbate Requirement of the 2-Oxoglutarate-Dependent Dioxygenases

In humans, the 2-oxoglutarate-dependent dioxygenases (2-OGDDs) catalyze hydroxylation reactions involved in cell metabolism, the biosynthesis of small molecules, DNA and RNA demethylation, the hypoxic response and the formation of collagen. The reaction is catalyzed by a highly oxidizing ferryl-oxo species produced when the active site non-heme iron engages molecular oxygen. Enzyme activity is specifically stimulated by l-ascorbic acid (ascorbate, vitamin C), an effect not well mimicked by other reducing agents. In this perspective article we discuss the reliance of the 2-OGDDs on ascorbate availability. We draw upon findings from studies with different 2-OGDDs to piece together a comprehensive theory for the specific role of ascorbate in supporting enzyme activity. Our discussion centers on the capacity for ascorbate to act as an efficient radical scavenger and its propensity to reduce and chelate transition metals. In addition, we consider the evidence supporting stereospecific binding of ascorbate in the enzyme active site.

Competing Reaction Pathways in Gas-Phase Oxidation of C6H6 by Protonated H2O2

Reactions between protonated hydrogen peroxide and benzene (and benzene-d6) have been studied in the gas phase using an FT-ICR mass spectrometer. Four competing paths for the bimolecular system were identified, namely, proton transfer, hydride abstraction, dissociative single-electron transfer, and an electrophilic addition of HO+ to give the Wheland intermediate [C6H6, OH]+ followed by a subsequent elimination of water. The three latter pathways correspond to three different ways to oxidize benzene. All reaction mechanisms have been modeled using quantum chemical methods, and the calculations are in agreement with the experimental observations. The total reaction rate proceeds at collision rate (slightly higher than the calculated Langevin capture rate), which exemplifies the high reactivity of H3O2+ toward arenes. These observations demonstrate a much richer chemical landscape than previously inferred from the corresponding condensed phase reaction, where only electrophilic substitution by solvated HO+ was described.

Correlating Structure with Spectroscopy in Ascorbate Peroxidase Compound II

Structural and spectroscopic investigations of compound II in ascorbate peroxidase (APX) have yielded conflicting conclusions regarding the protonation state of the crucial Fe(IV) intermediate. Neutron diffraction and crystallographic data support an iron(IV)-hydroxo formulation, whereas Mössbauer, X-ray absorption (XAS), and nuclear resonance vibrational spectroscopy (NRVS) studies appear consistent with an iron(IV)-oxo species. Here we examine APX with spectroscopy-oriented QM/MM calculations and extensive exploration of the conformational space for both possible formulations of compound II. We establish that irrespective of variations in the orientation of a vicinal arginine residue and potential reorganization of proximal water molecules and hydrogen bonding, the Fe-O distances for the oxo and hydroxo forms consistently fall within distinct, narrow, and nonoverlapping ranges. The accuracy of geometric parameters is validated by coupled-cluster calculations with the domain-based local pair natural orbital approach, DLPNO-CCSD(T). QM/MM calculations of spectroscopic properties are conducted for all structural variants, encompassing Mössbauer, optical, X-ray absorption, and X-ray emission spectroscopies and NRVS. All spectroscopic observations can be assigned uniquely to an Fe(IV)═O form. A terminal hydroxy group cannot be reconciled with the spectroscopic data. Under no conditions can the Fe(IV)═O distance be sufficiently elongated to approach the crystallographically reported Fe-O distance. The latter is consistent only with a hydroxo species, either Fe(IV) or Fe(III). Our findings strongly support the Fe(IV)═O formulation of APX-II and highlight unresolved discrepancies in the nature of samples used across different experimental studies.

Chimeric Biocatalyst Combining Peptidic and Nucleic Acid Components Overcomes the Performance and Limitations of the Native Horseradish Peroxidase

Chimeric peptide-DNAzyme (CPDzyme) is a novel artificial peroxidase that relies on the covalent assembly of DNA, peptides, and an enzyme cofactor in a single scaffold. An accurate control of the assembly of these different partners allows for the design of the CPDzyme prototype G4-Hemin-KHRRH, found to be >2000-fold more active (in terms of conversion number k_cat) than the corresponding but non-covalent G4/Hemin complex and, more importantly, >1.5-fold more active than the corresponding native peroxidase (horseradish peroxidase) when considering a single catalytic center. This unique performance originates in a series of gradual improvements, thanks to an accurate selection and arrangement of the different components of the CPDzyme, in order to benefit from synergistic interactions between them. The optimized prototype G4-Hemin-KHRRH is efficient and robust as it can be used under a wide range of non-physiologically relevant conditions [organic solvents, high temperature (95 °C), and in a wide range of pH (from 2 to 10)], thus compensating for the shortcomings of the natural enzymes. Our approach thus opens broad prospects for the design of ever more efficient artificial enzymes.

Common Reactivity and Properties of Heme Peroxidases: A DFT Study of Their Origin

Electronic structure calculations using the density-functional theory (DFT) have been performed to analyse the effect of water molecules and protonation on the heme group of peroxidases in different redox (ferric, ferrous, compounds I and II) and spin states. Shared geometries, spectroscopic properties at the Soret region, and the thermodynamics of peroxidases are discussed. B3LYP and M06-2X density functionals with different basis sets were employed on a common molecular model of the active site (Fe-centred porphine and proximal imidazole). Computed Gibbs free energies indicate that the corresponding aquo complexes are not thermodynamically stable, supporting the five-coordinate Fe(III) centre in native ferric peroxidases, with a water molecule located at a non-bonding distance. Protonation of the ferryl oxygen of compound II is discussed in terms of thermodynamics, Fe-O bond distances, and redox properties. It is demonstrated that this protonation is necessary to account for the experimental data, and computed Gibbs free energies reveal pK_a values of compound II about 8.5-9.0. Computation indicates that the general oxidative properties of peroxidase intermediates, as well as their reactivity towards water and protons and Soret bands, are mainly controlled by the iron porphyrin and its proximal histidine ligand.

Exploring the Factors which Result in Cytochrome P450 Catalyzed Desaturation Versus Hydroxylation

The cytochrome P450 family of monooxygenase enzymes have essential biological roles involving the selective oxidation of carbon-hydrogen bonds. They can also catalyze other important metabolic reactions including desaturation to form alkenes. Currently the factors that control the partition between P450 hydroxylation and desaturation pathways are poorly defined. The CYP199A4 enzyme from the bacterium Rhodopseudomonas palustris HaA2 catalyzes the oxidation of 4-ethyl- and 4-isopropyl- benzoic acids with hydroxylation and desaturation occurring in significant quantities. Here we demonstrate that 4-cyclopropylbenzoic acid is regioselectively hydroxylated by CYP199A4 at the benzylic carbon. In contrast, the oxidation of 4-n-propylbenzoic acid by CYP199A4 results in three major metabolites: an alkene from desaturation and two hydroxylation products at the benzylic (Cα) and Cβ carbons in similar quantities. Extending the length of the alkyl substituent resulted in 4-n-butylbenzoic acid being oxidized at the benzylic position (45%) and desaturated (55%). In contrast, 4-isobutylbenzoic generated very little alkene (5%) but was hydroxylated at the benzylic position (54%) and at the tertiary Cβ position (41%). The oxidation of 4-n-propylbenzoic acid by the F298 V mutant of CYP199A4 occurred with no hydroxylation at Cβ and a significant increase in metabolites arising from desaturation (73%). The X-ray crystal structures of CYP199A4 with each substrate revealed that they bind in the active site with the alkyl substituent positioned over the heme. However, the longer alkylbenzoic acids were bound in a different conformation as was 4-n-propylbenzoic acid in the F298 V mutant. Overall, the changes in metabolite distribution could be ascribed to bond strength differences and the position of the alkyl group relative to the heme.

Serial femtosecond crystallography approaches to understanding catalysis in iron enzymes

Enzymes with iron-containing active sites play crucial roles in catalysing a myriad of oxidative reactions essential to aerobic life. Defining the three-dimensional structures of iron enzymes in resting, oxy-bound intermediate and substrate-bound states is particularly challenging, not least because of the extreme susceptibility of the Fe(III) and Fe(IV) redox states to radiation-induced chemistry caused by intense X-ray or electron beams. The availability of novel sources such as X-ray free electron lasers has enabled structures that are effectively free of the effects of radiation-induced chemistry and allows time-resolved structures to be determined. Important to both applications is the ability to obtain in crystallo spectroscopic data to identify the redox state of the iron in any particular structure or timepoint.

Serial Femtosecond Crystallography Reveals the Role of Water in the One- or Two-Electron Redox Chemistry of Compound I in the Catalytic Cycle of the B-Type Dye-Decolorizing Peroxidase DtpB

Controlling the reactivity of high-valent Fe(IV)–O catalytic intermediates, Compounds I and II, generated in heme enzymes upon reaction with dioxygen or hydrogen peroxide, is important for function. It has been hypothesized that the presence (wet) or absence (dry) of distal heme pocket water molecules can influence whether Compound I undergoes sequential one-electron additions or a concerted two-electron reduction. To test this hypothesis, we investigate the role of water in the heme distal pocket of a dye-decolorizing peroxidase utilizing a combination of serial femtosecond crystallography and rapid kinetic studies. In a dry distal heme site, Compound I reduction proceeds through a mechanism in which Compound II concentration is low. This reaction shows a strong deuterium isotope effect, indicating that reduction is coupled to proton uptake. The resulting protonated Compound II (Fe(IV)–OH) rapidly reduces to the ferric state, giving the appearance of a two-electron transfer process. In a wet site, reduction of Compound I is faster, has no deuterium effect, and yields highly populated Compound II, which is subsequently reduced to the ferric form. This work provides a definitive experimental test of the hypothesis advanced in the literature that relates sequential or concerted electron transfer to Compound I in wet or dry distal heme sites.

Mechanistic insights into the chemistry of compound I formation in heme peroxidases: quantum chemical investigations of cytochrome c peroxidase

Peroxidases are heme containing enzymes that catalyze peroxide-dependant oxidation of a variety of substrates through forming key ferryl intermediates, compounds I and II. Cytochrome c peroxidase (Ccp1) has served for decades as a chemical model toward understanding the chemical biology of this heme family of enzymes. It is known to feature a distinctive electronic behaviour for its compound I despite significant structural similarity to other peroxidases. A water-assisted mechanism has been proposed over a dry one for the formation of compound I in similar peroxidases. To better identify the viability of these mechanisms, we employed quantum chemistry calculations for the heme pocket of Ccp1 in three different spin states. We provided comparative energetic and structural results for the six possible pathways that suggest the preference of the dry mechanism energetically and structurally. The doublet state is found to be the most preferable spin state for the mechanism to proceed and for the formation of the Cpd I ferryl-intermediate irrespective of the considered dielectric constant used to represent the solvent environment. The nature of the spin state has negligible effects on the calculated structures but great impact on the energetics. Our analysis was also expanded to explain the major contribution of key residues to the peroxidase activity of Ccp1 through exploring the mechanism at various in silico generated Ccp1 variants. Overall, we provide valuable findings toward solving the current ambiguity of the exact mechanism in Ccp1, which could be applied to peroxidases with similar heme pockets.

Discerning the feasibility of a no-water peroxidase mechanism in the doublet spin state irrespective of the environment surrounding the heme pocket.

Inhibitory effect of ascorbate on tryptophan 2,3-dioxygenase

Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) catalyze the same reaction, oxidative cleavage of L-tryptophan (L-Trp) to N-formyl-kynurenine. In both enzymes, the ferric (FeIII) form is inactive, and ascorbate (Asc) is frequently used as a reductant in in vitro assays to activate the enzymes by reducing the heme iron. Recently, it has been reported that Asc activates IDO2 by acting as a reductant, however, it is also a competitive inhibitor of the enzyme. Here, the effect of Asc on human TDO (hTDO) is investigated. Similar to its interaction with IDO2, Asc acts as both a reductant and a competitive inhibitor of hTDO in the absence of catalase, and its inhibitory effect was enhanced by the addition of H2O2. Interestingly, however, no inhibitory effect of Asc was observed in the presence of catalase. TDO is known to be activated by H2O2 and a ferryl-oxo (FeIV=O) intermediate (Compound II) is generated during the activation process. The observation that Asc acts as a competitive inhibitor of hTDO only in the absence of catalase can be explained by assuming that the target of Asc is Compound II. Asc seems to compete with L-Trp in an unusual manner.

Cryo-EM structures of intermediates suggest an alternative catalytic reaction cycle for cytochrome c oxidase

Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) to water. Their catalytic cycle has been considered to start with the oxidized form. Subsequent electron transfers lead to the E-state, the R-state (which binds oxygen), the P-state (with an already split dioxygen bond), the F-state and the O-state again. Here, we determined structures of up to 1.9 Å resolution of these intermediates by single particle cryo-EM. Our results suggest that in the O-state the active site contains a peroxide dianion and in the P-state possibly an intact dioxygen molecule, the F-state may contain a superoxide anion. Thus, the enzyme's catalytic cycle may have to be turned by 180 degrees.

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.

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.

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.

The Chemical Basis of Intracerebral Hemorrhage and Cell Toxicity With Contributions From Eryptosis and Ferroptosis

Intracerebral hemorrhage (ICH) is a particularly devastating event both because of the direct injury from space-occupying blood to the sequelae of the brain exposed to free blood components from which it is normally protected. Not surprisingly, the usual metabolic and energy pathways are overwhelmed in this situation. In this review article, we detail the complexity of red blood cell degradation, the contribution of eryptosis leading to hemoglobin breakdown into its constituents, the participants in that process, and the points at which injury can be propagated such as elaboration of toxic radicals through the metabolism of the breakdown products. Two prominent products of this breakdown sequence, hemin, and iron, induce a variety of pathologies including free radical damage and DNA breakage, which appear to include events independent from typical oxidative DNA injury. As a result of this confluence of damaging elements, multiple pathways of injury, cell death, and survival are likely engaged including ferroptosis (which may be the same as oxytosis but viewed from a different perspective) and senescence, suggesting that targeting any single cause will likely not be a sufficient strategy to maximally improve outcome. Combination therapies in addition to safe methods to reduce blood burden should be pursued.

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.

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.

X-ray-induced photoreduction of heme metal centers rapidly induces active-site perturbations in a protein-independent manner

Since the advent of protein crystallography, atomic-level macromolecular structures have provided a basis to understand biological function. Enzymologists use detailed structural insights on ligand coordination, interatomic distances, and positioning of catalytic amino acids to rationalize the underlying electronic reaction mechanisms. Often the proteins in question catalyze redox reactions using metal cofactors that are explicitly intertwined with their function. In these cases, the exact nature of the coordination sphere and the oxidation state of the metal is of utmost importance. Unfortunately, the redox-active nature of metal cofactors makes them especially susceptible to photoreduction, meaning that information obtained by photoreducing X-ray sources about the environment of the cofactor is the least trustworthy part of the structure. In this work we directly compare the kinetics of photoreduction of six different heme protein crystal species by X-ray radiation. We show that a dose of ∼40 kilograys already yields 50% ferrous iron in a heme protein crystal. We also demonstrate that the kinetics of photoreduction are completely independent from variables unique to the different samples tested. The photoreduction-induced structural rearrangements around the metal cofactors have to be considered when biochemical data of ferric proteins are rationalized by constraints derived from crystal structures of reduced enzymes.

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.

Assessment of malathion toxicity on cytophysiological activity, DNA damage and antioxidant enzymes in root of Allium cepa model

The current study was emphasized to assess the effect of malathion on root system (cell division and kinetics of the root elongation) and stress related parameters in Allium cepa L. The roots were exposed to different concentrations (0.05, 0.13, 0.26, 0.39 and 0.52 g/L) of malathion for different treatment periods (4, 8 and 18 h). The results revealed that malathion application affected the growth rate and cell division in root tips. The root elongation kinetics were impaired at 0.13 to 0.52 g/L concentrations. Reduction in tissue water content (TWC) indicated the limited osmotic adjustment due to membrane damage. Further, a decrease in sucrose content was observed in contrast to the accumulation of proline (upto 0.39 g/L). Moreover, malathion exposure elevated the levels of lipid peroxidation followed by changes in antioxidant enzymes status. The activities of ascorbate peroxidase (APX) and glutathione reductase (GR) were down-regulated whereas the activities of catalase (CAT), glutathione-S-transferase (GST) and superoxide dismutase (SOD) were up-regulated except in 0.52 g/L malathion. The molecular docking study of malathion with CAT, GST, SOD, APX and GR also supported of above results for their activity. All these physiological responses varied with increasing malathion concentration and duration of treatment. The single cell gel electrophoresis results showed that all concentrations of malathion induced DNA damage in root cells. The findings depicted that malathion application induces cytotoxic and phytotoxic effects mediated through oxidative stress and subsequent injuries.

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.

Methoxyphenol derivatives as reversible inhibitors of myeloperoxidase as potential antiatherosclerotic agents

Aim: To evaluate new chemical entities, based on ferulic acid scaffolds, as reversible myeloperoxidase inhibitors (MPOI). Methodology & results:In silico docking studies are performed with MPO protein as a target for several ferulic acid analogs followed by multiple in vitro assays to validate this approach. Two lead compounds 2a and 3 are identified with optimum docking and IC50 values: -7.95 kcal/mol, 0.9 μM and -8.35 kcal/mol, 8.5 μM, respectively. These MPOIs are able to inhibit oxidation of high-density lipoprotein and further promoted functionality of high-density lipoprotein. Conclusion: Lead analogs are potent MPOIs that exert specific effects on MPO-mediated oxidation as well as inflammatory pathways. It also acts as promoters of cholesterol efflux that sheds light on pharmacological approach in atherosclerosis treatment.

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.

Exploiting MATE efflux proteins to improve flavonoid accumulation in Camellia sinensis in silico

Flavonoids in tea plant are the important bioactive compounds for both human health and taste quality. Multidrug and Toxic compound Extrusion (MATE) proteins could improve flavonoid accumulations by transporting and sequestering the flavonoid in vacuoles. We identified 41 putative MATE genes in tea plants. The similar intron-exon structures of tea MATEs clustered within the same gene clade. The correlation analysis of tea flavonoid and transcriptome data showed that TEA006173 might be involve in the tea flavonoid accumulation. The RT-PCR results confirmed that TEA006173 showed high expression in the young leaf tissues. Tertiary structure prediction has shown that TEA006173 contained the 12 helices with three active pockets, comprising 13 critical residues. The present study provided the structural variations and expression patterns of tea MATEs and it would be helpful for taste and nutrient quality improvement in tea plant.

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.

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.

Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function

Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.

Living with Oxygen

Work on the electronic structures of metal–oxo complexes began in Copenhagen over 50 years ago. This work led to the prediction that tetragonal multiply bonded transition metal–oxos would not be stable beyond the iron–ruthenium–osmium oxo wall in the periodic table and that triply bonded metal–oxos could not be protonated, even in the strongest Brønsted acids. In this theory, only double bonded metal–oxos could attract protons, with basicities being a function of the electron donating ability of ancillary ligands. Such correlations of electronic structure with reactivity have gained importance in recent years, most notably owing to the widespread recognition that high-valent iron–oxos are intermediates in biological reactions critical to life on Earth.

In this Account, we focus attention on the oxygenations of inert organic substrates by cytochromes P450, as these reactions involve multiply bonded iron–oxos. We emphasize that P450 iron–oxos are strong oxidants, so strong that they would destroy nearby amino acids if substrates are not oxygenated rapidly; it is our view that these high-valent iron–oxos are such dangerous reactive oxygen species that Nature surely found ways to disable them. Looking more deeply into this matter, mainly by examining many thousands of structures in the Protein Data Bank, we have found that P450s and other enzymes that require oxygen for function have chains of tyrosines and tryptophans that extend from active-site regions to protein surfaces. Tyrosines are near the heme active sites in bacterial P450s, whereas tryptophan is closest in most human enzymes. High-valent iron–oxo survival times taken from hole hopping maps range from a few nanoseconds to milliseconds, depending on the distance of the closest Trp or Tyr residue to the heme. In our proposed mechanism, multistep hole tunneling (hopping) through Tyr/Trp chains guides the damaging oxidizing hole to the protein surface, where it can be quenched by soluble protein or small molecule reductants. As the Earth’s oxygenic atmosphere is believed to have developed about 2.5 billion years ago, the increase in occurrence frequency of tyrosine and tryptophan since the last universal evolutionary ancestor may be in part a consequence of enzyme protective functions that developed to cope with the environmental toxin, O₂.

The rise of neutron cryo-crystallography

The use of boiled-off liquid nitrogen to maintain protein crystals at 100 K during X-ray data collection has become almost universal. Applying this to neutron protein crystallography offers the opportunity to significantly broaden the scope of biochemical problems that can be addressed, although care must be taken in assuming that direct extrapolation to room temperature is always valid. Here, the history to date of neutron protein cryo-crystallography and the particular problems and solutions associated with the mounting and cryocooling of the larger crystals needed for neutron crystallography are reviewed. Finally, the outlook for further cryogenic neutron studies using existing and future neutron instrumentation is discussed.

Mechanistic Insight on the Activity and Substrate Selectivity of Nonheme Iron Dioxygenases

Nonheme iron dioxygenases catalyze vital reactions for human health particularly related to aging processes. They are involved in the biosynthesis of amino acids, but also the biodegradation of toxic compounds. Typically they react with their substrate(s) through oxygen atom transfer, although often with the assistance of a co-substrate like α-ketoglutarate that is converted to succinate and CO₂ . Many reaction processes catalyzed by the nonheme iron dioxygenases are stereoselective or regiospecific and hence understanding the mechanism and protein involvement in the selectivity is important for the design of biotechnological applications of these enzymes. To this end, I will review recent work of our group on nonheme iron dioxygenases and include background information on their general structure and catalytic cycle. Examples of stereoselective and regiospecific reaction mechanisms we elucidated are for the AlkB repair enzyme, prolyl-4-hydroxylase and the ergothioneine biosynthesis enzyme. Finally, I cover an example where we bioengineered S-p-hydroxymandelate synthase into the R-p-hydroxymandelate synthase.

Energy dispersive spectrometry and first principles studies on the oxidation of pentlandite

Experimental and computational studies were carried out to investigate the oxidation of pentlandite (Fe4.5Ni4.5S8). The oxidation product was first analyzed by energy dispersive spectrometry to reveal the elemental distribution at the cross section. Our experimental study shows that the Fe atoms in pentlandite migrated to the surface and were preferentially oxidized to form a thin layer of Fe2O3, whereas the Ni atoms remained at the center of the grain. Furthermore, density functional theory calculations were performed to investigate the adsorption and diffusion of atomic oxygen as well as the adsorption and dissociation of molecular oxygen on the (001) and (010) surfaces of pentlandite. From the calculated adsorption energies of atomic oxygen at the different sites of the (001) and (010) surfaces, we found that oxidation of the Fe sites was preferable to that of the Ni sites when exposed to an oxidizing atmosphere. For molecular oxygen adsorption on the surfaces of pentlandite, the bridge sites (Fe-Ni and Fe-Fe) were found to be the most favorable adsorption sites. The dissociative adsorption of O2 is thermodynamically more favorable than the molecular adsorption. Calculated dissociation barriers show that the oxidation is feasible during high temperature roasting.

Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins

As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.

Unveiling the water-associated conformational mobility in the active site of ascorbate peroxidase

We carried out comprehensive spectroscopic studies of wild type and mutants of ascorbate peroxidase (APX) to gain understanding of the conformational mobility of the active site. In this approach, three unnatural tryptophans were applied to replace the distal tryptophan (W41) in an aim to probe polarity/water environment near the edge of the heme-containing active site. 7-azatryptophan ((7-aza)Trp) is sensitive to environment polarity, while 2,7-azatryptophan ((2,7-aza)Trp) and 2,6-diazatryptophan ((2,6-aza)Trp) undergo excited-state water-catalyzed double and triple proton transfer, respectively, and are sensitive to the water network. The combination of their absorption, emission bands and the associated relaxation dynamics of these fluorescence probes, together with the Soret-band difference absorption and resonance Raman spectroscopy, lead us to unveil the water associated conformational mobility in the active site of APX. The results are suggestive of the existence of equilibrium between two different environments surrounding W41 in APX, i.e., the water-rich and water-scant forms with distinct fluorescence relaxation. Our results thus demonstrate for the first time the power of integrating multiple sensors (7-aza)Trp, (2,7-aza)Trp and (2,6-aza)Trp in probing the water environment of a specifically targeted Trp in proteins.

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.

Decarboxylation involving a ferryl, propionate, and a tyrosyl group in a radical relay yields heme b

The H₂O₂-dependent oxidative decarboxylation of coproheme III is the final step in the biosynthesis of heme b in many microbes. However, the coproheme decarboxylase reaction mechanism is unclear. The structure of the decarboxylase in complex with coproheme III suggested that the substrate iron, reactive propionates, and an active-site tyrosine convey a net 2e^-/2H⁺ from each propionate to an activated form of H₂O₂ Time-resolved EPR spectroscopy revealed that Tyr-145 formed a radical species within 30 s of the reaction of the enzyme-coproheme complex with H₂O₂ This radical disappeared over the next 270 s, consistent with a catalytic intermediate. Use of the harderoheme III intermediate as substrate or substitutions of redox-active side chains (W198F, W157F, or Y113S) did not strongly affect the appearance or intensity of the radical spectrum measured 30 s after initiating the reaction with H₂O₂, nor did it change the ∼270 s required for the radical signal to recede to ≤10% of its initial intensity. These results suggested Tyr-145 as the site of a catalytic radical involved in decarboxylating both propionates. Tyr-145^• was accompanied by partial loss of the initially present Fe(III) EPR signal intensity, consistent with the possible formation of Fe(IV)=O. Site-specifically deuterated coproheme gave rise to a kinetic isotope effect of ∼2 on the decarboxylation rate constant, indicating that cleavage of the propionate Cβ-H bond was partly rate-limiting. The inferred mechanism requires two consecutive hydrogen atom transfers, first from Tyr-145 to the substrate Fe/H₂O₂ intermediate and then from the propionate Cβ-H to Tyr-145^•.

Understanding heme proteins with hyperfine spectroscopy

Heme proteins are versatile proteins that are involved in a large number of biological processes. Many spectroscopic methods are used to gain insight into the different mechanistic processes governing heme-protein functions. Since many (intermediate) states of heme proteins are paramagnetic, electron paramagnetic resonance (EPR) methods, such as hyperfine spectroscopy, offer unique tools for these investigations. This perspective gives an overview of the use of state-of-the-art hyperfine spectroscopy in heme research, focusing on the advantages, limits and challenges of the different techniques.

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 Patterns of (Protonated) Compound II and Compound I of Cytochrome P450: Which is the Better Oxidant?

The cytochromes P450 are versatile enzymes in human physiology that perform substrate hydroxylation reactions extremely efficiently. In this work, we present results of a computational study on the reactivity patterns of Compound I, Compound II, and protonated Compound II with model substrates, and we address the question of which of these compounds is the most effective oxidant? All calculations, regardless of the substrate, implicated that Compound I is the superior oxidant of the three. However, Compound II and protonated Compound II were found to react with free energies of activation that are only a few kcal mol^-1 higher in energy than those obtained with Compound I. Therefore, Compound II and protonated Compound II should be able to react with aliphatic groups with moderate C-H bond strengths. We have analysed all results in detail and have given electronic, thermochemical, valence bond, and molecular orbital rationalizations on the reactivity differences and explained experimental product distributions. Overall, the findings implied that alternative oxidants could operate alongside Compound I in complex reaction mechanisms of enzymatic and synthetic iron porphyrinoid complexes.

Structure-Based Mechanism for Oxidative Decarboxylation Reactions Mediated by Amino Acids and Heme Propionates in Coproheme Decarboxylase (HemQ)

Coproheme decarboxylase catalyzes two sequential oxidative decarboxylations with H2O2 as the oxidant, coproheme III as substrate and cofactor, and heme b as the product. Each reaction breaks a C-C bond and results in net loss of hydride, via steps that are not clear. Solution and solid-state structural characterization of the protein in complex with a substrate analog revealed a highly unconventional H2O2-activating distal environment with the reactive propionic acids (2 and 4) on the opposite side of the porphyrin plane. This suggested that, in contrast to direct C-H bond cleavage catalyzed by a high-valent iron intermediate, the coproheme oxidations must occur through mediating amino acid residues. A tyrosine that hydrogen bonds to propionate 2 in a position analogous to the substrate in ascorbate peroxidase is essential for both decarboxylations, while a lysine that salt bridges to propionate 4 is required solely for the second. A mechanism is proposed in which propionate 2 relays an oxidizing equivalent from a coproheme compound I intermediate to the reactive deprotonated tyrosine, forming Tyr•. This residue then abstracts a net hydrogen atom (H•) from propionate 2, followed by migration of the unpaired propionyl electron to the coproheme iron to yield the ferric harderoheme and CO2 products. A similar pathway is proposed for decarboxylation of propionate 4, but with a lysine residue as an essential proton shuttle. The proposed reaction suggests an extended relay of heme-mediated e-/H+ transfers and a novel route for the conversion of carboxylic acids to alkenes.