On the mechanism of compound I formation from peroxidases and catalases

Advances in metal-organic framework-based nanozymes in ROS scavenging medicine

Reactive oxygen species (ROS) play important roles in regulating various physiological functions in the human body, however, excessive ROS can cause serious damage to the human body, considering the various limitations of natural enzymes as scavengers of ROS in the body, the development of better materials for the scavenging of ROS is of great significance to the biomedical field, and nanozymes, as a kind of nanomaterials which can show the activity of natural enzymes. Have a good potential for the development in the area of ROS scavenging. Metal-organic frameworks (MOFs), which are porous crystalline materials with a periodic network structure composed of metal nodes and organic ligands, have been developed with a variety of active nanozymes including catalase-like, superoxide dismutase-like, and glutathione peroxidase-like enzymes due to the adjustability of active sites, structural diversity, excellent biocompatibility, and they have shown a wide range of applications and prospects. In the present review, we first introduce three representative natural enzymes for ROS scavenging in the human body, methods for the detection of relevant enzyme-like activities and mechanisms of enzyme-like clearance are discussed, meanwhile, we systematically summarize the progress of the research on MOF-based nanozymes, including the design strategy, mechanism of action, and medical application, etc. Finally, the current challenges of MOF-based nanozymes are summarized, and the future development direction is anticipated. We hope that this review can contribute to the research of MOF-based nanozymes in the medical field related to the scavenging of ROS.

ROS-Scavenging Therapeutic Hydrogels for Modulation of the Inflammatory Response

Although reactive oxygen species (ROS) are essential for cellular processes, excessive ROS could be a major cause of various inflammatory diseases because of the oxidation of proteins, DNA, and membrane lipids. It has recently been suggested that the amount of ROS could thus be regulated to treat such physiological disorders. A ROS-scavenging hydrogel is a promising candidate for therapeutic applications because of its high biocompatibility, 3D matrix, and ability to be modified. Approaches to conferring antioxidant properties to normal hydrogels include embedding ROS-scavenging catalytic nanoparticles, modifying hydrogel polymer chains with ROS-adsorbing organic moieties, and incorporating ROS-labile linkers in polymer backbones. Such therapeutic hydrogels can be used for wound healing, cardiovascular diseases, bone repair, ocular diseases, and neurodegenerative disorders. ROS-scavenging hydrogels could eliminate oxidative stress, accelerate the regeneration process, and show synergetic effects with other drugs or therapeutic molecules. In this review, the mechanisms by which ROS are generated and scavenged in the body are outlined, and the effects of high levels of ROS and the resulting oxidative stress on inflammatory diseases are described. Next, the mechanism of ROS scavenging by hydrogels is explained depending on the ROS-scavenging agents embedded within the hydrogel. Lastly, the recent achievements in the development of ROS-scavenging hydrogels to treat various inflammation-associated diseases are presented.

A current perspective on hydrogen peroxide production in honey. A review

Hydrogen peroxide plays a key role in honey antibacterial activity. The production of H₂O₂ in honey requires glucose oxidase (GOx) that oxidizes glucose to gluconolactone and reduces molecular oxygen to hydrogen peroxide. The content of GOx of honeybee origin was believed to be the main predictor of H₂O₂ concentration in honey. The observed variations in H₂O₂ levels among honeys questioned however the direct GOx-H₂O₂ relationship and left its absence opened for exploration. Here, we evaluated principal causes underlying the imbalance in the quantitative enzyme-product relationship with respect to: (a) enzyme and the product inactivation or destruction by honey compounds; (b) non-enzymatic pathway of H₂O₂ formation, and (c) a potential contribution of enzymes with GOx activity originating from nectars and microorganisms inhabiting honey. We also bring new facts on the relationship between honey colloidal structure and H₂O₂ production that change our traditional understanding of honey function as antimicrobial agent.

Cystic Fibrosis and Pseudomonas aeruginosa: the Host-Microbe Interface

In human pathophysiology, the clash between microbial infection and host immunity contributes to multiple diseases. Cystic fibrosis (CF) is a classical example of this phenomenon, wherein a dysfunctional, hyperinflammatory immune response combined with chronic pulmonary infections wreak havoc upon the airway, leading to a disease course of substantial morbidity and shortened life span. Pseudomonas aeruginosa is an opportunistic pathogen that commonly infects the CF lung, promoting an accelerated decline of pulmonary function. Importantly, P. aeruginosa exhibits significant resistance to innate immune effectors and to antibiotics, in part, by expressing specific virulence factors (e.g., antioxidants and exopolysaccharides) and by acquiring adaptive mutations during chronic infection. In an effort to review our current understanding of the host-pathogen interface driving CF pulmonary disease, we discuss (i) the progression of disease within the primitive CF lung, specifically focusing on the role of host versus bacterial factors; (ii) critical, neutrophil-derived innate immune effectors that are implicated in CF pulmonary disease, including reactive oxygen species (ROS) and antimicrobial peptides (e.g., LL-37); (iii) P. aeruginosa virulence factors and adaptive mutations that enable evasion of the host response; and (iv) ongoing work examining the distribution and colocalization of host and bacterial factors within distinct anatomical niches of the CF lung.

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.

Spectroscopic and Kinetic Characterization of Peroxidase-Like π-Cation Radical Pinch-Porphyrin-Iron(III) Reaction Intermediate Models of Peroxidase Enzymes

The spectroscopic and kinetic characterization of two intermediates from the H₂O₂ oxidation of three dimethyl ester [(proto), (meso), (deuteroporphyrinato) (picdien)]Fe(III) complexes ([FePPPic], [FeMPPic] and [FeDPPic], respectively) pinch-porphyrin peroxidase enzyme models, with s = 5/2 and 3/2 Fe(III) quantum mixed spin (qms) ground states is described herein. The kinetic study by UV/Vis at λmax = 465 nm showed two different types of kinetics during the oxidation process in the guaiacol test for peroxidases (1-3 + guaiacol + H₂O₂ → oxidation guaiacol products). The first intermediate was observed during the first 24 s of the reaction. When the reaction conditions were changed to higher concentration of pinch-porphyrins and hydrogen peroxide only one type of kinetics was observed. Next, the reaction was performed only between pinch-porphyrins-Fe(III) and H₂O₂, resulting in only two types of kinetics that were developed during the first 0-4 s. After this time a self-oxidation process was observed. Our hypotheses state that the formation of the π-cation radicals, reaction intermediates of the pinch-porphyrin-Fe(III) family with the ligand picdien [N,N'-bis-pyridin-2-ylmethyl-propane-1,3-diamine], occurred with unique kinetics that are different from the overall process and was involved in the oxidation pathway. UV-Vis, ¹H-NMR and ESR spectra confirmed the formation of such intermediates. The results in this paper highlight the link between different spectroscopic techniques that positively depict the kinetic traits of artificial compounds with enzyme-like activity.

Production of dioxygen in the dark: dismutases of oxyanions

O₂-generating reactions are exceedingly rare in biology and difficult to mimic synthetically. Perchlorate-respiring bacteria enzymatically detoxify chlorite (ClO₂(-) ), the end product of the perchlorate (ClO(4)(-) ) respiratory pathway, by rapidly converting it to dioxygen (O₂) and chloride (Cl(-)). This reaction is catalyzed by a heme-containing protein, called chlorite dismutase (Cld), which bears no structural or sequence relationships with known peroxidases or other heme proteins and is part of a large family of proteins with more than one biochemical function. The original assumptions from the 1990s that perchlorate is not a natural product and that perchlorate respiration might be confined to a taxonomically narrow group of species have been called into question, as have the roles of perchlorate respiration and Cld-mediated reactions in the global biogeochemical cycle of chlorine. In this chapter, the chemistry and biochemistry of Cld-mediated O₂generation, as well as the biological and geochemical context of this extraordinary reaction, are described.

QM/MM molecular dynamics studies of metal binding proteins

Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM)) simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu) and main group (Mg) metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.

Mechanisms of oxidant generation by catalase

The enzyme catalase converts solar radiation into reactive oxidant species (ROS). In this study, we report that several bacterial catalases (hydroperoxidases, HP), including Escherichia coli HP-I and HP-II also generate reactive oxidants in response to ultraviolet B light (UVB). HP-I and HP-II are identical except for the presence of NADPH. We found that only one of the catalases, HPI, produces oxidants in response to UVB light, indicating a potential role for the nucleotide in ROS production. This prompts us to speculate that NADPH may act as a cofactor regulating ROS generation by mammalian catalases. Structural analysis of the NADPH domains of several mammalian catalases revealed that the nucleotide is bound in a constrained conformation and that UVB irradiation induces NADPH oxidation and positional changes. Biochemical and kinetic analysis indicate that ROS formation by the enzyme is enhanced by oxidation of the cofactor. Conformational changes following absorption of UVB light by catalase NADPH have the potential to facilitate ROS production by the enzyme.

Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase

Chlorite dismutase (Cld) is a heme enzyme capable of rapidly and selectively decomposing chlorite (ClO(2) (-)) to Cl(-) and O(2). The ability of Cld to promote O(2) formation from ClO(2) (-) is unusual. Heme enzymes generally utilize ClO(2) (-) as an oxidant for reactions such as oxygen atom transfer to, or halogenation of, a second substrate. The X-ray crystal structure of Dechloromonas aromatica Cld co-crystallized with the substrate analogue nitrite (NO(2) (-)) was determined to investigate features responsible for this novel reactivity. The enzyme active site contains a single b-type heme coordinated by a proximal histidine residue. Structural analysis identified a glutamate residue hydrogen-bonded to the heme proximal histidine that may stabilize reactive heme species. A solvent-exposed arginine residue likely gates substrate entry to a tightly confined distal pocket. On the basis of the proposed mechanism of Cld, initial reaction of ClO(2) (-) within the distal pocket generates hypochlorite (ClO(-)) and a compound I intermediate. The sterically restrictive distal pocket probably facilitates the rapid rebound of ClO(-) with compound I forming the Cl(-) and O(2) products. Common to other heme enzymes, Cld is inactivated after a finite number of turnovers, potentially via the observed formation of an off-pathway tryptophanyl radical species through electron migration to compound I. Three tryptophan residues of Cld have been identified as candidates for this off-pathway radical. Finally, a juxtaposition of hydrophobic residues between the distal pocket and the enzyme surface suggests O(2) may have a preferential direction for exiting the active site.

On the role of water in peroxidase catalysis: a theoretical investigation of HRP compound I formation

We have investigated the dynamics of water molecules in the distal pocket of horseradish peroxidase to elucidate the role that they may play in the formation of the principal active species of the enzymatic cycle (compound I, Por(o+)-Fe(IV)=O) upon reaction of the resting Fe(III) state with hydrogen peroxide. The equilibrium molecular dynamics simulations show that, in accord with experimental evidence, the active site access channel is hydrated with an average of two to three water molecules within 5 A from the bound hydrogen peroxide. Although the channel is always hydrated, the specific conformations in which a water molecule bridges H(2)O(2) and the distal histidine, which were found (Derat; et al. J. Am. Chem. Soc. 2007, 129, 6346.) to display a low-energy barrier for the initial acid-base step of the reaction, occur with low probability but are relevant within the time scale of catalysis. Metadynamics simulations, which were used to reconstruct the free-energy landscape of water motion in the access channel, revealed that preferred interaction sites within the channel are separated by small energy barriers (<1.5 kcal/mol). Most importantly, water-bridged conformations lie on a shoulder just 1 kcal/mol above one local minimum and thus are easily accessible. Such an energy landscape appears as a requisite for the effectiveness of compound I formation, whereby the H-bonding pattern involving reactants and catalytic residues (including the intervening water molecule) has to rearrange to deliver the proton to the distal OH moiety of the hydrogen peroxide and thereby lead to heterolytic O-O cleavage. Our study provides an example of a system for which the "reactive configurations" (i.e., structures characterized by a low barrier for the chemical transformation) correspond to a minor population of the system and show how equilibrium molecular dynamics and free-energy calculations may conveniently be used to ascertain that such reactive conformations are indeed accessible to the system. Once again, the MD and QM/MM combination shows that a single water molecule acts as a biocatalyst in the cycle of HRP.

The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations

The enzymatic cycle of hydroperoxidases involves the resting Fe(III) state of the enzyme and the high-valent iron intermediates Compound I and Compound II. These states might be characterized by X-ray crystallography and the transition pathways between each state can be investigated using atomistic simulations. Here we review our recent work in the modeling of two key steps of the enzymatic reaction of hydroperoxidases: the formation of Cpd I in peroxidase and the reduction of Cpd I in catalase. It will be shown that small conformational motions of distal side residues (His in peroxidases and His/Asn in catalases), not,or only partially, revealed by the available X-ray structures, play an important role in the catalytic processes examined.

Thirty years of microbial P450 monooxygenase research: Peroxo-heme intermediates—The central bus station in heme oxygenase catalysis

Oxygen has always been recognized as an essential element of many life forms, initially through its role as a terminal electron acceptor for the energy-generating pathways of oxidative phosphorylation. In 1955, Hayaishi et al. [Mechanism of the pyrocatechase reaction, J. Am. Chem. Soc. 77 (1955) 5450-5451] presented the most important discovery that changed this simplistic view of how Nature uses atmospheric dioxygen. His discovery, the naming and mechanistic understanding of the first "oxygenase" enzyme, has provided a wonderful opportunity and scientific impetus for four decades of researchers. This volume provides an opportunity to recognize the breakthroughs of the "Hayaishi School." Notable have been the prolific contributions of Professor Ishimura et al. [Oxygen and life. Oxygenases, Oxidases and Lipid Mediators, International Congress Series, Elsevier, Amsterdam, 2002], a first-generation Hayaishi product, to characterization of the cytochrome P450 monooxygenases.

The mechanism of Compound I formation revisited

The most recently proposed mechanisms for the formation of the Compound I intermediates of the peroxidases and catalases have been based on the crystallographic elucidation of the enzyme structures. It has been assumed that these mechanisms are compatible with an earlier proposal of the formation of a reversible enzyme-substrate intermediate called Compound 0, which was based on data that pre-dated the availability of the enzyme structures. However, it is argued here that this is not the case and some modifications of the existing mechanism are proposed which reconcile the structural, kinetic and energetic data for the reactions. This paper focuses attention on horseradish peroxidase isoenzyme C and particularly on the acid-base properties of the imidazole side chain of distal histidine 42. This imidazole group has an exceptionally low pK(a) value in the resting enzyme, which is higher in Compound I and higher still in Compound II. The pK(a) value must also be greatly increased following Compound 0 formation so that the imidazole can become an effective proton acceptor. An explanation is offered in a dielectric insertion (DI) model, in which the peroxide substrate, or fragments thereof, screens the influence of the positively charged heme iron on the pK(a) value of the imidazole group. It is proposed that Compound 0 is converted to a second intermediate, Compound 0*, by intramolecular proton transfer along a pre-existing hydrogen bond, a process which reduces the energy requirements of charge separation in the deprotonation of hydrogen peroxide.

Characterization of the Oxidase Activity in Mammalian Catalase

Catalase is a highly conserved heme-containing antioxidant enzyme known for its ability to degrade hydrogen peroxide into water and oxygen. In low concentrations of hydrogen peroxide, the enzyme also exhibits peroxidase activity. We report that mammalian catalase also possesses oxidase activity. This activity, which is detected in purified catalases, cell lysates, and intact cells, requires oxygen and utilizes electron donor substrates in the absence of hydrogen peroxide or any added cofactors. Using purified bovine catalase and 10-acetyl-3,7-dihydroxyphenoxazine as the substrate, the oxidase activity was found to be temperature-dependent and displays a pH optimum of 7-9. The Km for the substrate is 2.4 x 10(-4) m, and Vmax is 4.7 x 10(-5) m/s. Endogenous substrates, including the tryptophan precursor indole, the neurotransmitter precursor beta-phenylethylamine, and a variety of peroxidase and laccase substrates, as well as carcinogenic benzidines, were found to be oxidized by catalase or to inhibit this activity. Several dietary plant micronutrients that inhibit carcinogenesis, including indole-3-carbinol, indole-3-carboxaldehyde, ferulic acid, vanillic acid, and epigallocatechin-3-gallate, were effective inhibitors of the activity of catalase oxidase. Difference spectroscopy revealed that catalase oxidase/substrate interactions involve the heme-iron; the resulting spectra show time-dependent decreases in the ferric heme of the enzyme with corresponding increases in the formation of an oxyferryl intermediate, potentially reflecting a compound II-like intermediate. These data suggest a mechanism of oxidase activity involving the formation of an oxygen-bound, substrate-facilitated reductive intermediate. Our results describe a novel function for catalase potentially important in metabolism of endogenous substrates and in the action of carcinogens and chemopreventative agents.

Spectrophotometric investigations with hexa-coordinate ferric lignin peroxidase: does water retention at the active site influence catalysis?

Native lignin peroxidase (LIP) can adopt either a stable penta- or hexa-coordinate state. We have examined catalysis with hexa-coordinate ferric LIP as the starting material, using rapid scanning spectrophotometry. Initial two-electron oxidation of hexa-coordinate native LIP by H(2)O(2) (Compound I formation) was accompanied by a shifting isosbestic point (419-->416 nm), consistent with displacement of a resident water molecule, prior to the reaction of the ferric iron with H(2)O(2). The Compound I species derived from a hexa-coordinate ferric state shows an unusual peak at 520 nm, which may be due to water retention in the vicinity of the heme active site. Compound I reduction by veratryl alcohol showed saturation kinetics, which contrasts with the situation observed when Compound I is derived from a penta-coordinate ferric state. The data inferred that water can interfere with heme access by electron donors, altering the mechanism of Compound I reduction.

Roles of water in heme peroxidase and catalase mechanisms

A water molecule is coproduced with the Compound I intermediate in the reactions of native heme peroxidases and catalases with hydrogen peroxide. As a result of water release/rebinding from/to the coproduct formation site the Compound I intermediate may exist in two forms: a "wet" form, Compound I(H(2)O), in which a water molecule is present at or near the site of coproduct water formation, and Compound I, in which the coproduct water formation site is "dry." It is postulated that the absence or presence of a water molecule at this site provides the structural basis for a redox pathway switching mechanism, such that the transition states for 2-electron equivalent reduction of Compound I intermediates are accessible in the dry form, but that in the wet form only 1-electron equivalent processes are possible, unless release of water can be stimulated. This concept provides the basis of a general mechanism in which the classical functional distinction between catalases and peroxidases, as well as the more complex behavior observed in halide oxidation and halogenation reactions, appear as particular cases in which variations in the degree of retention of water at the coproduct formation site influence Compound I reactivity.

The structures of the horseradish peroxidase C-ferulic acid complex and the ternary complex with cyanide suggest how peroxidases oxidize small phenolic substrates

We have solved the x-ray structures of the binary horseradish peroxidase C-ferulic acid complex and the ternary horseradish peroxidase C-cyanide-ferulic acid complex to 2.0 and 1.45 A, respectively. Ferulic acid is a naturally occurring phenolic compound found in the plant cell wall and is an in vivo substrate for plant peroxidases. The x-ray structures demonstrate the flexibility and dynamic character of the aromatic donor binding site in horseradish peroxidase and emphasize the role of the distal arginine (Arg(38)) in both substrate oxidation and ligand binding. Arg(38) hydrogen bonds to bound cyanide, thereby contributing to the stabilization of the horseradish peroxidase-cyanide complex and suggesting that the distal arginine will be able to contribute with a similar interaction during stabilization of a bound peroxy transition state and subsequent O-O bond cleavage. The catalytic arginine is additionally engaged in an extensive hydrogen bonding network, which also includes the catalytic distal histidine, a water molecule and Pro(139), a proline residue conserved within the plant peroxidase superfamily. Based on the observed hydrogen bonding network and previous spectroscopic and kinetic work, a general mechanism of peroxidase substrate oxidation is proposed.

Structural analysis of compound I in hemoproteins: study on Proteus mirabilis catalase

Ferryl catalysis has attracted considerable interest, because a diverse variety of enzymes use ferryl intermediates to perform difficult chemistry. The structure of the reactional intermediate compound I of Proteus mirabilis catalase (PMC) has been solved using time-resolved X-ray diffraction techniques and single crystal microspectrophotometry. Formation of compound I is characterized by significant changes in the absorbance spectrum, and the creation of an oxoferryl group on the distal side of the heme. This group is clearly visible in the X-ray electron density maps. An unidentified electron density, likely to be an anion because of the nature of its environment, appears during the reaction, in a site distant from the heme. The structure of compound I in PMC is compared with that of compound I in cytochrome c peroxidase (CCP).

Reversible inhibition and irreversible inactivation of catalase in presence of hydrogen peroxide

Spectroscopic and kinetic investigations have been carried out on catalase from bovine liver and from Aspergillus niger to address the mechanism of activity loss at high hydrogen peroxide concentrations (0.01 to 2 M). The mammalian enzyme was both reversibly inhibited and irreversibly inactivated in the presence of hydrogen peroxide, whereas the fungal enzyme did not show any reversible inhibition. A comparison of reaction rates with catalase preparations containing different proportions of Compound III indicated that the formation of Compound III is responsible for the reversible inhibition of bovine liver catalase at high H2O2 concentrations. Superoxide radical did not appear to be the inactivating species in this mechanism. Kinetic modelling emphasises the role of Compound III in both types of activity loss. It shows that the higher activity of A. niger catalase at high substrate concentration, compared to bovine liver catalase, the lack of reversible inhibition of the former and its lower rate of irreversible inactivation may be attributed both to a high rate of conversion of Compound III into native form and to a low rate of conversion of Compound I to Compound II.

2.2 A structure of oxy-peroxidase as a model for the transient enzyme: peroxide complex

The Fe+3-OOH complex of peroxidases has a very short half life, and its structure cannot be determined by conventional methods. The Fe+2-O2 complex provides a useful structural model for this intermediate, as it differs by only one electron and one proton from the transient Fe+3-OOH complex. We therefore determined the crystal structure of the Fe+2-O2 complex formed by a yeast cytochrome c peroxidase mutant with Trp 191 replaced by Phe. The refined structure shows that dioxygen can form a hydrogen bond with the conserved distal His residue, but not with the conserved distal Arg residue. When the transient Fe+3-OOH complex is modelled in a similar orientation, the active site of peroxidase appears to be optimized for catalysing proton transfer between the vicinal oxygen atoms of the peroxy-anion.

Histidine 52 is a critical residue for rapid formation of cytochrome c peroxidase compound I

The crystal structure and reactivity with hydrogen peroxide are reported for a mutant of a cloned cytochrome c peroxidase [CcP(MI)], in which the conserved distal His (His-52) is replaced with Leu. The reaction of the H52L enzyme with peroxide was examined as a function of pH in 0.1 M phosphate buffers and buffers in which nitrate was used to adjust the ionic strength. The pH-independent bimolecular rate constant for the reaction of H52L with peroxide was 731 +/- 44 and 236 +/- 14 M-1 s-1 in phosphate and nitrate-containing buffers, respectively. This represents a 10(5)-fold decrease in rate relative to the CcP(MI) parent under comparable conditions. Single-crystal diffraction studies showed that no dramatic changes in the structure or in the accessibility of the heme binding site were caused by the mutation. Rather, the mutation caused significant structural changes only at residue 52 and the nearby active-site water molecules. The residual reactivity of the H52L enzyme with peroxide was pH- and buffer-dependent. In nitrate-containing buffer, the apparent bimolecular rate constant for the reaction with peroxide decreased with decreasing pH; the loss of reactivity correlated with protonation of a group with an apparent pKA = 4.5. Protonation of the group caused a loss of reactivity with peroxide. This is in contrast to the CcP(MI) parent enzyme, as well as all other mutants that have been examined, where the loss of reactivity correlates with protonation of an enzyme group with an apparent pKA = 5.4.(ABSTRACT TRUNCATED AT 250 WORDS)

A step towards understanding the folding mechanism of horseradish peroxidase. Tryptophan fluorescence and circular dichroism equilibrium studies

The guanidinium chloride denaturation/renaturation of the holo- and apo-horseradish peroxidase isoenzyme c (HRP) has been studied by fluorescence and circular dichroism spectroscopies. A distinct equilibrium intermediate of the apoprotein could be detected at low concentrations of guanidinium chloride (0.5 M). This intermediate has a secondary structure content like that of the native protein but a poorly defined tertiary structure. Renaturation of the apo-HRP is reversible and 100% activity could be obtained after addition of a twofold excess of free haem. The denaturation of the holo-HRP is more complex and occurs in two distinct steps; unfolding of the protein backbone and loss of the haem. The denatured protein folds back to its native conformation but the incorporation of the haem occurs only after the secondary structure is formed. Ca2+ appears to be important for the stability of the protein as the apo-HRP is more resistant to denaturation in the presence of Ca2+. The free-energy change during unfolding of the apo-HRP was determined in the absence and presence of Ca2+ and found to be 9.2 kJ/mol and 16.7 kJ/mol, respectively. The importance of Ca2+ to the protein stability was also supported by studies on the loss of the haem from the protoporphyrin-IX-apo-HRP complex.

A spectrophotometric method for determination of catalase activity in small tissue samples

A simple and rapid method for determination of catalase activity in small tissue samples is described. Using a new approach, we have exploited the peroxidatic function of catalase for the determination of enzyme activity. The method was based on the reaction of the enzyme with methanol in the presence of an optimal concentration of hydrogen peroxide. The formaldehyde produced was measured spectrophotometrically with 4-amino-3-hydrazino-5-mercapto-1,2,4-triazole (Purpald) as a chromogen. With this method, a detection limit of 12.5 ng of purified catalase from bovine liver was possible, and it was successfully applied to microgram amounts of mouse liver and pancreatic islet homogenates. The catalase activity in liver was about 50 times higher than that in pancreatic islets.

Hemes and hemoproteins. 5: Kinetics of the peroxidatic activity of microperoxidase-8: model for the peroxidase enzymes

The peroxidatic activity of the heme octapeptide from cytochrome c, microperoxidase-8 (MP-8), was assayed at 25 degrees C under conditions where formation of Compound I is rate limiting. In the pH range 6-9, the reaction rate increased linearly with a slope close to unity. The active form of the substrate is the hydroperoxide anion, HO2-, and an extrapolated second-order rate constant was obtained for the reaction of aquoMP-8 with HO2- of 3.7 X 10(8) M-1 sec-1, which is close to the second-order rate constants reported for reaction of the peroxidase enzymes with H2O2. Comparison with published data shows that the Fe3+ ion of MP-8 reacts as expected with simple anions, electrons, and HO2-, while the analogous reactions of the enzymes all show a requirement for one H+. We conclude that the peroxidase enzymes activate H2O2 under physiological conditions through a pH-independent, H+-coupled binding of the required H2O2-. The peroxidase activity of MP-8 can be increased more than tenfold by the presence of the guanidinium ion, which is ascribed to formation of the ion-pair GuaH+HO2-; this suggests a role for the invariant distal Arg in the enzymes.

The formation of ES of cytochrome-c peroxidase: a comparison with lactoperoxidase and horseradish peroxidase

The activation energy for the formation of the first red compound, ES, for cytochrome-c peroxidase (ferrocytochrome-c: hydrogen-peroxide oxidoreductase, EC 1.11.1.5) by i-propyl hydroperoxide and the rate constants for the formation of ES with various hydroperoxides have been determined. Multivariate data analysis by the partial least-squares model in latent variables has been used to compare the rate constants with the corresponding rate constants for the formation of compound I from lactoperoxidase and two isoenzymes of horseradish peroxidase. The results show that the rate of formation of ES from cytochrome-c peroxidase is highly correlated with the pKa of the hydroperoxides. The activation energy for the formation of ES with i-propyl hydroperoxide is close to the corresponding value for hydrogen peroxide.

Peroxidase-catalyzed N-demethylation reactions: deuterium solvent isotope effects

The effect of D2O on the kinetic parameters for the hydroperoxide-supported N-demethylation of N,N-dimethylaniline catalyzed by chloroperoxidase and horseradish peroxidase was investigated in order to assess the roles of exchangeable hydrogens in the demethylation reaction. The initial rate of the chloroperoxidase-catalyzed N-demethylation of N,N-dimethylaniline supported by ethyl hydroperoxide exhibited a pL optimum (where L denotes H or D) of 4.5 in both H2O and D2O. The solvent isotope effect on the initial rate of the chloroperoxidase-catalyzed demethylation reaction was independent of pL, suggesting that the solvent isotope effect is not due to a change in the pK of a rate-controlling ionization in D2O. The solvent isotope effect on the Vmax for the chloroperoxidase-catalyzed demethylation reaction was 3.66 +/- 0.62. In contrast, the solvent isotope effect on the Vmax for the horseradish peroxidase catalyzed demethylation reaction was approximately 1.5 with either ethyl hydroperoxide or hydrogen peroxide as the oxidant, indicating that the exchange of hydrogens in the enzyme and hydroperoxide for deuterium in D2O has little effect on the rate of the demethylation reaction. The solvent isotope effect on the Vmax/KM for ethyl hydroperoxide in the chloroperoxidase-catalyzed demethylation reaction was 8.82 +/- 1.57, indicating that the rate of chloroperoxidase compound I formation is substantially decreased in D2O. This isotope effect is suggested to arise from deuterium exchange of the hydroperoxide hydrogen and of active-site residues involved in compound I formation. A solvent isotope effect of 2.96 +/- 0.57 was observed on the Vmax/KM for N,N-dimethylaniline in the chloroperoxidase-catalyzed reaction.(ABSTRACT TRUNCATED AT 250 WORDS)

The active center of catalase

The refined structure of beef liver catalase (I. Fita, A. M. Silva, M. R. N. Murthy & M. G. Rossmann, unpublished results) is here examined with regard to possible catalytic mechanisms. The distal side of the deeply buried heme pocket is connected with the surface of the molecule by one (or possibly two) channel. The electron density representing the heme group, in each of the two crystallographically independent subunits, is consistent with degradation of the porphyrin rings. The heme group appears to be buckled, reflecting the high content of bile pigment in liver catalase. The spatial organization on the proximal side (where the fifth ligand of the iron is located) shows an elaborate network of interactions. The distal side contains the substrate pocket. The limited space in this region severely constrains possible substrate positions and orientations. The N delta atom of the essential His74 residue hydrogen bonds with O gamma of Ser113, which in turn hydrogen bonds to a water molecule associated with the propionic carbonylic group of pyrrole III. These interactions are also visible in the refined structure of Penicillium vitale catalase (B. K. Vainshtein, W. R. Melik-Adamyan, V. V. Barynin, A. A. Vagin, A. I. Grebenko, V. V. Borisov, K. S. Bartels, I. Fita, & M. G. Rossmann, unpublished results). Model building suggests a pathway for a catalase mechanism (compound I formation, as well as catalatic and peroxidatic reactions). There are some similarities in compound I formation of catalase and cytochrome c peroxidase.

Kinetics of yeast cytochrome c peroxidase compound I formation with modified substrates (peroxybenzoic acids)

The kinetics of formation of Compound I of yeast cytochrome c peroxidase (ferrocytochrome c:hydrogen-peroxide oxidoreductase, EC 1.11.1.5) with a series of peroxybenzoic acids were studied. Reactivity is affected not only by protein ionization, as in the reaction with H2O2, but also by substrate ionization. The reactivity of negatively charged substrates is markedly lower than that of uncharged species, implying that electrostatic factors profoundly influence substrate binding. The rate constants for neutral peroxybenzoic acids carrying electron-withdrawing substituents increase with increasing peroxy acid pKa. This behaviour suggests that, as previously discussed for reactions of turnip peroxidases, formation of peroxy anion by ionization of substrate within the active site is kinetically important. The results support the mechanism of cytochrome c peroxidase Compound I formation which has been proposed by Poulos and Kraut (J. Biol. Chem. 225 (1980), 8199-8205) on the basis of enzyme structural studies.

Evidence for heme pi cation radical species in compound I of horseradish peroxidase and catalase

Magnetic circular dichroism spectra are reported for the compound I species of beef liver catalase (hydrogen-peroxide: hydrogen-peroxide oxidoreductase, EC 1.11.1.6) and horseradish peroxidase (donor: hydrogen-peroxide oxidoreductase, EC 1.11.1.7) and the pi cation radical derivatives of porphyrins that have been suggested as models of the electronic configuration of the heme in the compound I species of these enzymes. Comparison of the magnetic circular dichroism spectra of the compound I species with the spectra of [Co(octaethylporphyrin)]2Br and [Co(octaethylporphyrin)]2ClO4 indicates that in both the intermediate enzyme species the heme has been oxidized to a pi cation radical. While there is a clear distinction between the magnetic circular dichroism spectra of the 2A2u porphyrin [Co(III)octaethylporphyrin]2ClO4, and the 2A1u porphyrin, [Co(III)octaethylporphyrin]2Br, such specific differences are not observed in the spectra of the two enzymes. Analysis of our data suggests that the ground states in the two enzymes are far more similar than the ground states in the two model porphyrins.

Kinetic studies of the reaction of ferric soybean leghemoglobins with hydrogen peroxide, cyanide and nicotinic acid

A kinetic study of the reaction of two soybean leghemoglobins (components a and c) with hydrogen peroxide to form the oxidized compound (leghemoglobin IV) has been carried out over the pH range 2.5--10. Three different ionization processes of leghemoglobins with pKa values of 3,4.7 +/- 0.2 and 8.2 +/- 0.1 are required to explain the rate/pH profiles. Protonation of the former group and ionization of the latter cause a decrease in the rate of reaction of the hemoproteins with H2O2. The results are compared to those obtained for the reactions of plant peroxidases and myoglobin with H2O2. The results obtained from the kinetic study of cyanide binding to soybean leghemoglobins indicate that CN- is the reactive species. Two ionization processes of leghemoglobins with pKa values of 4.7 +/- 0.2 and 8.2 +/- 0.1 affect the reaction rates. The association and dissociation rate constants corresponding to nicotinic acid binding to leghemoglobins a and c have been measured over the pH range 2.5--7. The dissociation rate constant is affected by ionization of a group with pKa less than 2.5 for both leghemoglobin-nicotinate complexes. In this pH range the association rate constant is only affected by ionization of a group with pKa value of 4.7 +/- 0.2. The analysis of these results shows that both ionization processes corresponding to ring nitrogen atom of the ligand (pKa approximately equal to 4.9) and to a heme-linked group (pKa approximately equal to 4.7 +/- 0.2) influence the association rate constant. Furthermore, it appears that in the binding site of leghemoglobins the pKa value corresponding to ionization of the ring nitrogen atom of nicotinic acid is shifted from the normal value of 4.9 to a value of less than 2.5. This pecularity might explain the exceptional reactivity of leghemoglobins for nicotinic acid, over a large pH range. For both cyanide and nicotinic acid binding reactions, the ionizable group of leghemoglobins with pKa value of 4.7 +/- 0.2 seems to act as an electrostatic gate. When the group is deprotonated, it restricts the access of anion ligands to the heme pocket. For all the three reactions studied, leghemoglobin a reacts about twice as fast as leghemoglobin c.

The action of chloride peroxidase on 4-chloroaniline. N-oxidation and ring halogenation

Chloride peroxidase catalyses both the ring halogenation and N-oxidation reactions of 4-chloroaniline by H2O2 and either KCl or KBr. In the absence of any halide salt only the N-oxidation reaction was observed, with the resulting conversion of 4-chloroaniline into 4-chloronitrosobenzene. The N-oxidation reaction proceeded even more rapidly in the presence of Cl- or Br-, in spite of the fact that ring halogenation was also a rapid reaction. The enhancement of N-oxidation was highly dependent on the pH of the media and displayed an optimum in the region of pH 3.5-4.0. No rate enhancement was observed above pH 5.5. KF partially inhibited the rate of N-oxidation in a pH-dependent manner. On the basis of calculated catalytic-centre activity the N-oxidation reaction was the major reaction at pH 3.5 or higher, whereas the ring-halogenation reaction became the major reaction below pH 3.5. In the presence of high concentrations of 4-chloroaniline relative to H2O2 the reaction intermediate, 4-chlorophenylhydroxylamine, was detected for the first time in a chloride peroxidase-catalysed reaction with this arylamine substrate. These findings were interpreted on the basis of current knowledge concerning the mechanism of action of chloride peroxidase.

Magnetic circular dichroism studies on the electronic configuration of catalase compounds I and II

Absorption and magnetic circular dichroism spectra of native catalase, compound I and compound II have been measured and the data compared with that observed previously for horseradish peroxidase. The native catalase data at pH 6.9 are characteristic of a high-spin ferric porphyrin and are similar to the data reported for the ferric myoglobin and ferric horseradish peroxidase at pH 7. Oxidation of native catalase by peroxoacetic acid forms the compound I species that is identified by its low absorbance in the 400 nm Soret region and a series of overlapping bands between 450 nm and 680 nm. The magnetic circular dichroism spectra of compound I of catalase closely resembles that previously obtained for horseradish peroxidase compound I. These results indicate that the ground state of the heme pi-system is the same in both catalase and horseradish peroxidase compound I species. The compound II data show that the ratio of the magnetic circular dichroism intensity for the Soret to alpha A terms is 0.5 which means that there is a redistribution of angular momentum between the pi* excited states that give rise to the Soret and alpha-bands compared with the horseradish peroxidase compound II data where the ratio of the analogous A term intensities has a value of about 3. In addition, the magnetic CD spectra of both the catalase and horseradish peroxidase compound II species are reminiscent of typical metalloporphyrin spectra which lack charge-transfer transitions and where the metal d-orbitals are decoupled from the porphyrin pi-system.

Magnetic circular dichroism studies of bovine liver catalase

Absorption, circular dichroism (CD) and magnetic circular dichroism (MCD) spectra of beef liver catalase at pH 5.0 and 6.9, and its complexes with NaF, KCNO, NaCNS, NaN3 and NaCN, have been measured between 250 nm and 700 nm at room temperature. The pH 6.9 native catalase MCD shows the presence of several additional transitions not resolved in the absorption spectrum. While these bands can be seen in the spectra of all the derivatives, with the exception of the cyanide, their relative intensities changes considerably between complexes. Of special interest in the MCD of ferric hemes is the signal intensity at about 400 nm and 620 nm. The data indicate that the MCD intensity at 620 nm increases as the high spin iron porphyrin fraction increases, reaching a maximum with the fluoride complex. The 430 nm band intensity increases as the proportion of low spin iron increases, reaching a maximum with the cyanide complex. The MCD spectra also indicate clearly the existence of spin mixtures in the complexes with CNO-, CNS-, and N3-, where both the 430 nm and 620 nm bands have appreciable intensity. It is significant that despite almost identical absorption spectra the CNS- complex has higher fraction of low spin iron than either the CNO- or the N3- species. The differences between the pH 5 and 6.9 MCD spectra of the native catalase suggest that the environment of the heme centre is sensitive to protonation.