EPR Evidence for a Tyrosyl Radical Intermediate in Bovine Liver Catalase

A remarkable peroxidase-like behavior of the catalase KatA from the pathogenic bacteria Helicobacter pylori: The oxidation reaction with formate as substrate and the stabilization of an [Fe(IV) = O Trp•] intermediate assessed by multifrequency EPR spectroscopy

We have characterized the catalytic cycle of the Helicobacter pylori KatA catalase (HPC). H. pylori is a human and animal pathogen responsible for gastrointestinal infections. Multifrequency (9-285 GHz) EPR spectroscopy was applied to identify the high-valent intermediates (5 ≤ pH ≤ 8.5). The broad (2000 G) 9-GHz EPR spectrum consistent with the [Fe(IV) = O Por•+] intermediate was detected, and showed a clear pH dependence on the exchange-coupling of the radical (delocalized over the porphyrin moiety) due to the magnetic interaction with the ferryl iron. In addition, Trp• (for pH ≤ 6) and Tyr• (for 5 ≤ pH ≤ 8.5) species were distinguished by the advantageous resolution of their g-values in the 285-GHz EPR spectrum. The unequivocal identification of the high-valent intermediates in HPC by their distinct EPR spectra allowed us to address their reactivity towards substrates. The stabilization of an [Fe(IV) = O Trp•] species in HPC, unprecedented in monofunctional catalases and possibly involved in the oxidation of formate to the formyloxyl radical at pH ≤ 6, is reminiscent of intermediates previously identified in the catalytic cycle of bifunctional catalase-peroxidases. The 2e- oxidation of formate by the [Fe(IV) = O Por•+] species, both at basic and acidic pH conditions, involving a 1H+/2e- oxidation in a cytochrome P450 peroxygenase-like reaction is proposed. Our findings demonstrate that moonlighting by the H. pylori catalase includes formate oxidation, an enzymatic reaction possibly related to the unique strategy of the neutrophile bacterium for gastric colonization, that is the release of CO2 to regulate the pH in the acidic environment.

Polarised neutron scattering from dynamic polarised nuclei 1972-2022

With the inauguration of the small-angle instrument D11 of the Institute Laue-Langevin (ILL) in September 1972 neutron scattering revolutionized methods of contrast variation. Very soon D11 was oversubscribed by proposals relying on isotopic substitution of hydrogen isotopes. At the same time in Oxford first experiments of polarised neutron diffraction from dynamic polarised protons in lanthanum magnesium nitrate crystals demonstrated the great utility of this approach. In the early eighties a new type of polarised target material led to a boom of contrast variation by nuclear polarisation. The new samples of frozen solutions of macromolecules lent themselves to small-angle scattering. Often in collaboration with research centres of High Energy Physics various groups in Europe and Japan started experiments of polarized neutron scattering from dynamic polarised protons. Techniques of NMR and EPR considerably enlarged the spectrum of nuclear contrast variation. This is shown with time-resolved polarised neutron scattering from dynamic polarized proton spins of a free radical and of tyrosyl doped catalase using D22 at the ILL.

Monofunctional Heme-Catalases

The review focuses on four issues that are critical for the understanding of monofunctional catalases. How hydrogen peroxide (H2O2) reaches the active site and outcompetes water molecules to be able to function at a very high rate is one of the issues examined. Part of the answer is a gate valve system that is instrumental to drive out solvent molecules from the final section of the main channel. A second issue relates to how the enzyme deals with an unproductive reactive compound I (Cpd I) intermediate. Peroxidatic two and one electron donors and the transfer of electrons to the active site from NADPH and other compounds are reviewed. The new ascribed catalase reactions are revised, indicating possible measurement pitfalls. A third issue concerns the heme b to heme d oxidation, why this reaction occurs only in some large-size subunit catalases (LSCs), and the possible role of singlet oxygen in this and other modifications. The formation of a covalent bond between the proximal tyrosine with the vicinal residue is analyzed. The last issue refers to the origin and function of the additional C-terminal domain (TD) of LSCs. The TD has a molecular chaperone activity that is traced to a gene fusion between a Hsp31-type chaperone and a small-size subunit catalase (SSC).

Control of Tyrosyl Radical Stabilization by {SiO2@Oligopeptide} Hybrid Biomimetic Materials

Tyrosine radicals are notoriously short-lived/unstable in solution, while they present an impressive degree of stability and versatility in bioenzymes. Herein, we have developed a library of hybrid biomimetic materials (HBMs), which consists of tyrosine-containing oligopeptides covalently grafted on SiO₂ nanoparticles, and studied the formation, lifetime, and redox properties of tyrosyl radicals. Using electron paramagnetic resonance spectroscopy, we have studied the radical-spin distribution as a probe of the local microenvironment of the tyrosyl radicals in the HBMs. We find that the lifetime of the tyrosyl radical can be enhanced by up to 6 times, by adjusting three factors, namely, a proximal histidine, the length of the oligopeptide, and the interface with the SiO₂ nanomatrix. This is shown to be correlated to a significant lowering of E_1/2 from +736 mV, in free tyrosine, to +548 mV in the {12-peptide}@SiO₂ material. Moreover, we show that grafting on SiO₂ lowers the E_1/2 of tyrosine radicals by ∼50 mV in all oligopeptides. Analysis of the spin-distribution by EPR reveals that the positioning of a histidine at a H-bonding distance from the tyrosine further favors tyrosine radical stabilization.

Effect of sequestering intrinsic iron on the electron paramagnetic resonance signals in powdered soy proteins

This investigation examined iron in powdered soy protein products using electron paramagnetic resonance (EPR) spectroscopy, and the effect that selectively binding free iron in isolated soy protein (ISP) had on the occurrence of metastable radicals in powdered soy proteins. EPR analyses of soybean defatted flour, commercial ISP and laboratory ISP samples revealed a peak at g = 4.3 characteristic of high-spin ferric iron in a rhombic-coordinated environment. Commercial ISP samples examined contained higher levels of the rhombic ferric iron than laboratory-prepared ISP samples. During the first 6 wk of storage the primary singlet EPR signal at g = 2.0049 in the commercial ISP samples approximately doubled, and the laboratory prepared samples increased by about 9-fold. The EPR signal was initially about 4-times higher in the freshly prepared commercial samples compared to the corresponding laboratory ISP. Laboratory ISP samples prepared with added deferoxamine to sequester endogenous iron exhibited a large increase in the high-spin ferric iron EPR signal at g = 4.3. ISP treated with deferoxamine also exhibited a multiple-line EPR signal at about g = 2.007, instead of the typical singlet signal at g = 2.0049. The power at which the signal amplitude was half-saturated also changed from about 1 mW in the control ISP to about 20 mW in the deferoxamine treated ISP. The multiple-line EPR spectrum from the ISP treated with deferoxamine increased during storage over a 6-wk period by about 6-fold. The observed changes in EPR line-shape, g-value, and power saturation with the deferoxamine treatment indicate that the primary free-radical signal in powdered ISP samples may be from stabilized tyrosine radicals with spin densities distributed over the aromatic ring.

The reaction mechanisms of heme catalases: an atomistic view by ab initio molecular dynamics

Catalases are ubiquitous enzymes that prevent cell oxidative damage by degrading hydrogen peroxide to water and oxygen (2H(2)O(2) → 2H(2)O+O(2)) with high efficiency. The enzyme is first oxidized to a high-valent iron intermediate, known as Compound I (Cpd I, Por(·+)-Fe(IV)=O) which, at difference from other hydroperoxidases, is reduced back to the resting state by further reacting with H(2)O(2). The normal catalase activity is reduced if Cpd I is consumed in a competing side reaction, forming a species named Cpd I*. In recent years, Density Functional Theory (DFT) methods have unraveled the electronic configuration of these high-valent iron species, helping to assign the intermediates trapped in the crystal structures of oxidized catalases. It has been demonstrated that the a priori assumption that the H(+)/H(-) type of mechanism for Cpd I reduction leads to the generation of singlet oxygen is not justified. Moreover, it has been shown by ab initio metadynamics simulations that two pathways are operative for Cpd I reduction: a His-mediated mechanism (described as H·/H(+) + e(-)) in which the distal His acts as an acid-base catalyst and a direct mechanism (described as H·/H·) in which the distal His does not play a direct role. Independently of the mechanism, the reaction proceeds by two one-electron transfers rather than one two-electron transfer, as previously assumed. Electron transfer to Cpd I, regardless of whether the electron is exogenous or endogenous, facilitates protonation of the oxoferryl group, to the point that formation of Cpd I* may be controlled by the easiness of protonation of reduced Cpd I.

Classical catalase: ancient and modern

This review describes the historical difficulties in devising a kinetically satisfactory mechanism for the classical catalase after its identification as a unique catalytic entity in 1902 and prior to the breakthrough 1947 analysis by Chance and co-workers which led to the identification of peroxide compounds I and II. The role of protons in the formation of these two ferryl complexes is discussed and current problems of inhibitory ligand and hydrogen donor binding at the active site are outlined, especially the multiple roles involving formate or formic acid. A previous mechanism of NADPH-dependent catalase protection against substrate inhibition is defended. A revised model linking the catalytic ('catalatic') action and the one-electron side reactions involving compound II is suggested. And it is concluded that, contrary to an idea proposed in 1963 that eukaryotic catalase might be a 'fossil enzyme', current thinking gives it a central role in the redox protective processes of long term importance for human and other eukaryotic and prokaryotic life.

Human catalase: looking for complete identity

Catalases are well studied enzymes that play critical roles in protecting cells against the toxic effects of hydrogen peroxide. The ubiquity of the enzyme and the availability of substrates made heme catalases the focus of many biochemical and molecular biology studies over 100 years. In human, this has been implicated in various physiological and pathological conditions. Advancement in proteomics revealed many of novel and previously unknown features of this mysterious enzyme, but some functional aspects are yet to be explained. Along with discussion on future research area, this mini-review compile the information available on the structure, function and mechanism of action of human catalase.

Characterization of the peroxidase mechanism upon reaction of prostacyclin synthase with peracetic acid. Identification of a tyrosyl radical intermediate

Prostacyclin synthase (PGIS) is a membrane-bound class III cytochrome P450 that catalyzes an isomerization of prostaglandin H(2), an endoperoxide, to prostacyclin. We report here the characterization of the PGIS intermediates in reactions with other peroxides, peracetic acid (PA), and iodosylbenzene. Rapid-scan stopped-flow experiments revealed an intermediate with an absorption spectrum similar to that of compound ES (Cpd ES), which is an oxo-ferryl (Fe(IV)O) plus a protein-derived radical. Cpd ES, formed upon reaction with PA, has an X-band (9 GHz) EPR signal of g = 2.0047 and a half-saturation power, P(1/2), of 0.73 mW. High-field (130 GHz) EPR reveals the presence of two species of tyrosyl radicals in Cpd ES with their g-tensor components (g(x), g(y), g(z)) of 2.00970, 2.00433, 2.00211 and 2.00700, 2.00433, 2.00211 at a 1:2 ratio, indicating that one is involved in hydrogen bonding and the other is not. The line width of the g = 2 signal becomes narrower, while its P(1/2) value becomes smaller as the reaction proceeds, indicating migration of the unpaired electron to an alternative site. The rate of electron migration ( approximately 0.2 s(-1)) is similar to that of heme bleaching, suggesting the migration is associated with the enzymatic inactivation. Moreover, a g = 6 signal that is presumably a high-spin ferric species emerges after the appearance of the amino acid radical and subsequently decays at a rate comparable to that of enzymatic inactivation. This loss of the g = 6 species thus likely indicates another pathway leading to enzymatic inactivation. The inactivation, however, was prevented by the exogenous reductant guaiacol. The studies of PGIS with PA described herein provide a mechanistic model of a peroxidase reaction catalyzed by the class III cytochromes P450.

An oxyferrous heme/protein-based radical intermediate is catalytically competent in the catalase reaction of Mycobacterium tuberculosis catalase-peroxidase (KatG)

A mechanism accounting for the robust catalase activity in catalase-peroxidases (KatG) presents a new challenge in heme protein enzymology. In Mycobacterium tuberculosis, KatG is the sole catalase and is also responsible for peroxidative activation of isoniazid, an anti-tuberculosis pro-drug. Here, optical stopped-flow spectrophotometry, rapid freeze-quench EPR spectroscopy both at the X-band and at the D-band, and mutagenesis are used to identify catalase reaction intermediates in M. tuberculosis KatG. In the presence of millimolar H2O2 at neutral pH, oxyferrous heme is formed within milliseconds from ferric (resting) KatG, whereas at pH 8.5, low spin ferric heme is formed. Using rapid freeze-quench EPR at X-band under both of these conditions, a narrow doublet radical signal with an 11 G principal hyperfine splitting was detected within the first milliseconds of turnover. The radical and the unique heme intermediates persist in wild-type KatG only during the time course of turnover of excess H2O2 (1000-fold or more). Mutation of Met255, Tyr229, or Trp107, which have covalently linked side chains in a unique distal side adduct (MYW) in wild-type KatG, abolishes this radical and the catalase activity. The D-band EPR spectrum of the radical exhibits a rhombic g tensor with dual gx values (2.00550 and 2.00606) and unique gy (2.00344) and gz values (2.00186) similar to but not typical of native tyrosyl radicals. Density functional theory calculations based on a model of an MYW adduct radical built from x-ray coordinates predict experimentally observed hyperfine interactions and a shift in g values away from the native tyrosyl radical. A catalytic role for an MYW adduct radical in the catalase mechanism of KatG is proposed.

On the functional role of a water molecule in clade 3 catalases: a proposal for the mechanism by which NADPH prevents the formation of compound II

X-ray structures of the 13 different monofunctional heme catalases published to date were scrutinized in order to gain insight in the mechanism by which NADPH in Clade 3 catalases may protect the reactive ferryloxo intermediate Compound I (Cpd I; por (*+)Fe (IV)O) against deactivation to the catalytically inactive intermediate Compound II (Cpd II; porFe (IV)O). Striking similarities in the molecular network of the protein subunits encompassing the heme center and the surface-bound NADPH were found for all of the Clade 3 catalases. Unique features in this region are the presence of a water molecule (W1) adjacent to the 4-vinyl group of heme and a serine residue or a second water molecule hydrogen-bonded to both W1 and the carbonyl group of a threonine-proline linkage, with the proline in van der Waals contact with the dihydronicotinamide group of NADPH. A mechanism is proposed in which a hydroxyl anion released from W1 undergoes reversible nucleophilic addition to the terminal carbon of the 4-vinyl group of Cpd I, thereby producing a neutral porphyrin pi-radical ferryloxo (HO-por (*)Fe (IV)O) species of reduced reactivity. This structure is suggested to be the elusive Cpd II' intermediate proposed in previous studies. An accompanying proton-shifting process along the hydrogen-bonded network is believed to facilitate the NADPH-mediated reduction of Cpd I to ferricatalase and to serve as a funnel for electron transfer from NADPH to the heme center to restore the catalase Fe (III) resting state. The proposed reaction paths were fully supported as chemically reasonable and energetically feasible by means of density functional theory calculations at the (U)B3LYP/6-31G* level. A particularly attractive feature of the present mechanism is that the previously discussed formation of protein-derived radicals is avoided.

Three different tyrosyl radicals identified in L-tyrosine HCl crystals upon gamma-irradiation: magnetic characterization and temporal evolution

High-frequency electron paramagnetic resonance (EPR) and X-band electron-nuclear double resonance (ENDOR) spectroscopies were used to investigate the effect of gamma-irradiation on single crystals of L-tyrosine hydrochloride at room temperature. The oxidation product is the tyrosyl radical formed by hydrogen abstraction from the phenolic group; interestingly, on freshly irradiated crystals, two tyrosyl radicals were identified, characterized by slightly different magnetic parameters. In particular, one of the two radicals, with a gxx value of 2.00621, has its phenoxyl oxygen strongly hydrogen-bonded to one or more donors; to our knowledge, this is the lower gxx value reported for tyrosyl radicals. These two oxidation radicals are found to evolve very slowly to a third, single more stable radical conformation. To interpret the experimental data, a possible molecular scenario is presented, where the process of radical formation can be seen as a hydrogen atom transfer or a proton-coupled electron transfer. These processes seem to be controlled by the specific network of hydrogen-bond interactions present in the crystal. The results are discussed in relation to their relevance for the interpretation of EPR spectra of tyrosyl radicals in biological systems.

The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations

The structures of Helicobacter pylori (HPC) and Penicillium vitale (PVC) catalases, each with two subunits in the crystal asymmetric unit, oxidized with peroxoacetic acid are reported at 1.8 and 1.7 A resolution, respectively. Despite the similar oxidation conditions employed, the iron-oxygen coordination length is 1.72 A for PVC, close to what is expected for a Fe=O double bond, and 1.80 and 1.85 A for HPC, suggestive of a Fe-O single bond. The structure and electronic configuration of the oxoferryl heme and immediate protein environment is investigated further by QM/MM density functional theory calculations. Four different active site electronic configurations are considered, Por*+-FeIV=O, Por*+-FeIV=O...HisH+, Por*+-FeIV-OH+ and Por-FeIV-OH (a protein radical is assumed in the latter configuration). The electronic structure of the primary oxidized species, Por*+-FeIV=O, differs qualitatively between HPC and PVC with an A2u-like porphyrin radical delocalized on the porphyrin in HPC and a mixed A1u-like "fluctuating" radical partially delocalized over the essential distal histidine, the porphyrin, and, to a lesser extent, the proximal tyrosine residue. This difference is rationalized in terms of HPC containing heme b and PVC containing heme d. It is concluded that compound I of PVC contains an oxoferryl Por*+-FeIV=O species with partial protonation of the distal histidine and compound I of HPC contains a hydroxoferryl Por-FeIV-OH with the second oxidation equivalent delocalized as a protein radical. The findings support the idea that there is a relation between radical migration to the protein and protonation of the oxoferryl bond in catalase.

Freeze-quenched iron-oxo intermediates in cytochromes P450

Since the discovery of cytochromes P450 and their assignment to heme proteins a reactive iron-oxo intermediate as the hydroxylating species has been discussed. It is believed that the electronic structure of this intermediate corresponds to an iron(IV)-porphyrin-pi-cation radical system (Compound I). To trap this intermediate the reaction of P450 with oxidants (shunt pathway) has been used. The common approaches are stopped-flow experiments with UV-visible spectroscopic detection or rapid-mixing/freeze-quench studies with EPR and Mössbauer spectroscopic characterization of the trapped intermediate. Surprisingly, the two approaches seem to give conflicting results. While the stopped-flow data indicate the formation of a porphyrin-pi-cation radical, no such species is seen by EPR spectroscopy, although the Mössbauer data indicate iron(IV) for P450cam (CYP101) and P450BMP (CYP102). Instead, radicals on tyrosine and tryptophan residues are observed. These findings are reviewed and discussed with respect to intramolecular electron transfer from aromatic amino acids to a presumably transiently formed porphyrin-pi-cation radical.

Moving a Phenol Hydroxyl Group from the Surface to the Interior of a Protein: Effects on the Phenol Potential and pKA

De novo protein design and electrochemistry were used to measure changes in the potential and pK(A) of a phenol when its OH group is moved from a solvent-exposed to a sequestered protein position. A "phenol rotation strategy" was adopted in which phenols, containing a SH in position 4, 3, or 2 relative to the OH group, were bound to a buried protein site. The alpha(3)C protein used here is a tryptophan to cysteine variant of the structurally defined alpha(3)W protein (Dai et al. (2002) J. Am. Chem. Soc. 124, 10952-10953). The protein characteristics of alpha(3)C and the three mercaptophenol-alpha(3)C (MP-alpha(3)C) proteins are shown to be close to those of alpha(3)W. Moreover, the phenol OH group is fully solvent exposed in 4MP-alpha(3)C and more sequestered in 3MP-alpha(3)C and 2MP-alpha(3)C. Here we compare the redox properties of the three mercaptophenols when bound to alpha(3)C and to cysteine free in water. The pK(A) and E(peak) values are essential identical when 4MP is ligated to alpha(3)C relative to when it is free in solution. In contrast, these values are increased in 3MP-alpha(3)C and 2MP-alpha(3)C relative to the solvated compounds. The E(peak) vs pH plots all display a approximately 59 mV/pH unit dependence. We conclude that interactions with the OH group dominate the phenol redox characteristics. In 3MP-alpha(3)C and 2MP-alpha(3)C, hydrogen bonds between the protein and the bound phenols appear to either stabilize the reduced phenol or destabilize the radical, relative to the aqueous buffer, raising the potential by 0.11 and 0.12 V, respectively.

Exploring amino-acid radical chemistry: protein engineering and de novo design

Amino-acid radical enzymes are often highly complex structures containing multiple protein subunits and cofactors. These properties have in many cases hampered the detailed characterization of their amino-acid redox cofactors. To address this problem, a range of approaches has recently been developed in which a common strategy is to reduce the complexity of the radical-containing system. This work will be reviewed and it includes the light-induced generation of aromatic radicals in small-molecule and peptide systems. Natural redox proteins, including the blue copper protein azurin and a bacterial photosynthetic reaction center, have been engineered to introduce amino-acid radical chemistry. The redesign strategies to achieve this remarkable change in the properties of these proteins will be described. An additional approach to gain insights into the properties of amino-acid radicals is to synthesize de novo designed model proteins in which the redox chemistry of these species can be studied. Here we describe the design, synthesis and characteristics of monomeric three-helix bundle and four-helix bundle proteins designed to study the redox chemistry of tryptophan and tyrosine. This work demonstrates that de novo protein design combined with structural, electrochemical and quantum chemical analyses can provide detailed information on how the protein matrix tunes the thermodynamic properties of tryptophan.

Reaction of haem containing proteins and enzymes with hydroperoxides: The radical view

The reaction between hydroperoxides and the haem group of proteins and enzymes is important for the function of many enzymes but has also been implicated in a number of pathological conditions where oxygen binding proteins interact with hydrogen peroxide or other peroxides. The haem group in the oxidized Fe3+ (ferric) state reacts with hydroperoxides with a formation of the Fe4+=O (oxoferryl) haem state and a free radical primarily located on the pi-system of the haem. The radical is then transferred to an amino acid residue of the protein and undergoes further transfer and transformation processes. The free radicals formed in this reaction are reviewed for a number of proteins and enzymes. Their previously published EPR spectra are analysed in a comparative way. The radicals directly detected in most systems are tyrosyl radicals and the peroxyl radicals formed on tryptophan and possibly cysteine. The locations of the radicals in the proteins have been reported as follows: Tyr133 in soybean leghaemoglobin; alphaTyr42, alphaTrp14, betaTrp15, betaCys93, (alphaTyr24-alphaHis20), all in the alpha- and beta-subunits of human haemoglobin; Tyr103, Tyr151 and Trp14 in sperm whale myoglobin; Tyr103, Tyr146 and Trp14 in horse myoglobin; Trp14, Tyr103 and Cys110 in human Mb. The sequence of events leading to radical formation, transformation and transfer, both intra- and intermolecularly, is considered. The free radicals induced by peroxides in the enzymes are reviewed. Those include: lignin peroxidase, cytochrome c peroxidase, cytochrome c oxidase, turnip isoperoxidase 7, bovine catalase, two isoforms of prostaglandin H synthase, Mycobacterium tuberculosis and Synechocystis PCC6803 catalase-peroxidases.

A new method of identifying the site of tyrosyl radicals in proteins

Protein-bound tyrosyl radicals catalyze many important enzymatic reactions. They can also initiate oxidative damage to cells. Here we report a new method of computer simulation of tyrosyl radical electron paramagnetic resonance spectra. The method enables the determination of the rotational conformation of the phenoxyl ring in a radical with unprecedented accuracy (approximately 2 degrees ). When coupled with a new online database, all tyrosine residues in a protein can be screened for that particular conformation. For the first time we show relationships between the spin density on atom C1 (rho(C1)) and the principal g-factors measured by electron paramagnetic resonance spectroscopy (rho(C1) on g(x) is shown to be linear). The new method enables the accurate determination of rho(C1) in all known tyrosyl radicals, evaluates the likelihood of a hydrogen bond, and determines the possibility of a rho(C1) distribution in the radicals. This information, together with the accurately determined rotational conformation, is frequently sufficient to allow for an unambiguous identification of the site of radical formation. The possibility of a similar relationship between rho(C) and g(x) in other radicals, e.g., tryptophanyl, is discussed.

Tryptophan or tyrosine? On the nature of the amino acid radical formed following hydrogen peroxide treatment of cytochrome c oxidase

It has been reported that different amino acid radicals are formed following the addition of hydrogen peroxide to cytochrome c oxidase (CcO) from bovine heart or from Paracoccus denitrificans. A broad unresolved signal in the electron paramagnetic resonance (EPR) spectra of bovine CcO has been assigned to a tryptophan radical, probably Trp126 [Rigby et al. Biochemistry 2000, 39, 5921-5928]. In the P. denitrificans enzyme, a similarly broad signal but with a well-resolved hyperfine structure was shown to originate from a tyrosyl radical and was tentatively assigned to the active site Tyr280 [MacMillan et al. Biochemistry 1999, 38, 9179-9184]. We confirm that the EPR signal from P. denitrificans CcO can be simulated using spectral parameters typical for known Tyr radicals in other systems. However, the rotational conformation of the phenolic ring of Tyr280 is inconsistent with our simulation. Instead, the simulation parameters we used correspond to the rotational conformation of ring that matches very accurately the conformation found in Tyr167, a residue that is close enough ( approximately 10 A) to the binuclear centre to readily donate an electron. The broad unresolved EPR signal in the bovine oxidase has been thought previously to be inconsistent with a tyrosyl radical. However, we have simulated a hypothetical EPR spectrum arising from a Tyr129 radical (the equivalent of Tyr167 in P. denitrificans CcO) and showed that it is similar to the observed broad signal. The possibility exists, therefore, that the homological tyrosine amino acid (Tyr167/Tyr129) is responsible for the EPR spectrum in both the Paraccoccus and the bovine enzyme. This correspondence between the two enzymes at least allows the possibility that this radical may have functional importance.

Protein-based radicals in the catalase-peroxidase of synechocystis PCC6803: a multifrequency EPR investigation of wild-type and variants on the environment of the heme active site

Catalase-peroxidases are bifunctional heme enzymes with a high structural homology to peroxidases from prokaryotic origin and a catalatic activity comparable to monofunctional catalases. These unique features of catalase-peroxidases make them good systems to study and understand the role of alternative electron pathways both in catalases and peroxidases. In particular, it is of interest to study the poorly understood role of tyrosyl and tryptophanyl radicals as alternative cofactors in the catalytic cycle of catalases and peroxidases. In this work, we have used a powerful combination of multifrequency EPR spectroscopy, isotopic labeling of tryptophan and tyrosine residues, and site-directed mutagenesis to unequivocally identify the reactive intermediates formed by the wild-type Synechocystis PCC6803 catalase-peroxidase. Selected variants of the heme distal and proximal sides of the Synechocystis enzyme were investigated. Variants on the aromatic residues of the short stretch located relatively close to the heme and spanning the distal and proximal sides were also investigated. In the wild-type enzyme, the EPR signal of the catalases and peroxidases (typical) Compound I intermediate [Fe(IV)=O por.+] was observed. Two protein-based radical intermediates were also detected and identified as a Tyr. and a Trp. . The site of Trp. is proposed to be Trp 106, a residue belonging to the conserved short stretch in catalase-peroxidases and located at a 7-8 A distance to the heme propionate groups. An extensive hydrogen-bonding network on the heme distal side, involving Trp122, His123, Arg119, seven structural waters, the heme 6-propionate group, and Trp106, is proposed to have a key role on the formation of the tryptophanyl radical. We used high-field EPR spectroscopy (95-285 GHz) to resolve the g-anisotropy of the protein-based radicals in Synechocystis catalase-peroxidase. The broad gx component of the HF EPR spectrum of the Tyr. in Synechocystis catalase-peroxidase was consistent with a distributed electropositive protein environment to the tyrosyl radical.

Tyrosine radical formation in the reaction of wild type and mutant cytochrome P450cam with peroxy acids: a multifrequency EPR study of intermediates on the millisecond time scale

We report a multifrequency (9.6-, 94-, 190-, and 285-GHz) EPR study of a freeze-quenched intermediate obtained from reaction of substrate-free cytochrome P450cam (CYP101) and its Y96F and Y96F/Y75F mutants with peroxy acids. It is generally assumed that in such a shunt reaction an intermediate [Fe(IV)=O, porphyrin-pi-cation radical] is formed, which should be identical to the species in the natural reaction cycle. However, for the wild type as well as for the mutant proteins, a porphyrin-pi-cation radical is not detectable within 8 ms. Instead, EPR signals corresponding to tyrosine radicals are obtained for the wild type and the Y96F mutant. Replacement of both Tyr-96 and Tyr-75 by phenylalanine leads to the disappearance of the tyrosine EPR signals. EPR studies at 285 GHz on freeze-quenched wild type and Y96F samples reveal g tensor components for the radical (stretched g(x) values from 2.0078 to 2.0064, g(y) = 2.0043, and g(z) = 2.0022), which are fingerprints for tyrosine radicals in a heterogeneous polar environment. The measurements at 94 GHz using a fundamental mode microwave resonator setup confirm the 285-GHz study. From the simulation of the hyperfine structure in the 94-GHz EPR spectra the signals have been assigned to Tyr-96 in the wild type and to Tyr-75 in the Y96F mutant. We suggest that a transiently formed Fe(IV)=O porphyrin-pi-cation radical intermediate in P450cam is reduced by intramolecular electron transfer from these tyrosines within 8 ms.

Role of radical formation at tyrosine 193 in the allene oxide synthase domain of a lipoxygenase-AOS fusion protein from coral

Coral allene oxide synthase (cAOS), a fusion protein with 8R-lipoxygenase in Plexaura homomalla, is a hemoprotein with sequence similarity to catalases. cAOS reacts rapidly with the oxidant peracetic acid to form heme compound I and intermediate II. Concomitantly, an electron paramagnetic resonance (EPR) signal with tyrosyl radical-like features, centered at a g-value of 2.004-2.005, is formed. The radical is identified as tyrosyl by changes in EPR spectra when deuterated tyrosine is incorporated in cAOS. The radical location in cAOS is determined by mutagenesis of Y193 and Y209. Upon oxidation, native cAOS and mutant Y209F exhibit the same radical spectrum, but no significant tyrosine radical forms in mutant Y193H, implicating Y193 as the radical site in native cAOS. Estimates of the side chain torsion angles for the radical at Y193, based on the beta-proton isotropic EPR hyperfine splitting, A(iso), are theta(1) = 21 to 30 degrees and theta(2) = -99 to -90 degrees. The results show that cAOS can cleave nonsubstrate hydroperoxides by a heterolytic path, although a homolytic course is likely taken in converting the normal substrate, 8R-hydroperoxyeicosatetraenoic acid (8R-HpETE), to product. Coral AOS achieves specificity for the allene oxide formed by selection of the homolytic pathway normally, while it inactivates by the heterolytic path with nonoptimal substrates. Accordingly, with the nonoptimal substrate, 13R-hydroperoxyoctadecadienoic acid (13R-HpODE), mutant Y193H is inactivated after turning over significantly fewer substrate molecules than required to inactivate native cAOS or the Y209F mutant because it cannot absorb oxidizing equivalents by forming a radical at Y193.

Spectroscopic studies of peroxyacetic acid reaction intermediates of cytochrome P450cam and chloroperoxidase

It is generally assumed that the putative compound I (cpd I) in cytochrome P450 should contain the same electron and spin distribution as is observed for cpd I of peroxidases and catalases and many synthetic cpd I analogues. In these systems one oxidation equivalent resides on the Fe(IV)=O unit (d(4), S=1) and one is located on the porphyrin (S'=1/2), constituting a magnetically coupled ferryl iron-oxo porphyrin pi-cation radical system. However, this laboratory has recently reported detection of a ferryl iron (S=1) and a tyrosyl radical (S'=1/2), via Mössbauer and EPR studies of 8 ms-reaction intermediates of substrate-free P450cam from Pseudomonas putida, prepared by a freeze-quench method using peroxyacetic acid as the oxidizing agent [Schünemann et al., FEBS Lett. 479 (2000) 149]. In the present study we show that under the same reaction conditions, but in the presence of the substrate camphor, only trace amounts of the tyrosine radical are formed and no Fe(IV) is detectable. We conclude that camphor restricts the access of the heme pocket by peroxyacetic acid. This conclusion is supported by the additional finding that binding of camphor and metyrapone inhibit heme bleaching at room temperature and longer reaction times, forming only trace amounts of 5-hydroxy-camphor, the hydroxylation product of camphor, during peroxyacetic acid oxidation. As a control we performed freeze-quench experiments with chloroperoxidase from Caldariomyces fumago using peroxyacetic acid under the identical conditions used for the substrate-free P450cam oxidations. We were able to confirm earlier findings [Rutter et al., Biochemistry 23 (1984) 6809], that an antiferromagnetically coupled Fe(IV)=O porphyrin pi-cation radical system is formed. We conclude that CPO and P450 behave differently when reacting with peracids during an 8-ms reaction time. In P450cam the formation of Fe(IV) is accompanied by the formation of a tyrosine radical, whereas in CPO Fe(IV) formation is accompanied by the formation of a porphyrin radical.

Conformational analysis of the tyrosine dipeptide analogue in the gas phase and in aqueous solution by a density functional/continuum solvent model

The conformational behavior of a dipeptide analogue of tyrosine (TDA) has been investigated by density functional methods using the polarizable continuum model (PCM) for the description of solvent effects. Our study points out the interplay of backbone and side chain contributions in determining the relative stabilities of energy minima. In particular, stabilizing interactions between the NH bond and the aromatic ring have a significant effect. The topology of the potential energy surface is significantly modified in aqueous solution due to a general widening of low energy regions and to a stabilization of helical structures.

2D-hyperfine sublevel correlation spectroscopy of tyrosyl radicals

Hyperfine sublevel correlation (HYSCORE) spectroscopy has been used to study the tyrosyl radicals in Photosystem II and bovine liver catalase. The HYSCORE data allow a complete resolution of all the 1H hyperfine tensors of these radicals. The present work shows that the proper analysis of the HYSCORE data allows the complete assignment of the 1H-hyperfine tensors in tyrosine radicals and this offers an alternative experimental tool relative to ENDOR.

Tyrosine iminoxyl radical formation from tyrosyl radical/nitric oxide and nitrosotyrosine

The quenching of the Y(D)(.) tyrosyl radical in photosystem II by nitric oxide was reported to result from the formation of a weak tyrosyl radical-nitric oxide complex (Petrouleas, V., and Diner, B. A. (1990) Biochim. Biophys. Acta 1015, 131-140). This radical/radical reaction is expected to generate an electron spin resonance (ESR)-silent 3-nitrosocyclohexadienone species that can reversibly regenerate the tyrosyl radical and nitric oxide or undergo rearrangement to form 3-nitrosotyrosine. It has been proposed that 3-nitrosotyrosine can be oxidized by one electron to form the tyrosine iminoxyl radical (>C=N-O*). This proposal was put forth as a result of ESR detection of the iminoxyl radical intermediate when photosystem II was exposed to nitric oxide (Sanakis, Y., Goussias, C., Mason, R. P., and Petrouleas, V. (1997) Biochemistry 36, 1411-1417). A similar iminoxyl radical was detected in prostaglandin H synthase-2 (Gunther, M. R., Hsi, L. C., Curtis, J. F., Gierse, J. K., Marnett, L. J., Eling, T. E., and Mason, R. P. (1997) J. Biol. Chem., 272, 17086-17090). Although the iminoxyl radicals detected in the photosystem II and prostaglandin H synthase-2 systems strongly suggest a mechanism involving 3-nitrosotyrosine, the iminoxyl radical ESR spectrum was not unequivocally identified as originating from tyrosine. We report here the detection of the non-protein L-tyrosine iminoxyl radical generated by two methods: 1) peroxidase oxidation of synthetic 3-nitroso-N-acetyl-L-tyrosine and 2) peroxidase oxidation of free L-tyrosine in the presence of nitric oxide. A newly developed ESR technique that uses immobilized enzyme was used to perform the ESR experiments. Analysis of the high resolution ESR spectrum of the tyrosine iminoxyl radical generated from free tyrosine and nitric oxide reveals a 28.4-G isotropic nitrogen hyperfine coupling and a 2.2-G proton hyperfine coupling assigned to the proton originally ortho to the phenoxyl oxygen.

Catalytic control of redox reactivities of coenzyme analogs by metal ions

Redox coenzymes and analogs have their own redox reactivities for both thermal and photochemical redox reactions. The redox activities of coenzymes can be tuned by using metal ions that can bind the redox coenzymes and analogs. Quantitative measure to determine the Lewis acidity of a variety of metal ions is given in relation to the catalytic reactivities. The mechanistic viability of metal ion catalysis in redox reactions of coenzyme analogs is described by showing a number of examples of both thermal and photochemical reactions that are made possible to proceed by controlling the redox reactivities of coenzymes with metal ions.

Comparative electron paramagnetic resonance study of radical intermediates in turnip peroxidase isozymes

The occurrence of isozymes in plant peroxidases is poorly understood. Turnip roots contain seven season-dependent isoperoxidases with distinct physicochemical properties. In the work presented here, multifrequency electron paramagnetic resonance spectroscopy has been used to characterize the Compound I intermediate obtained by the reaction of turnip isoperoxidases 1, 3, and 7 with hydrogen peroxide. The broad (2500 G) Compound I EPR spectrum of all three peroxidases was consistent with the formation of an exchange-coupled oxoferryl-porphyrinyl radical species. A dramatic pH dependence of the exchange interaction of the [Fe(IV)=O por(*+)] intermediate was observed for all three isoperoxidases and for a pH range of 4.5-7.7. This result provides substantial experimental evidence for previous proposals concerning the protein effect on the ferro- or antiferromagnetic character of the exchange coupling of Compound I based on model complexes. Turnip isoperoxidase 7 exhibited an unexpected pH effect related to the nature of the Compound I radical. At basic pH, a narrow radical species ( approximately 50 G) was formed together with the porphyrinyl radical. The g anisotropy of the narrow radical Delta(g) = 0.0046, obtained from the high-field (190 and 285 GHz) EPR spectrum, was that expected for tyrosyl radicals. The broad g(x) edge of the Tyr* spectrum centered at a low g(x) value (2.00660) strongly argues for a hydrogen-bonded tyrosyl radical in a heterogeneous microenvironment. The relationship between tyrosyl radical formation and the higher redox potential of turnip isozyme 7, as compared to that of isozyme 1, is discussed.

Multifrequency high-field EPR study of the tryptophanyl and tyrosyl radical intermediates in wild-type and the W191G mutant of cytochrome c peroxidase

Multifrequency (95, 190, and 285 GHz) high-field electron paramagnetic resonance (EPR) spectroscopy has been used to characterize radical intermediates in wild-type and Trp191Gly mutant cytochrome c peroxidase (CcP). The high-field EPR spectra of the exchange-coupled oxoferryl--trytophanyl radical pair that constitutes the CcP compound I intermediate [(Fe(IV)=O) Trp*(+)] were analyzed using a spin Hamiltonian that incorporated a general anisotropic spin-spin interaction term. Perturbation expressions of this Hamiltonian were derived, and their limitations under high-field conditions are discussed. Using numerical solutions of the completely anisotropic Hamiltonian, its was possible to simulate accurately the experimental data from 9 to 285 GHz using a single set of spin parameters. The results are also consistent with previous 9 GHz single-crystal studies. The inherent superior resolution of high-field EPR spectroscopy permitted the unequivocal detection of a transient tyrosyl radical that was formed 60 s after the addition of 1 equiv of hydrogen peroxide to the wild-type CcP at 0 degrees C and disappeared after 1 h. High-field EPR was also used to characterize the radical intermediate that was generated by hydrogen peroxide addition to the W191G CcP mutant. The g- values of this radical (g(x)= 2.00660, g(y) = 2.00425, and g(z)= 2.00208), as well as the wild-type transient tyrosyl radical, are essentially identical to those obtained from the high-field EPR spectra of the tyrosyl radical generated by gamma-irradiation of crystals of tyrosine hydrochloride (g(x)= 2.00658, g(y) = 2.00404, and g(z) = 2.00208). The low g(x)-value indicated that all three of the tyrosyl radicals were in electropositive environments. The broadening of the g(x) portion of the HF-EPR spectrum further indicated that the electrostatic environment was distributed. On the basis of these observations, possible sites for the tyrosyl radical(s) are discussed.

Sensitivity of tyrosyl radical g-values to changes in protein structure: a high-field EPR study of mutants of ribonucleotide reductase

The local electrostatic environment plays a critical role in determining the physicochemical properties of reactive radicals in proteins. High-field electron paramagnetic resonance (HF-EPR) spectroscopy has been used to determine the sensitivity of the tyrosyl radical g-values to local electrostatic environment. Site-specific mutants of ribonucleotide reductase from Escherichia coli were used to study the effect of introducing a charge group on the HF-EPR spectrum of the stable tyrosyl (Y122) radical. The changes affected by the mutations were small, but measurable. Mutation of isoleucine-74 to an arginine (I74R) or lysine (I74K) induced disorder in the hyperfine interactions. Similar effects were observed for the mutation of valine-136 to an arginine (V136R) or asparagine (V136N). For five or six mutants studied, the g(x)() component of the g-tensor was distributed. For the isoleucine-74 to lysine (I74K) and leucine-77 to phenylalanine (L77F) mutants, a shift of 1 x 10(-)(4) in g(x)() value was also detected. For the I74K mutant, it is shown that the shift is consistent with the introduction of a charged residue, but cannot be distinguished from changes in the electrostatic effect of the nearby diiron center. For the L77F mutant, the shift is induced by the diiron center. Using existing tyrosyl radical g-tensor measurements, we have developed a simple effective charge model that allows us to rationalize the effect of the local electrostatic environments in a number of proteins.

Effects of metal ions on physicochemical properties and redox reactivity of phenolates and phenoxyl radicals: mechanistic insight into hydrogen atom abstraction by phenoxyl radical-metal complexes

Phenolate and phenoxyl radical complexes of a series of alkaline earth metal ions as well as monovalent cations such as Na+ and K+ have been prepared by using 2,4-di-tert-butyl-6-(1,4,7,10-tetraoxa-13-aza-cyclopentadec-13-ylmethyl)phenol (L1H) and 2,4-di-tert-butyl-6-(1,4,7,10,13-pentaoxa-16-aza-cyclooctadec-16-ylmethyl)phenol (L2H) to examine the effects of the cations on the structure, physicochemical properties and redox reactivity of the phenolate and phenoxyl radical complexes. Crystal structures of the Mg2+- and Ca2+-complexes of L1- as well as the Ca2+- and Sr2+-complexes of L2- were determined by X-ray crystallographic analysis, showing that the crown ether rings in the Ca2+-complexes are significantly distorted from planarity, whereas those in the Mg2+- and Sr2+-complexes are fairly flat. The spectral features (UV-vis) as well as the redox potentials of the phenolate complexes are also influenced by the metal ions, depending on the Lewis acidity of the metal ions. The phenoxyl radical complexes are successfully generated in situ by the oxidation of the phenolate complexes with (NH4)(2)[Ce4+(NO3)6] (CAN). They exhibited strong absorption bands around 400 nm together with a broad one around 600-900 nm, the latter of which is also affected by the metal ions. The phenoxyl radical-metal complexes are characterized by resonance Raman, ESI-MS, and ESR spectra, and the metal ion effects on those spectroscopic features are also discussed. Stability and reactivity of the phenoxyl radical-metal complexes are significantly different, depending on the type of metal ions. The disproportionation of the phenoxyl radicals is significantly retarded by the electronic repulsion between the metal cation and a generated organic cation (Ln+), leading to stabilization of the radicals. On the other hand, divalent cations decelerate the rate of hydrogen atom abstraction from 10-methyl-9,10-dihydroacridine (AcrH2) and its 9-substituted derivatives (AcrHR) by the phenoxyl radicals. On the basis of primary kinetic deuterium isotope effects and energetic consideration of the electron-transfer step from AcrH2 to the phenoxyl radical-metal complexes, we propose that the hydrogen atom abstraction by the phenoxyl radical-alkaline earth metal complexes proceeds via electron transfer followed by proton transfer.

Characterization of the coral allene oxide synthase active site with UV-visible absorption, magnetic circular dichroism, and electron paramagnetic resonance spectroscopy: evidence for tyrosinate ligation to the ferric enzyme heme iron

Coral allene oxide synthase (AOS), a hemoprotein with weak sequence homology to catalase, is the N-terminal domain of a naturally occurring fusion protein with an 8R-lipoxygenase. AOS converts 8R-hydroperoxyeicosatetraenoic acid to the corresponding allene oxide. The UV--visible absorption and magnetic circular dichroism spectra of ferric AOS and of its cyanide and azide complexes, and the electron paramagnetic resonance spectra of native AOS (high-spin, g = 6.56, 5.22, 2.00) and of its cyanide adduct (low-spin, g = 2.86, 2.24, 1.60) closely resemble the corresponding spectra of bovine liver catalase (BLC). These results provide strong evidence for tyrosinate ligation to the heme iron of AOS as has been established for catalases. On the other hand, the positive circular dichroism bands in the Soret region for all three derivatives of ferric AOS are almost the mirror image of those in catalase. In addition, the cyanide affinity of native AOS (K(d) = 10 mM at pH 7) is about 3 orders of magnitude lower than that of BLC. Thus, while these results conclusively support a common tyrosinate-ligated heme in AOS as in catalase, significant differences exist in the interaction between their respective heme prosthetic groups and protein environments, and in the access of small molecules to the heme iron.

The electronic and vibrational structures of iron-oxo porphyrin with a methoxide or cysteinate axial ligand

Hybrid density functional theory (DFT) calculations for the electronic and vibrational structures of compound I species with a methoxide (MeO-) (1) or cysteinate (CysS-) (2) axial ligand are carried out in order to elucidate the natures of a methoxide-coordinating new type of compound I species (Bull. Chem. Soc. Jpn. 71 (1998) 1343) and cysteinate-coordinating compound I species of chloroperoxidase (CPO-I) and cytochrome P450s (P450-I). DFT computations of 1 and 2 demonstrate that these "anionic" ligands are a spin carrier; 70% (80%) of a spin density resides on the O (S) atom of the axial ligand and 30% (20%) is distributed on the porphyrin ring. These results suggest that for the generation of the compound I species, one electron is removed from the iron centers and the rest of the one electron is supplied from the oxidizable axial ligands instead of the iron centers or the porphyrin ring. Vibrational analyses demonstrate that the Fe=O bond is more strongly activated in 1 compared with 2 with the stretching mode at 849 cm(-1) (878 cm(-1)) for the doublet state1a (2a) and at 814 cm(-1) (875 cm(-1)) in the quartet state 1b (2b). This reverse order of the Fe=O bond strength with respect to the axial donor strength should have relevance to the significantly oxidized character of the CysS- axial ligand. In conjunction with the recent results of the extensive resonance Raman (RR) studies, some interpretations of unsettled RR results for compound I of chloroperoxidase (CPO-I) and a synthetic compound I species [O=FeIV(TMP*+)(alcohol)] (J. Am. Chem. Soc. 113 (1991) 6542) concerning the O=Fe stretching frequencies are discussed.

Intermediates in the reaction of substrate-free cytochrome P450cam with peroxy acetic acid

Freeze-quenched intermediates of substrate-free cytochrome 57Fe-P450(cam) in reaction with peroxy acetic acid as oxidizing agent have been characterized by EPR and Mossbauer spectroscopy. After 8 ms of reaction time the reaction mixture consists of approximately 90% of ferric low-spin iron with g-factors and hyperfine parameters of the starting material; the remaining approximately 10% are identified as a free radical (S' = 1/2) by its EPR and as an iron(IV) (S= 1) species by its Mossbauer signature. After 5 min of reaction time the intermediates have disappeared and the Mossbauer and EPR-spectra exhibit 100% of the starting material. We note that the spin-Hamiltonian analysis of the spectra of the 8 ms reactant clearly reveals that the two paramagnetic species, e.g. the ferryl (iron(IV)) species and the radical, are not exchanged coupled. This led to the conclusion that under the conditions used, peroxy acetic acid oxidized a tyrosine residue (probably Tyr-96) into a tyrosine radical (Tyr*-96), and the iron(III) center of substrate-free P450(cam) to iron(IV).

Electron paramagnetic resonance and electron nuclear double resonance spectroscopic identification and characterization of the tyrosyl radicals in prostaglandin H synthase 1

The tyrosyl radicals generated in reactions of ethyl hydrogen peroxide with both native and indomethacin-pretreated prostaglandin H synthase 1 (PGHS-1) were examined by low-temperature electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopies. In the reaction of peroxide with the native enzyme at 0 degrees C, the tyrosyl radical EPR signal underwent a continuous reduction in line width and lost intensity as the incubation time increased, changing from an initial, 35-G wide doublet to a wide singlet of slightly smaller line width and finally to a 25-G narrow singlet. The 25-G narrow singlet produced by self-inactivation was distinctly broader than the 22-G narrow singlet obtained by indomethacin treatment. Analysis of the narrow singlet EPR spectra of self-inactivated and indomethacin-pretreated enzymes suggests that they reflect conformationally distinct tyrosyl radicals. ENDOR spectroscopy allowed more detailed characterization by providing hyperfine couplings for ring and methylene protons. These results establish that the wide doublet and the 22-G narrow singlet EPR signals arise from tyrosyl radicals with different side-chain conformations. The wide-singlet ENDOR spectrum, however, is best accounted for as a mixture of native wide-doublet and self-inactivated 25-G narrow-singlet species, consistent with an earlier EPR study [DeGray et al. (1992) J. Biol. Chem. 267, 23583-23588]. We conclude that a tyrosyl residue other than the catalytically essential Y385 species is most likely responsible for the indomethacin-inhibited, narrow-singlet spectrum. Thus, this inhibitor may function by redirecting radical formation to a catalytically inactive side chain. Either radical migration or conformational relaxation at Y385 produces the 25-G narrow singlet during self-inactivation. Our ENDOR data also indicate that the catalytically active, wide-doublet species is not hydrogen bonded, which may enhance its reactivity toward the fatty-acid substrate bound nearby.

Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism

Human catalase is an heme-containing peroxisomal enzyme that breaks down hydrogen peroxide to water and oxygen; it is implicated in ethanol metabolism, inflammation, apoptosis, aging and cancer. The 1. 5 A resolution human enzyme structure, both with and without bound NADPH, establishes the conserved features of mammalian catalase fold and assembly, implicates Tyr370 as the tyrosine radical, suggests the structural basis for redox-sensitive binding of cognate mRNA via the catalase NADPH binding site, and identifies an unexpectedly substantial number of water-mediated domain contacts. A molecular ruler mechanism based on observed water positions in the 25 A-long channel resolves problems for selecting hydrogen peroxide. Control of water-mediated hydrogen bonds by this ruler selects for the longer hydrogen peroxide and explains the paradoxical effects of mutations that increase active site access but lower catalytic rate. The heme active site is tuned without compromising peroxide binding through a Tyr-Arg-His-Asp charge relay, arginine residue to heme carboxylate group hydrogen bonding, and aromatic stacking. Structures of the non-specific cyanide and specific 3-amino-1,2, 4-triazole inhibitor complexes of human catalase identify their modes of inhibition and help reveal the catalytic mechanism of catalase. Taken together, these resting state and inhibited human catalase structures support specific, structure-based mechanisms for the catalase substrate recognition, reaction and inhibition and provide a molecular basis for understanding ethanol intoxication and the likely effects of human polymorphisms.

A protein radical and ferryl intermediates are generated by linoleate diol synthase, a ferric hemeprotein with dioxygenase and hydroperoxide isomerase activities

Linoleate diol synthase (LDS) was isolated as a hemeprotein from the fungus Gaeumannomyces graminis. LDS converts linoleate sequentially to 8R-hydroperoxylinoleate (8-HPODE) through an 8-dioxygenase by insertion of molecular oxygen and to 7S,8S-dihydroxylinoleate through a hydroperoxide isomerase by intramolecular oxygen transfer. Light absorption and EPR spectra of LDS indicated that the heme iron was ferric and mainly high spin. Oxygen consumption during catalysis started after a short time lag which was reduced by 8-HPODE. Catalysis declined due to suicide inactivation. Stopped flow studies with LDS and 8-HPODE at 13 degreesC showed a rapid decrease in light absorption at 406 nm within 35 ms with a first order rate constant of 90-120 s-1. Light absorption at 406 nm then increased at a rate of approximately 4 s-1, whereas the absorption at 421 nm increased after a lag time of approximately 5 ms at a rate of approximately 70 s-1. EPR spectra at 77 K of LDS both with linoleic acid and 8-HPODE showed a transient doublet when quenched after incubation on ice for 3 s (major hyperfine splitting 2.3 millitesla; g = 2.005), indicating a protein radical. The relaxation properties of the protein radical suggested interaction with a metal center. 8-HPODE generated about twice as much radical as linoleic acid, and the 8-HPODE-induced radical appeared to be stable. Our results suggest that LDS may form, in analogy with prostaglandin H synthases, ferryl intermediates and a protein radical during catalysis.

Formation of a tyrosyl radical in xanthine oxidase

Treatment of xanthine oxidase with ferricenium at high pH gives rise to an EPR signal not previously seen with this enzyme. The signal is apparently isotropic at 9 GHz with a gavg of approximately 2 and once generated is stable to pH 6.0, so long as the sample is kept in the dark. Treatment of the signal-giving species with hydroxyurea results in complete loss of the signal, indicating that the signal is radical-based. Pretreatment of the enzyme with iodoacetate has no effect on signal formation with ferricenium. The ferricenium-generated EPR signal shows proton hyperfine coupling that is not lost upon exchange into D2O and bears considerable resemblance to the tyrosyl radical of the photosynthetic reaction center and other systems. These observations lead us to interpret the new ferricenium-generated EPR signal of xanthine oxidase as arising from a tyrosyl radical, the result of one-electron oxidation of a protein tyrosinate residue. Kinetic parameters for the reductive half-reaction of ferricenium-treated xanthine oxidase with xanthine were determined by stopped-flow spectrophotometry; kred and KDxanthine (15 s-1 and 12 microM, respectively) were essentially unchanged. Addition of 2-hydroxy-6-methylpurine (in the presence of 2 mg/mL catalase and superoxide dismutase) generated the "very rapid" MoV EPR signal while preserving the ferricenium-derived EPR signal, providing a further indication that the modified enzyme remains fully functional and the presence of the tyrosyl radical does not impact turnover by the enzyme. Coupling of the two signals was not evident, nor was coupling to the two 2Fe-2S centers or the flavin semiquinone evident. The implications of covalent modifications of proteins mediated by ferricenium are discussed.

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).