Electron paramagnetic resonance analyses of horseradish peroxidase in situ and after purification

In Vitro Heme Coordination of a Dye-Decolorizing Peroxidase-The Interplay of Key Amino Acids, pH, Buffer and Glycerol

Dye-decolorizing peroxidases (DyPs) have gained interest for their ability to oxidize anthraquinone-derived dyes and lignin model compounds. Spectroscopic techniques, such as electron paramagnetic resonance and optical absorption spectroscopy, provide main tools to study how the enzymatic function is linked to the heme-pocket architecture, provided the experimental conditions are carefully chosen. Here, these techniques are used to investigate the effect of active site perturbations on the structure of ferric P-class DyP from Klebsiella pneumoniae (KpDyP) and three variants of the main distal residues (D143A, R232A and D143A/R232A). Arg-232 is found to be important for maintaining the heme distal architecture and essential to facilitate an alkaline transition. The latter is promoted in absence of Asp-143. Furthermore, the non-innocent effect of the buffer choice and addition of the cryoprotectant glycerol is shown. However, while unavoidable or indiscriminate experimental conditions are pitfalls, careful comparison of the effects of different exogenous molecules on the electronic structure and spin state of the heme iron contains information about the inherent flexibility of the heme pocket. The interplay between structural flexibility, key amino acids, pH, temperature, buffer and glycerol during in vitro spectroscopic studies is discussed with respect to the poor peroxidase activity of bacterial P-class DyPs.

Synthesis, Kinetic Study, and Spectroscopic Analysis of Peroxidase-like Pinch-Porphyrin Fe(III) Complexes

In the present manuscript, we report the kinetic and spectroscopic analysis of six new pinch-porphyrins: protoporphyrin-picpenta 1, mesoporphyrin-picpenta 2, deuteroporphyrin-picpenta 3, protoporphyrin-picocta 4, mesoporphyrin-picocta 5, and deuteroporphyrin-picocta 6. The Michaelis-Menten enzymatic pathway and the guaiacol test confirmed the ability of the compounds to function like new peroxidase models. UV-vis, ¹H NMR, and electron spin resonance studies are in accordance with porphyrin-Fe(III) molecules with the quantum phenomena called quantum mixed spin (qms, s = 3/2, s = 5/2). Importantly, the influence of the presence of the s = 3/2 spin state in the compounds and its critical role for the catalytic capacity is proven here, which was the original hypothesis in our research group. The compounds with higher populations of the s = 3/2 spin state have increased peroxidase activity.

An Efficient Proton-Coupled Electron-Transfer Process during Oxidation of Ferulic Acid by Horseradish Peroxidase: Coming Full Cycle

Quantum mechanics/molecular mechanics calculations were utilized to study the process of oxidation of a native substrate (ferulic acid) by the active species of horseradish peroxidase (Dunford, H. B. Heme Peroxidases; Wiley-VCH: New York, 1999), Compound I and Compound II, and the manner by which the enzyme returns to its resting state. The results match experimental findings and reveal additional novel features. The calculations demonstrate that both oxidation processes are initiated by a proton-coupled electron-transfer (PCET) step, in which the active species of the enzyme participate only as electron-transfer partners, while the entire proton-transfer event is being relayed from the substrate to and from the His42 residue by a water molecule (W402). The reason for the observed (Henriksen, A; Smith, A. T.; Gajhede, M. J. Biol. Chem. 1999, 274, 35005-35011) similar reactivities of Compound I and Compound II toward ferulic acid is that the reactive isomer of Compound II is the, hitherto unobserved, Por(*)(+)Fe(III)OH isomer that resembles Compound I. The PCET mechanism reveals that His42 and W402 are crucial moieties and they determine the function of the HRP enzyme and account for its ability to perform substrate oxidation (Poulos, T. L. Peroxidases and Cytochrome P450. In The Porphyrin Handbook; Kadish, K. M., Smith, K. M., Guilard, R., Eds.; Academic Press: New York, 2000; Vol. 4, pp 189). In view of the results, the possibility of manipulating substrate oxidation by magnetic fields is an intriguing possibility.

Structures of the high-valent metal-ion haem–oxygen intermediates in peroxidases, oxygenases and catalases

Peroxidases, oxygenases and catalases have similar high-valent metal-ion intermediates in their respective reaction cycles. In this review, haem-based examples will be discussed. The intermediates of the haem-containing enzymes have been extensively studied for many years by different spectroscopic methods like UV-Vis, EPR (electron paramagnetic resonance), resonance Raman, Mössbauer and MCD (magnetic circular dichroism). The first crystal structure of one of these high-valent intermediates was on cytochrome c peroxidase in 1987. Since then, structures have appeared for catalases in 1996, 2002, 2003, putatively for cytochrome P450 in 2000, for myoglobin in 2002, for horseradish peroxidase in 2002 and for cytochrome c peroxidase again in 1994 and 2003. This review will focus on the most recent structural investigations for the different intermediates of these proteins. The structures of these intermediates will also be viewed in light of quantum mechanical (QM) calculations on haem models. In particular quantum refinement, which is a combination of QM calculations and crystallography, will be discussed. Only small structural changes accompany the generation of these intermediates. The crystal structures show that the compound I state, with a so called pi-cation radical on the haem group, has a relatively short iron-oxygen bond (1.67-1.76A) in agreement with a double-bond character, while the compound II state or the compound I state with a radical on an amino acid residue have a relatively long iron-oxygen bond (1.86-1.92A) in agreement with a single-bond character where the oxygen-atom is protonated.

How O2 binds to heme: reasons for rapid binding and spin inversion

We have used density functional methods to calculate fully relaxed potential energy curves of the seven lowest electronic states during the binding of O(2) to a realistic model of ferrous deoxyheme. Beyond a Fe-O distance of approximately 2.5 A, we find a broad crossing region with five electronic states within 15 kJ/mol. The almost parallel surfaces strongly facilitate spin inversion, which is necessary in the reaction of O(2) with heme (deoxyheme is a quintet and O(2) a triplet, whereas oxyheme is a singlet). Thus, despite a small spin-orbit coupling in heme, the transition probability approaches unity. Using reasonable parameters, we estimate a transition probability of 0.06-1, which is at least 15 times larger than for the nonbiological Fe-O(+) system. Spin crossing is anticipated between the singlet ground state of bound oxyheme, the triplet and septet dissociation states, and a quintet intermediate state. The fact that the quintet state is close in energy to the dissociation couple is of biological importance, because it explains how both spin states of O(2) may bind to heme, thereby increasing the overall efficiency of oxygen binding. The activation barrier is estimated to be <15 kJ/mol based on our results and Mössbauer experiments. Our results indicate that both the activation energy and the spin-transition probability are tuned by the porphyrin as well as by the choice of the proximal heme ligand, which is a histidine in the globins. Together, they may accelerate O(2) binding to iron by approximately 10(11) compared with the Fe-O(+) system. A similar near degeneracy between spin states is observed in a ferric deoxyheme model with the histidine ligand hydrogen bonded to a carboxylate group, i.e. a model of heme peroxidases, which bind H(2)O(2) in this oxidation state.

The charge transfer band in horseradish peroxidase correlates with heme in-plane distortions induced by calcium removal

Horseradish peroxidase C (HRPC) is a class III peroxidase whose structure is stabilized by the presence of two endogenous calcium atoms. Calcium removal has been shown to decrease the enzymatic activity of the enzyme. The spin state of the iron, a mixture of high spin (HS) and mixed quantum spin state (QS) consisting of intermediate spin (IS) 3/2 + (HS) 5/2, is also significantly affected by calcium removal, going from a predominant QS component to a predominant HS component upon removal of one calcium. Removal of both calcium ions, however, results in the appearance of a significant LS contribution, easily monitored in the charge transfer (CT) band region by low-T absorption. Normal structural decomposition (NSD) calculations of the in-plane (ip) modes of the heme extracted from HRPC native and Ca(2+)-depleted models show that removal of the proximal calcium is associated with perturbed E(u) and increased A(1g) ip distortions of the heme. The effect of complete or distal calcium removal on the heme also results in increased A(1g) ip distortions, but in significantly decreased E(u) distortions. The overall effect is to decrease the nonplanarity of the heme: the total ip distortion of the native HRPC heme is 0.200 and 0.134 A for the Ca(2+)-depleted species. Our NSD results corroborate the role proposed for the protein matrix, namely to fine-tune the active site by inducing subtle changes in heme planarity and spin state of the iron.

Resonance Raman spectroscopy study of change of iron spin state in horseradish peroxidase C induced by removal of calcium

Resonance Raman spectroscopy is used to probe the effect of calcium depletion on the heme group of horseradish peroxidase C at pH 8. Polarized Raman spectra are recorded with an argon ion laser at eight different wavelengths to provide a sound database for a reliable spectral decomposition. Upon calcium depletion, the spectrum is indicative of a predominantly pentacoordinated high spin state of the heme iron coexisting with small fractions of hexacoordinated high and low spin states. The dominant quantum mixed spin state of native ferric horseradish peroxidase, which is characteristic for class III peroxidases, is not detectable in the spectrum of the enzyme with partial distal Ca(2+) depletion. The quenching of the quantum mixed spin state and the predominance of the pentacoordinated high spin state are likely to arise from distortions induced by distal calcium depletion, which translates into a weaker Fe-N(epsilon)(His) bond and a more tilted imidazole. A correlation is proposed between the lower enzyme activity and the elimination of the pentacoordinated quantum mixed state upon Ca(2+) depletion.

Heme structural perturbation of PEG-modified horseradish peroxidase C in aromatic organic solvents probed by optical absorption and resonance Raman dispersion spectroscopy

The heme structure perturbation of poly(ethylene glycol)-modified horseradish peroxidase (HRP-PEG) dissolved in benzene and toluene has been probed by resonance Raman dispersion spectroscopy. Analysis of the depolarization ratio dispersion of several Raman bands revealed an increase of rhombic B(1g) distortion with respect to native HRP in water. This finding strongly supports the notion that a solvent molecule has moved into the heme pocket where it stays in close proximity to one of the heme's pyrrole rings. The interactions between the solvent molecule, the heme, and the heme cavity slightly stabilize the hexacoordinate high spin state without eliminating the pentacoordinate quantum mixed spin state that is dominant in the resting enzyme. On the contrary, the model substrate benzohydroxamic acid strongly favors the hexacoordinate quantum mixed spin state and induces a B(2g)-type distortion owing to its position close to one of the heme methine bridges. These results strongly suggest that substrate binding must have an influence on the heme geometry of HRP and that the heme structure of the enzyme-substrate complex (as opposed to the resting state) must be the key to understanding the chemical reactivity of HRP.

Analysis of heme structural heterogeneity in Mycobacterium tuberculosis catalase-peroxidase (KatG)

Mycobacterium tuberculosis catalase-peroxidase (KatG) is a heme enzyme considered important for virulence, which is also responsible for activation of the anti-tuberculosis pro-drug isoniazid. Here, we present an analysis of heterogeneity in KatG heme structure using optical, resonance Raman, and EPR spectroscopy. Examination of ferric KatG under a variety of conditions, including enzyme in the presence of fluoride, chloride, or isoniazid, and at different stages during purification in different buffers allowed for assignment of spectral features to both five- and six-coordinate heme. Five-coordinate heme is suggested to be representative of "native" enzyme, since this species was predominant in the enzyme examined immediately after one chromatographic protocol. Quantum mechanically mixed spin heme is the most abundant form in such partially purified enzyme. Reduction and reoxidation of six-coordinate KatG or the addition of glycerol or isoniazid restored five-coordinate heme iron, consistent with displacement of a weakly bound distal water molecule. The rate of formation of KatG Compound I is not retarded by the presence of six-coordinate heme either in wild-type KatG or in a mutant (KatG[Y155S]) associated with isoniazid resistance, which contains abundant six-coordinate heme. These results reveal a number of similarities and differences between KatG and other Class I peroxidases.

Mutation of residues critical for benzohydroxamic acid binding to horseradish peroxidase isoenzyme C

Aromatic substrate binding to peroxidases is mediated through hydrophobic and hydrogen bonding interactions between residues on the distal side of the heme and the substrate molecule. The effects of perturbing these interactions are investigated by an electronic absorption and resonance Raman study of benzohydroxamic acid (BHA) binding to a series of mutants of horseradish peroxidase isoenzyme C (HRPC). In particular, the Phe179 --> Ala, His42 --> Glu variants and the double mutant His42 --> Glu:Arg38 --> Leu are studied in their ferric state at pH 7 with and without BHA. A comparison of the data with those previously reported for wild-type HRPC and other distal site mutants reaffirms that in the resting state mutation of His42 leads to an increase of 6-coordinate aquo heme forms at the expense of the 5-coordinate heme state, which is the dominant species in wild-type HRPC. The His42Glu:Arg38Leu double mutant displays an enhanced proportion of the pentacoordinate heme state, similar to the single Arg38Leu mutant. The heme spin states are insensitive to mutation of the Phe179 residue. The BHA complexes of all mutants are found to have a greater amount of unbound form compared to the wild-type HRPC complex. It is apparent from the spectral changes induced on complexation with BHA that, although Phe179 provides an important hydrophobic interaction with BHA, the hydrogen bonds formed between His42 and, in particular, Arg38 and BHA assume a more critical role in the binding of BHA to the resting state.

Ionic strength and pH effect on the Fe(III)-imidazolate bond in the heme pocket of horseradish peroxidase: an EPR and UV-visible combined approach

The effects of chloride, dihydrogenphosphate and ionic strength on the spectroscopic properties of horseradish peroxidase in aqueous solution at pH=3.0 were investigated. A red-shift (lambda=408 nm) of the Soret band was observed in the presence of 40 mM chloride; 500 mM dihydrogenphosphate or chloride brought about a blue shift of the same band (lambda=370 nm). The EPR spectrum of the native enzyme at pH 3.0 was characterized by the presence of two additional absorption bands in the region around g=6, with respect to pH 6.5. Chloride addition resulted in the loss of these features and in a lower rhombicity of the signal. A unique EPR band at g=6.0 was obtained as a result of the interaction between HRP and dihydrogenphosphate, both in the absence and presence of 40 mM Cl-. We suggest that a synergistic effect of low pH, Cl- and ionic strength is responsible for dramatic modifications of the enzyme conformation consistent with the Fe(II)-His170 bond cleavage. Dihydrogenphosphate as well as high chloride concentrations are shown to display an unspecific effect, related to ionic strength. A mechanistic explanation for the acid transition of HRP, previously observed by Smulevich et al. [Biochemistry 36 (1997) 640] and interpreted as a pure pH effect, is proposed.

The quantum mixed-spin heme state of barley peroxidase: A paradigm for class III peroxidases

Electronic absorption and resonance Raman (RR) spectra of the ferric form of barley grain peroxidase (BP 1) at various pH values, at both room temperature and 20 K, are reported, together with electron paramagnetic resonance spectra at 10 K. The ferrous forms and the ferric complex with fluoride have also been studied. A quantum mechanically mixed-spin (QS) state has been identified. The QS heme species coexists with 6- and 5-cHS hemes; the relative populations of these three spin states are found to be dependent on pH and temperature. However, the QS species remains in all cases the dominant heme spin species. Barley peroxidase appears to be further characterized by a splitting of the two vinyl stretching modes, indicating that the vinyl groups are differently conjugated with the porphyrin. An analysis of the currently available spectroscopic data for proteins from all three peroxidase classes suggests that the simultaneous occurrence of the QS heme state as well as the splitting of the two vinyl stretching modes is confined to class III enzymes. The former point is discussed in terms of the possible influences of heme deformations on heme spin state. It is found that moderate saddling alone is probably not enough to cause the QS state, although some saddling may be necessary for the QS state.

Understanding heme cavity structure of peroxidases: comparison of electronic absorption and resonance Raman spectra with crystallographic results

Electronic absorption and resonance Raman spectra of various peroxidases and selected site-directed mutants are reported. These results and the X-ray crystal structure data are critically analyzed and underline the differences that exist between the crystal and solution states. The effect of the vinyl conjugation on the electronic absorption maxima and the influence of the ligand nature on the wavelength of the charge-transfer (CT1) band are shown to be useful probes of subtle interactions in the heme pocket. The spectroscopic differences observed between the three classes of peroxidases are discussed in terms of their structural diversity.

Electron paramagnetic resonance studies of ferric cytochrome c' from photosynthetic bacteria

Electronic ground nature of ferric cytochromes c' isolated from five photosynthetic bacteria. Chromatium vinosum ATCC 17899, Rhodobacter capsulatus ATCC 11166, Rhodopseudomonas palustris ATCC 17001, Rhodospirillum molischianum ATCC 14031, and Rhodospirillum rubrum ATCC 11170 has been investigated by electron paramagnetic resonance (EPR) spectroscopy. EPR spectra indicate that the electronic ground state of five ferric cytochromes c' is a quantum mechanical admixed-spin state of a high spin (S = 5/2) and an intermediate spin (S = 3/2) at pH 7.2 and is high-spin state at pH 11.0. At physiological pH, however, the content of an intermediate spin state differs with the bacterial source of the protein: approximately 50%, Chromatium vinosum; approximately 40%, Rhodobacter capsulatus and Rhodopseudomonas palustris; approximately 10%, Rhodospirillum molischianum and Rhodospirillum rubrum. Computer simulation of the spectra supports this diversity of the contribution of an intermediate spin state. Model studies of the ferric porphyrin complexes suggest that the correlation between content of an intermediate spin state and heme iron displacement from the mean heme plane. Therefore, the variation of the content of an intermediate spin state observed in the present study reflects the subtle difference in the degree of heme iron displacement among the proteins.

Novel ligand binding properties of the myoglobin substituted with monoazahemin

The iron complex of alpha-azamesoporphyrin XIII was combined with apomyoglobin to investigate influence of the meso nitrogen on ligand binding properties in the reconstituted protein. Stoichiometric complex formation between the two components was confirmed, and conservation of the native coordination structures in the resultant myoglobin was established with spectroscopic criteria and apparently normal ligand binding. The visible absorption spectra of various ferric and ferrous derivatives are characteristic with less intense Soret peaks and enhanced visible bands. The electron paramagnetic resonance spectrum with g = 5.2 suggests an anomalous intermediate spin (S = 3/2) character for the aquomet protein. The oxygen affinity of reduced azaheme myoglobin, 0.010 mm Hg, is 50 times larger than that of the native myoglobin. In addition, azaheme myoglobin forms stable complexes with imidazole, pyridine, or cyanide in ferrous state. All of these new properties were consistently explained in terms of stronger equatorial ligand field of the heme iron in a narrower coordination cavity. Similarities of azaheme to verdoheme were also pointed out.

Purification and properties of a halophilic catalase-peroxidase from Haloarcula marismortui

A heme protein, hCP, from the extreme halophile, Haloarcula marismortui, showing both peroxidatic and catalatic activity has been purified and characterized as a catalase-peroxidase. Catalatic activity is enhanced by molar concentrations of NaCl or (NH4)2SO4, while peroxidase activity decreases with increasing salt concentration. Optimal pH values are 6.0 for peroxidatic activity assayed in absence of NaCl and 7.5 for catalatic activity assayed in molar concentrations of NaCl. The two activities present saturation behaviour with increasing H2O2 concentration with apparent Km values of 0.5 and 2.5 mM for the peroxidatic and catalatic activities, respectively. A molecular mass of 81,292 +/- 9 Da was measured for the polypeptide by mass spectroscopy. One heme group (protoporphyrin IX with an iron atom in the ferric state) is associated with one molecule of hCP. Its amino-acid composition shows hCP to contain a high proportion of acidic residues. The EPR spectrum of the NO-compound of reduced (ferrous) hCP strongly suggests that the proximal ligand of the heme is the imidazole group of a histidine residue.

Resonance Raman spectroscopy shows different temperature-dependent coordination equilibria for native horseradish and cytochrome c peroxidase

Resonance Raman spectra are reported for native horseradish peroxidase (HRP) and cytochrome c peroxidase (CCP) at 290, 77 and 9 K, using 406.7 nm excitation, in resonance with the Soret electronic transition. The spectra reveal temperature-dependent equilibria involving changes in coordination or spin state. At 290 K and pH 6.5, CCP contains a mixture of 5- and 6-coordinate high-spin FeIII heme while at 9 K the equilibrium is shifted entirely to the 6-coordinate species. The spectra indicate weak binding of H2O to the heme Fe, consistent with the long distance, 2.4 A, seen in the crystal structure. At 290 K HRP also contains a mixture of high-spin FeIII hemes with the 5-coordinate form predominant. At low temperature, a small 6-coordinate high-spin component remains but the 5-coordinate high-spin spectrum is replaced by another which is characteristic either of 6-coordinate low-spin or 5-coordinate intermediate spin heme. The latter species is definitely indicated by previous EPR studies at low temperature. This behavior implies that, in contrast to CCP, the distal coordination site of HRP is only partially occupied by H2O at any temperature and that lowering the temperature significantly weakens the Fe-proximal imidazole bond. Consistent with this inference, the 77 K spectrum of reduced HRP shows an appreciable fraction of molecules having an Fe-imidazole stretching frequency of 222 cm-1, a value indicating weakened H-bonding of the proximal imidazole.

Temperature dependence in the absorption spectra of beef liver catalase

The spin characteristics of the ferric heme groups in native beef liver catalase, and in the complexes formed by reaction with fluoride, cyanide, azide, thiocyanate, and cyanate ions have been studied using absorption spectroscopy over the temperature range of 4-285 K. The azide, isothiocyanate, and isocyanate complexes of catalase are considered to be high-spin ferric heme complexes at room temperature, but undergo a thermal spin change below 300 K. The temperature dependence of these absorption spectra, however, cannot be analyzed in terms of simple Boltzmann distributions between two S = 1/2 and S = 5/2 spin states. The data show that these spin changes occur over a very narrow temperature range, but do not result in the formation of completely, low-spin complexes. The data also suggest that the thermal spin changes that occur below the glassing temperature of the solvent are dependent upon the conformational changes which take place within the protein itself with a change in temperature, and which directly affect the environment of the heme group.

High-pressure proton nuclear magnetic resonance studies of hemoproteins. Pressure-induced structural change in heme environments of myoglobin, hemoglobin, and horseradish peroxidase

Hyperfine shifted proton NMR spectra of metmyoglobin, methemoglobin, and their complexes with azide, imidazole, and cyanide as well as the spectrum of native horseradish peroxidase were obtained at high pressures up to 2000 atm with a specially designed high-pressure cell for 220-MHz superconducting NMR spectrometer. For the azide complexes of metmyoglobin, in all of which the iron atoms are in thermal spin equilibrium between high- and low-spin states, the increased pressure shifted their heme methyl proton signals to the upfield side. For the cyanide complexes of metmyoglobin and methemoglobin and for the fluoride complex of metmyoglobin, which are in purely low- and high-spin states, respectively, the spectra were almost insensitive to changes in pressure up to 2000 atm. The heme methyl proton signals of aquometmyoglobin, its formate complex, and horseradish peroxidase showed appreciable upfield shifts upon pressurization. These results were interpreted to indicate that the primary effect of pressure on the hemoprotein structure is to shift the spin equilibrium in favor of the low-spin form. Hemichrome formation of methemoglobin at high pressures was also observed, and the effect of pressure on the heme environmental structure of deoxyhemoglobin and deoxymyoglobin was also discussed.