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Sumithran S, Sono M, Raner GM, Dawson JH. Single turnover studies of oxidative halophenol dehalogenation by horseradish peroxidase reveal a mechanism involving two consecutive one electron steps: Toward a functional halophenol bioremediation catalyst. J Inorg Biochem 2012; 117:316-21. [DOI: 10.1016/j.jinorgbio.2012.09.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 09/18/2012] [Accepted: 09/18/2012] [Indexed: 10/27/2022]
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Silaghi-Dumitrescu R, Reeder B, Nicholls P, Cooper C, Wilson M. Ferryl haem protonation gates peroxidatic reactivity in globins. Biochem J 2007; 403:391-5. [PMID: 17214588 PMCID: PMC1876371 DOI: 10.1042/bj20061421] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 01/02/2007] [Accepted: 01/10/2007] [Indexed: 02/04/2023]
Abstract
Ferryl (Fe(IV)=O) species are involved in key enzymatic processes with direct biomedical relevance; among others, the uncontrolled reactivities of ferryl Mb (myoglobin) and Hb (haemoglobin) have been reported to be central to the pathology of rhabdomyolysis and subarachnoid haemorrhage. Rapid-scan stopped-flow methods have been used to monitor the spectra of the ferryl species in Mb and Hb as a function of pH. The ferryl forms of both proteins display an optical transition with pK approximately 4.7, and this is assigned to protonation of the ferryl species itself. We also demonstrate for the first time a direct correlation between Hb/Mb ferryl reactivity and ferryl protonation status, simultaneously informing on chemical mechanism and toxicity and with broader biochemical implications.
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Affiliation(s)
- Radu Silaghi-Dumitrescu
- *Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, U.K
- †Domeniul Chimie, Universitatea Babeş-Bolyai, Str. Arany János 11, RO-3400 Cluj-Napoca, Romania
| | - Brandon J. Reeder
- *Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, U.K
| | - Peter Nicholls
- *Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, U.K
| | - Chris E. Cooper
- *Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, U.K
| | - Michael T. Wilson
- *Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, U.K
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Abstract
Density functional calculations are performed to investigate the protonation state of the compound II intermediate (Cpd II) of the catalase reaction cycle. Several scenarios are considered, depending on the protonation state of the active center (heme) and the catalytic His residue. Only the form with a protonated Fe==O unit (i.e. Fe--OH) is in agreement with the recent high-resolution crystal structure, while the traditional description of Cpd II as an oxoferryl species corresponds to a configuration slightly higher in energy. The computed Fe--O stretch frequency is in agreement with the available experimental data. Molecular dynamics simulations show that the pocket water remains in the region between the His61 and Asn133 catalytic residues, but it occasionally tries to escape towards the main channel in a concerted motion with the Asn133 residue. A possible role for this residue in the process of ligand entry/escape from the binding pocket is proposed.
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Affiliation(s)
- Carme Rovira
- Centre de Recerca en Química Teòrica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.
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Terner J, Palaniappan V, Gold A, Weiss R, Fitzgerald MM, Sullivan AM, Hosten CM. Resonance Raman spectroscopy of oxoiron(IV) porphyrin π-cation radical and oxoiron(IV) hemes in peroxidase intermediates. J Inorg Biochem 2006; 100:480-501. [PMID: 16513173 DOI: 10.1016/j.jinorgbio.2006.01.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Accepted: 01/04/2006] [Indexed: 11/15/2022]
Abstract
The catalytic cycle intermediates of heme peroxidases, known as compounds I and II, have been of long standing interest as models for intermediates of heme proteins, such as the terminal oxidases and cytochrome P450 enzymes, and for non-heme iron enzymes as well. Reports of resonance Raman signals for compound I intermediates of the oxo-iron(IV) porphyrin pi-cation radical type have been sometimes contradictory due to complications arising from photolability, causing compound I signals to appear similar to those of compound II or other forms. However, studies of synthetic systems indicated that protein based compound I intermediates of the oxoiron(IV) porphyrin pi-cation radical type should exhibit vibrational signatures that are different from the non-radical forms. The compound I intermediates of horseradish peroxidase (HRP), and chloroperoxidase (CPO) from Caldariomyces fumago do in fact exhibit unique and characteristic vibrational spectra. The nature of the putative oxoiron(IV) bond in peroxidase intermediates has been under discussion in the recent literature, with suggestions that the Fe(IV)O unit might be better described as Fe(IV)-OH. The generally low Fe(IV)O stretching frequencies observed for proteins have been difficult to mimic in synthetic ferryl porphyrins via electron donation from trans axial ligands alone. Resonance Raman studies of iron-oxygen vibrations within protein species that are sensitive to pH, deuteration, and solvent oxygen exchange, indicate that hydrogen bonding to the oxoiron(IV) group within the protein environment contributes to substantial lowering of Fe(IV)O frequencies relative to those of synthetic model compounds.
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Affiliation(s)
- James Terner
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284-2006, USA.
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Pinakoulaki E, Pfitzner U, Ludwig B, Varotsis C. Direct detection of Fe(IV)[double bond]O intermediates in the cytochrome aa3 oxidase from Paracoccus denitrificans/H2O2 reaction. J Biol Chem 2003; 278:18761-6. [PMID: 12637529 DOI: 10.1074/jbc.m211925200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We report the first evidence for the formation of the "607- and 580-nm forms" in the cytochrome oxidase aa3/H2O2 reaction without the involvement of tyrosine 280. The pKa of the 607-580-nm transition is 7.5. The 607-nm form is also formed in the mixed valence cytochrome oxidase/O2 reaction in the absence of tyrosine 280. Steady-state resonance Raman characterization of the reaction products of both the wild-type and Y280H cytochrome aa3 from Paracoccus denitrificans indicate the formation of six-coordinate low spin species, and do not support, in contrast to previous reports, the formation of a porphyrin pi-cation radical. We observe three oxygen isotope-sensitive Raman bands in the oxidized wild-type aa3/H2O2 reaction at 804, 790, and 358 cm-1. The former two are assigned to the Fe(IV)[double bond]O stretching mode of the 607- and 580-nm forms, respectively. The 14 cm-1 frequency difference between the oxoferryl species is attributed to variations in the basicity of the proximal to heme a3 His-411, induced by the oxoferryl conformations of the heme a3-CuB pocket during the 607-580-nm transition. We suggest that the 804-790 cm-1 oxoferryl transition triggers distal conformational changes that are subsequently communicated to the proximal His-411 heme a3 site. The 358 cm-1 mode has been found for the first time to accumulate with the 804 cm-1 mode in the peroxide reaction. These results indicate that the mechanism of oxygen reduction must be reexamined.
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Jantschko W, Furtmüller PG, Allegra M, Livrea MA, Jakopitsch C, Regelsberger G, Obinger C. Redox intermediates of plant and mammalian peroxidases: a comparative transient-kinetic study of their reactivity toward indole derivatives. Arch Biochem Biophys 2002; 398:12-22. [PMID: 11811944 DOI: 10.1006/abbi.2001.2674] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A comparative study on the reactivity of five indole derivatives (tryptamine, N-acetyltryptamine, tryptophan, melatonin, and serotonin), with the redox intermediates compound I (k2) and compound II (k3) of the plant enzyme horseradish peroxidase (HRP) and the two mammalian enzymes lactoperoxidase (LPO) and myeloperoxidase (MPO), was performed using the sequential-mixing stopped-flow technique. The calculated bimolecular rate constants (k2, k3) revealed substantial differences regarding the oxidazibility of the substrates by redox intermediates at pH 7.0 and 25 degrees C. With HRP it was shown that k2 and k3 are mainly determined by the reduction potential (Eo') of the substrate with k2 being 7-45 times higher than k3. Compound I of mammalian peroxidases was a much better oxidant than HRP compound I with the consequence that the influence of the indole structure on k2 of LPO and MPO was small varying by a factor of only 88 and 38, respectively, which is in strong contrast to a factor of 160,000 determined for k2 of HRP. Interestingly, the k3 values for all three enzymes were very similar. Oxidation of substrates by mammalian peroxidase compound II is strongly constrained by the nature of the substrate. The k3 values for the five indoles varied by a factor of 3,570 (LPO) and 200,000 (MPO), suggesting that the reduction potential of compound II of mammalian peroxidase is less positive than that of compound I, which is in contrast to the plant enzyme.
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Affiliation(s)
- Walter Jantschko
- Institute of Chemistry, University of Agricultural Sciences, Muthgasse 18, Vienna, A-1190, Austria
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Proshlyakov DA, Pressler MA, Babcock GT. Dioxygen activation and bond cleavage by mixed-valence cytochrome c oxidase. Proc Natl Acad Sci U S A 1998; 95:8020-5. [PMID: 9653133 PMCID: PMC20922 DOI: 10.1073/pnas.95.14.8020] [Citation(s) in RCA: 244] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Elucidating the structures of intermediates in the reduction of O2 to water by cytochrome c oxidase is crucial to understanding both oxygen activation and proton pumping by the enzyme. In the work here, the reaction of O2 with the mixed-valence enzyme, in which only heme a3 and CuB in the binuclear center are reduced, has been followed by time-resolved resonance Raman spectroscopy. The results show that O==O bond cleavage occurs within the first 200 micros after reaction initiation; the presence of a uniquely stable Fe---O---O(H) peroxy species is not detected. The product of this rapid reaction is a heme a3 oxoferryl (FeIV==O) species, which requires that an electron donor in addition to heme a3 and CuB must be involved. The available evidence suggests that the additional donor is an amino acid side chain. Recent crystallographic data [Yoshikawa, S., Shinzawa-Itoh, K., Nakashima, R., Yaono, R., Yamashita, E., Inoue, N., Yao, M., Fei, M. J., Libeu, C. P., Mizushima, T., et al. Science, in press; Ostermeier, C., Harrenga, A. , Ermler, U. & Michel, H. (1997) Proc. Natl. Acad. Sci. USA 94, 10547-10553] show that one of the CuB ligands, His240, is cross-linked to Tyr244 and that this cross-linked tyrosyl is ideally positioned to participate in dioxygen activation. We propose a mechanism for O---O bond cleavage that proceeds by concerted hydrogen atom transfer from the cross-linked His---Tyr species to produce the product oxoferryl species, CuB2+---OH-, and the tyrosyl radical. This mechanism provides molecular structures for two key intermediates that drive the proton pump in oxidase; moreover, it has clear analogies to the proposed O---O bond forming chemistry that occurs during O2 evolution in photosynthesis.
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Affiliation(s)
- D A Proshlyakov
- Chemistry Department and Laser Laboratory, Michigan State University, East Lansing, Michigan 48824-1322, USA
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Patel PK, Mondal MS, Modi S, Behere DV. Kinetic studies on the oxidation of phenols by the horseradish peroxidase compound II. BIOCHIMICA ET BIOPHYSICA ACTA 1997; 1339:79-87. [PMID: 9165102 DOI: 10.1016/s0167-4838(96)00219-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Oxidation of substituted phenols by horseradish peroxidase compound II were studied using stopped-flow technique. Dissociation constants (K(D)) of HRP-II-phenol complexes were deduced from the kinetic data. Magnitudes of K(D) fall in a relatively narrow range of 3-11 mM. These are comparable to 3-10 mM reported for the binding of substituted phenols to native HRP, suggesting that the mode of binding of phenols to native HRP and HRP compound II may be similar. pH dependence of the apparent second order rate constants (k(app)) of the reactions of all the phenols were determined. The k(app) values of reactions other than the reaction of tyrosine, were observed to increase in the acidic region but decreased in the alkaline region. The increase was attributed to the deprotonation of distal carboxylic acid residue on enzyme with pK(a) values of 4.2-5.2. For tyrosine, however, the apparent second-order rate constant was observed to further increase non linearly on increasing the pH in the alkaline region. Results were interpreted quantitatively on the basis that protonated form of the enzyme reacted with the protonated form of the phenol with different individual rate constants.
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Affiliation(s)
- P K Patel
- Chemical Physics Group, Tata Institute of Fundamental Research, Navy Nagar, Bombay, India
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Proshlyakov DA, Paeng IR, Paeng KJ, Kitagawa T. Resonance Raman studies of compounds I and II ofarthromyces ramosus peroxidase: Close similarities in their Raman spectra but distinct oxygen exchangeability of the Fe=O heme. ACTA ACUST UNITED AC 1996. [DOI: 10.1002/(sici)1520-6343(1996)2:5<317::aid-bspy5>3.0.co;2-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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11
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Sharonov YuA, Pismensky VF, Yarmola EG. Contribution of protein conformation to heme stereochemistry and reactivity. Low-temperature magnetic circular dichroism data. J Biomol Struct Dyn 1989; 7:207-24. [PMID: 2818870 DOI: 10.1080/07391102.1989.10507761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Visible and near infrared magnetic circular dichroism (MCD) spectra of heme proteins and enzymes as well as those of a protein-free heme bound to 2-methylimidazole were recorded and compared at 4.2 K in unrelaxed metastable and relaxed equilibrium heme stereochemistry. The relaxed and unrelaxed stereochemistries of a 5-coordinate ferrous heme were generated by chemical reduction of iron at room temperature before freezing the sample and by photolysis of CO or O2 complexes at 4.2 K, respectively. The results are discussed in terms of a protein contribution into energies of the Fe-N epsilon(His) and Fe-N(pyrrols) bonds and their change on a ligand binding. We observed and analyzed cases of weak (myoglobin, hemoglobin) and strong (leghemoglobin, peroxidases) constraints imposed by the protein conformation on the proximal heme stereochemistry by comparing the bond energies in proteins with those in the protoheme-(2-methylimidazole) model compound. The role of a protein moiety in modulating the ligand binding properties of leghemoglobin and the heme reactivity of horseradish peroxidase is discussed.
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Affiliation(s)
- Sharonov YuA
- Institute of Molecular Biology, USSR Academy of Sciences, Moscow
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13
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Kuo CF, Fridovich I. Stimulation of the activity of horseradish peroxidase by nitrogenous compounds. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68997-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Nakajima R, Yamazaki I. The mechanism of oxyperoxidase formation from ferryl peroxidase and hydrogen peroxide. J Biol Chem 1987. [DOI: 10.1016/s0021-9258(18)61544-3] [Citation(s) in RCA: 132] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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15
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Dunford HB, Adeniran AJ. Hammett rho sigma correlation for reactions of horseradish peroxidase compound II with phenols. Arch Biochem Biophys 1986; 251:536-42. [PMID: 3800384 DOI: 10.1016/0003-9861(86)90361-9] [Citation(s) in RCA: 86] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The rates of reduction of horseradish peroxidase compound II by p-methoxyphenol (4-hydroxyanisole) have been studied from pH 6.0 to 10.5. The kinetics are influenced by an acid group of pKa 8.7 on compound II. The acidic form of compound II is reactive; the basic form is not. Only the electrically neutral, unionized form of p-methoxyphenol is reactive. Fifteen different phenols were reacted with compound II at either pH 7.6 or pH 7.0 (three of them at both pH's). Rate constants varied from zero for p-nitrophenol to 3.2 X 10(7) M-1 for p-aminophenol. The reactive m- and p-substituted phenols yield a rho value of -4.6 +/- 0.5 when plotted according to the Hammett relation. This compares to the rho value of -6.9 obtained for horseradish peroxidase compound I reactions with phenols (1976, D. Job and H. B. Dunford, Eur. J. Biochem. 66, 607). The difference in sensitivity of compounds I and II to electron donating substituents on the phenols can be explained in terms of the relative simplicity of the reactions. Electron donation occurs to the electron-deficient porphyrin pi-cation radical of compound I accompanied by single proton addition to the protein. For compound II the electron is fed to the ferryl group at the center of the porphyrin in a reaction accompanied by two proton additions to the ferryl oxygen atom, one from the protein and the other from the substrate or solvent. This is followed by loss of water from the inner coordination sphere of the ferric ion. The relative reactivities of three o-substituted phenols can be explained in terms of steric hindrance which is minimal for a single o-substituent.
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Hashimoto S, Nakajima R, Yamazaki I, Tatsuno Y, Kitagawa T. Oxygen exchange between the Fe(IV) = O heme and bulk water for the A2 isozyme of horseradish peroxidase. FEBS Lett 1986; 208:305-7. [PMID: 3780970 DOI: 10.1016/0014-5793(86)81038-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Resonance Raman spectra were observed for compound II of horseradish peroxidase A2, and the Fe(IV) = O stretching Raman line was identified at 775 cm-1. This Raman line shifted to 741 cm-1 upon a change of solvent from H2(16)O to H2(18)O, indicating occurrence of the oxygen exchange between the Fe(IV) = O heme and bulk water. The oxygen exchange took place only at the acidic side of the heme-linked ionization with pKa = 6.9.
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Makino R, Uno T, Nishimura Y, Iizuka T, Tsuboi M, Ishimura Y. Coordination structures and reactivities of compound II in iron and manganese horseradish peroxidases. A resonance Raman study. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(19)83923-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Hashimoto S, Tatsuno Y, Kitagawa T. Resonance Raman evidence for oxygen exchange between the FeIV = O heme and bulk water during enzymic catalysis of horseradish peroxidase and its relation with the heme-linked ionization. Proc Natl Acad Sci U S A 1986; 83:2417-21. [PMID: 3458206 PMCID: PMC323308 DOI: 10.1073/pnas.83.8.2417] [Citation(s) in RCA: 105] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Raman spectroscopic studies of compound II of horseradish peroxidase show that the oxygen atom in the FeIV = O group of the heme is rapidly exchanged in H2O at pH 7.0 but not in an alkaline solution (pH 11.0). This conclusion is based on studies of shift in the FeIV = O stretching mode of compound II in H2(18)O; further studies show that the FeIV = O heme is hydrogen-bonded to an amino acid residue of the protein in neutral solutions but not in the alkaline solution. Deprotonation of this residue takes place with the midpoint pH at 8.8 and accordingly corresponds to the so-called heme-linked ionization. It is concluded that this hydrogen-bonded proton plays an important part in the oxygen exchange mechanism. From this it seems clear that this hydrogen-bonded proton has an essential role in the acid/base catalysis of this enzyme and that alkaline deactivation of this enzyme can be attributed to the lack of a hydrogen-bonded proton at high pH.
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Heme-linked ionization of horseradish peroxidase compound II monitored by the resonance Raman Fe(IV)=O stretching vibration. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39637-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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A molecular orbital study on the oxidation of hydrogen donor molecules by peroxidase compound II. J Theor Biol 1983. [DOI: 10.1016/0022-5193(83)90352-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Teraoka J, Kitagawa T. Structural implication of the heme-linked ionization of horseradish peroxidase probed by the Fe-histidine stretching Raman line. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69554-2] [Citation(s) in RCA: 178] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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The oxidation-reduction potentials of compound I/compound II and compound II/ferric couples of horseradish peroxidases A2 and C. J Biol Chem 1979. [DOI: 10.1016/s0021-9258(19)86816-3] [Citation(s) in RCA: 189] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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