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Ullmann GM. The Coupling of Protonation and Reduction in Proteins with Multiple Redox Centers: Theory, Computational Method, and Application to Cytochrome c3. J Phys Chem B 2000. [DOI: 10.1021/jp000711j] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. Matthias Ullmann
- Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., TPC-15, La Jolla, California 92037
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Czjzek M, Payan F, Guerlesquin F, Bruschi M, Haser R. Crystal structure of cytochrome c3 from Desulfovibrio desulfuricans Norway at 1.7 A resolution. J Mol Biol 1994; 243:653-67. [PMID: 7966289 DOI: 10.1016/0022-2836(94)90039-6] [Citation(s) in RCA: 84] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The crystal structure of cytochrome c3 (M(r) 13,000) from Desulfovibrio desulfuricans (118 residues, four heme groups) has been crystallographically refined to 1.7 A resolution using a simulated annealing method, based on the structure-model at 2.5 A resolution, already published. The final R-factor for 10,549 reflections was 0.198 covering the range from 5.5 to 1.7 A resolution. The individual temperature factors were refined for a total of 1059 protein atoms, together with 126 bound solvent molecules. The structure has been analyzed with respect to its detailed conformational properties, secondary structure features, temperature factor behaviour, bound solvent sites and heme geometry and ligation. The characteristic secondary structures of the polypeptide chain of this molecule are one extended alpha-helix, a short beta-strand and 13 reverse turns. The four heme groups are located in different structural environments, all highly exposed to solvent. The particular structural features of the heme environments are compared to the four hemes of the cytochrome c3 from Desulfovibrio vulgaris Miyazaki.
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Affiliation(s)
- M Czjzek
- CNRS-Marseille, Laboratoire de Cristallographie et Cristallisation des Macromolécules Biologiques, URA 1296 Faculté de Médicine-Nord, Marseille, France
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Bertrand P, Asso M, Mbarki O, Camensuli P, More C, Guigliarelli B. Individual redox characteristics and kinetic properties of the hemes in cytochromes c3: new methods of investigation. Biochimie 1994; 76:524-36. [PMID: 7880891 DOI: 10.1016/0300-9084(94)90176-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The elucidation of the role of the four hemes in cytochromes c3 requires several complementary approaches. The measurements and the assignment of the redox potentials resort to magnetic spectroscopies, EPR and NMR, which are able to discriminate the hemes. The origin of the differences between the redox properties of the hemes can be studied by comparing their thermodynamic parameters delta S and delta H, as measured by the temperature dependence of their individual potentials. Lastly, the available data concerning the electron exchange between cytochromes c3 and their redox partners can be analysed through a detailed kinetic model which provides important information on the role of the different hemes.
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Affiliation(s)
- P Bertrand
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Université de Provence, Centre St-Jérome, Marseille, France
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Czjzek M, Payan F, Haser R. Molecular and structural basis of electron transfer in tetra- and octa-heme cytochromes. Biochimie 1994; 76:546-53. [PMID: 7880893 DOI: 10.1016/0300-9084(94)90178-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The first three-dimensional structure of a dimeric, octa-heme cytochrome c3 (M(r) 26000) from Desulfovibrio desulfuricans Norway, established at 2.2 A resolution, is briefly presented and compared to the known 3-D-structures of different C3-type tetraheme cytochromes, in order to contribute to a better understanding of the function of multiheme clusters and of the role of conserved amino acids implicated in possible electron transfer pathways. The dimeric protein crystallizes in the space group P3(1)21 with a = 73.01 A, c = 61.81 A and the asymmetric unit contains one monomer subunit, the dimer being generated by the crystallographic two-fold axis. The 3-D-structure was solved using the molecular replacement method with a model based on the structure of the tetraheme cytochrome c3 (M(r) 13000) from D desulfuricans Norway, presently refined at 1.7 A resolution. The monomeric subunit has the same overall fold as all cytochromes c3 (M(r) 13000). Moreover, the heme core of all examined cytochromes c3 is highly conserved, but differences appear concerning the heme environments and the histidines, axial ligands of the heme-iron atoms.
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Affiliation(s)
- M Czjzek
- Laboratoire de Cristallographie et Cristallisation des Macromolécules Biologiques, URA 1296, CNRS, Marseille, France
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6
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Abstract
C-type cytochromes are classified into two main groups: i) cytochromes which give fast electrochemical responses at the conventional electrodes in the absence of any promoter (eg multi-heme cytochromes c3); ii) cytochromes which need the presence of promoters or the use of modified electrodes to exhibit fast electrochemical responses (eg one-heme mitochondrial cytochrome c). In the latter case, careful design of electrode surface and composition of the solution are required for the attainment of rapid and reversible electron-exchange reactions. Some general considerations are given on the 'electrochemical model'. In particular, binding interactions between the electrode and the protein can take place in a similar manner to that occurring between physiological partner proteins. Electrochemistry when coupled to other physical techniques can give more complete insights in the relationship between the redox properties, structure and function of c-type cytochromes. In particular, in the case of polyheme cytochromes, promising results are expected from the study of site-directed mutagenesis-modified cytochrome c3.
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Affiliation(s)
- P Bianco
- Laboratoire de Chimie et Electrochimie des Complexes, Université de Provence, Marseille, France
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Affiliation(s)
- I B Coutinho
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Portugal
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Salgueiro CA, Turner DL, Santos H, LeGall J, Xavier AV. Assignment of the redox potentials to the four haems in Desulfovibrio vulgaris cytochrome c3 by 2D-NMR. FEBS Lett 1992; 314:155-8. [PMID: 1333991 DOI: 10.1016/0014-5793(92)80963-h] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Using 2D-NMR the four haems of Desulfovibrio vulgaris (Hildenborough) cytochrome c3 within the X-ray structure were fully cross assigned according to their redox potential. The strategy used was based on a complete network of chemical exchange connectivities between the NMR signals obtained for all oxidation levels to the corresponding ones in the fully reduced spectrum [1992, Eur. J. Biochem., in press]. This unequivocal cross-assignment disagrees with earlier results obtained for the similar protein from Desulfovibrio vulgaris (Miyazaki F.).
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Affiliation(s)
- C A Salgueiro
- Centro de Tecnologia Química e Biológica, Oeiras, Portugal
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9
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Site-directed mutagenesis of tetraheme cytochrome c3. Modification of oxidoreduction potentials after heme axial ligand replacement. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)41862-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Coletta M, Catarino T, LeGall J, Xavier AV. A thermodynamic model for the cooperative functional properties of the tetraheme cytochrome c3 from Desulfovibrio gigas. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 202:1101-6. [PMID: 1662600 DOI: 10.1111/j.1432-1033.1991.tb16476.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A thermodynamic model is presented to describe the redox behaviour of the tetraheme cytochrome c3 from Desulfovibrio gigas. This molecule displays different intrinsic redox potentials for the four hemes and during the redox titration process, interactions among different hemes occur, thus altering the values of redox potentials according to which of the hemes are oxidized [Santos, H., Moura, J.J.G., Moura, I., LeGall, J. & Xavier, A.V. (1984) Eur. J. Biochem. 141, 283-296]. This complex cooperative behaviour [Xavier, A.V. (1986) J. Inorg. Biochem. 28, 239-243] has been analyzed here using an I2H4-interaction network [Cornish-Bowden, A. & Koshland, D.E. Jr (1970) J. Biol. Chem. 245, 6241-6250] coupled to a proton-linked equilibrium between two tertiary structures. Such a formalism, which requires a reduced number of parameters, is able to fully account quantitatively for the pH dependence of the NMR redox-titration curves. The 'redox-Bohr' effect is discussed in terms of the available structure and thermodynamic data and a functional mechanism is proposed.
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Affiliation(s)
- M Coletta
- CNR Center for Molecular Biology, University of Rome La Sapienza, Italy
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Moreno C, Campos A, Teixeira M, LeGall J, Montenegro MI, Moura I, van Dijk C, Moura JG. Simulation of the electrochemical behavior of multi-redox systems. Current potential studies on multiheme cytochromes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 202:385-93. [PMID: 1662131 DOI: 10.1111/j.1432-1033.1991.tb16386.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The direct unmediated electrochemical response of the tetrahemic cytochrome c3 isolated from sulfate reducers Desulfovibrio baculatus (DSM 1743) and D. vulgaris (strain Hildenborough), was evaluated using different electrode systems [graphite (edge cut), gold, semiconductor (InO2) and mercury)] and different electrochemical methods (cyclic voltammetry and differential pulse voltammetry). A computer program was developed for the theoretical simulation of a complete cyclic voltammetry curve, based on the method proposed by Nicholson and Shain [Nicholson, R.S. & Shain, I. (1964) Anal. Chem. 36, 706-723], using the Gauss-Legendre method for calculation of the integral equations. The experimental data obtained for this multi-redox center protein was deconvoluted in to the four redox components using theoretically generated cyclic voltammetry curves and the four mid-point reduction potentials determined. The pH dependence of the four reduction potentials was evaluated using the deconvolution method described.
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Affiliation(s)
- C Moreno
- Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Portugal
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Park JS, Kano K, Niki K, Akutsu H. Full assignment of heme redox potentials of cytochrome c3 of D. vulgaris Miyazaki F by 1H-NMR. FEBS Lett 1991; 285:149-51. [PMID: 1648512 DOI: 10.1016/0014-5793(91)80746-p] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Site-specific heme assignment of the 1H-NMR spectrum of cytochrome c3 of D. vulgaris Miyazaki F, a tetraheme protein, was established. The major reduction of the heme turned out to take place in the order of hemes I, III, IV and II (numbering in the crystal structure). The hemes with the smallest and greatest solvent accessibility were reduced at the highest and lowest potentials on average, respectively. A cooperative interheme interaction was attributed to a pair of the closest hemes, namely, hemes III and IV. This assignment can provide the physiochemical basis for the elucidation of electron transfer of this protein.
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Affiliation(s)
- J S Park
- Department of Physical Chemistry, Faculty of Engineering, Yokohoma National University, Japan
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Dolla A, Leroy G, Guerlesquin F, Bruschi M. Identification of the site of interaction between cytochrome c3 and ferredoxin using peptide mapping of the cross-linked complex. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1058:171-7. [PMID: 1646631 DOI: 10.1016/s0005-2728(05)80234-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Structural studies carried out on a cross-linked complex between cytochrome c3 and ferredoxin I, both isolated from Desulfovibrio desulfuricans Norway, allowed the identification of the site of interaction between the two redox proteins. Staphylococcus aureus proteinase and chymotrypsin digestions led to characterization of peptides containing both cytochrome c3 and ferredoxin sequences. The cytochrome c3 sequences involved in the three isolated cross-linked peptides contained several lysine residues localized around the heme 4 crevice. This analysis stressed the peculiar role of lysines 100, 101, 103, 104 and 113, which could be considered as major cross-link sites, as opposed to the lysines 75, 79 and 82, which could be considered as minor cross-link sites. One cross-linked peptide, containing two ferredoxin sequences joined to one cytochrome c3 sequence, had been isolated, suggesting the possibility of more than one cross-link per covalent complex. All these results led to the identification of heme 4 of cytochrome c3 as the site of interaction for the ferredoxin I. This study confirms the proposal that could be deduced from the hypothetical structure of the complex built by computer graphics modelling (Cambillau, C., Frey, M., Mosse, J., Guerlesquin, F. and Bruschi, M. (1988) Proteins: struct., funct. genet. 4, 63-70).
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Affiliation(s)
- A Dolla
- Laboratoire de Chimie Bactérienne du CNRS, Marseille, France
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Dolla A, Guerlesquin F, Bruschi M, Haser R. Ferredoxin electron transfer site on cytochrome c3. Structural hypothesis of an intramolecular electron transfer pathway within a tetra-heme cytochrome. J Mol Recognit 1991; 4:27-33. [PMID: 1657066 DOI: 10.1002/jmr.300040105] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To specify electron exchanges involving Desulfovibrio desulfuricans Norway tetra-heme cytochrome c3, the chemical modification of arginine 73 residue, was performed. Biochemical and biophysical studies have shown that the modified cytochrome retains its ability to both interact and act as an electron carrier with its redox partners, ferredoxin and hydrogenase. Moreover, the chemical modification effects on the cytochrome c3 1H NMR spectrum were similar to that induced by the presence of ferredoxin. This suggests that arginine 73 is localized on the cytochrome c3 ferredoxin interacting site. The identification of heme 4, the closest heme to arginine 73, as the ferredoxin interacting heme helps us to hypothesize about the role of the three other hemes in the molecule. A structural hypothesis for an intramolecular electron transfer pathway, involving hemes 4, 3 and 1, is proposed on the basis of the crystal structures of D. vulgaris Miyazaki and D. desulfuricans Norway cytochromes c3. The unique role of some structural features (alpha helix, aromatic residues) intervening between the heme groups, is proposed.
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Affiliation(s)
- A Dolla
- Laboratoire de Chimie Bactérienne, Centre National de la Recherche Scientifique, Marseille, France
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Guigliarelli B, Bertrand P, More C, Haser R, Gayda JP. Single-crystal electron paramagnetic resonance study of cytochrome c3 from Desulfovibrio desulfuricans Norway Strain. Assignment of the heme midpoint redox potentials. J Mol Biol 1990; 216:161-6. [PMID: 2172551 DOI: 10.1016/s0022-2836(05)80067-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A single crystal of cytochrome c3 from Desulfovibrio desulfuricans Norway is studied by electron paramagnetic resonance at low temperature. The orientation of the principal axis corresponding to the largest g value is determined for the 12 heme groups in the crystal unit cell. The comparison of these directions to the normals to the heme planes, determined from the crystallographic data at 2.5 A resolution, gives strong evidence for the following assignment of the midpoint redox potentials to the heme groups H1 to H4, defined in the three-dimensional structure: -150 mV is assigned to H3, -300 mV to H4, -330 mV to H1 and -355 mV to H2. This assignment is in agreement with a partial correspondence previously established from an independent study performed on cytochrome c3 in solution.
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Affiliation(s)
- B Guigliarelli
- Laboratoire d'Electronique des Milieux Condensés, URA-CNRS 784, Université de Provence, Centre de St. Jérôme, Marseille, France
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Fan KJ, Akutsu H, Kyogoku Y, Niki K. Estimation of microscopic redox potentials of a tetraheme protein, cytochrome c3 of Desulfovibrio vulgaris, Miyazaki F, and partial assignments of heme groups. Biochemistry 1990; 29:2257-63. [PMID: 2159795 DOI: 10.1021/bi00461a008] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The microscopic formal redox potentials of a tetraheme protein, cytochrome c3 from Desulfovibrio vulgaris, Miyazaki F, were estimated from the chemical shifts of the heme methyl signals in its 1H NMR spectrum. All chemical shifts in the five macroscopic oxidation states were determined for eight of the heme methyl protons by the saturation-transfer method. The electron-distribution probability at each heme in each oxidation state was estimated directly from the chemical shifts. To minimize errors due to interheme pseudocontact contributions, the average electron-distribution probability was used for calculation of the microscopic formal redox potentials. By introducing interacting potentials, 32 parameters were reduced to 10. The 10 parameters were determined analytically from the 9 independent electron-distribution probabilities and 2 macroscopic formal redox potentials. The results showed the presence of a strong positive interaction between a pair of particular hemes. The microscopic formal redox potential changes dramatically with the extent of reduction because of the intramolecular interheme interactions. NMR signals of two hemes were assigned to particular hemes in the crystal structures by nuclear Overhauser effect experiments. The results showed that the hemes with the highest and lowest redox potentials in the one-electron reduction process correspond to hemes I and IV in the crystal structure.
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Affiliation(s)
- K J Fan
- Department of Physical Chemistry, Faculty of Engineering, Yokohama National University, Japan
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Cytochrome c3-ferredoxin I covalent complex: evidence for an intramolecular electron exchange in cytochrome c3. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1989. [DOI: 10.1016/s0005-2728(89)80348-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Meyer TE, Cusanovich MA. Structure, function and distribution of soluble bacterial redox proteins. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 975:1-28. [PMID: 2660909 DOI: 10.1016/s0005-2728(89)80196-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- T E Meyer
- Department of Biochemistry, University of Arizona, Tucson 85721
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Moura I, Teixeira M, Huynh BH, LeGall J, Moura JJ. Assignment of individual heme EPR signals of Desulfovibrio baculatus (strain 9974) tetraheme cytochrome c3. A redox equilibria study. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 176:365-9. [PMID: 2843371 DOI: 10.1111/j.1432-1033.1988.tb14290.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An EPR redox titration was performed on the tetraheme cytochrome c3 isolated from Desulfovibrio baculatus (strain 9974), a sulfate-reducer. Using spectral differences at different poised redox states of the protein, it was possible to individualize the EPR g-values of each of the four hemes and also to determine the mid-point redox potentials of each individual heme: heme 4 (-70 mV) at gmax = 2.93, gmed = 2.26 and gmin = 1.51; heme 3 (-280 mV) at gmax = 3.41; heme 2 (-300 mV) at gmax = 3.05, gmed = 2.24 and gmin = 1.34; and heme 1 (-355 mV) at gmx = 3.18. A previously described multi-redox equilibria model used for the interpretation of NMR data of D. gigas cytochrome c3 [Santos, H., Moura, J.J.G., Moura, I., LeGall, J. & Xavier, A. V. (1984) Eur. J. Biochem. 141, 283-296] is discussed in terms of the EPR results.
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Affiliation(s)
- I Moura
- Centro de Quimica Estrutural Complexo I, UNL, Lisboa, Portugal
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