EPR determination of interaction redox potentials in a multiheme cytochrome: cytochrome c3 from Desulfovibrio desulfuricans Norway

Very Low-Frequency Broadband Electron Paramagnetic Resonance Spectroscopy of Metalloproteins

A previously developed spectrometer for broadband electron paramagnetic resonance (EPR) spectroscopy of dilute randomly oriented systems has been considerably modified to extend the frequency reach down to the hundred MHz range and to boost concentration sensitivity by 1 to 2 orders of magnitude. The instrument is now suitable for the study of biological systems in particular metalloproteins. As a proof of concept, examples from the class of low-spin ferric hemoproteins are studied in terms of frequency-dependent changes in their EPR spectra. Mono-heme cytochrome c EPR is determined by g-strain over a wide frequency range, whereas a combination of unresolved ligand hyperfine interaction and concentration-dependent intermolecular dipolar interaction becomes dominant at very low frequencies. In the four heme containing cytochrome c₃, g-strain combines with intramolecular dipolar interaction over the full-studied frequency range of 0.23–12.0 GHz. It is concluded that the point-dipole approach is inappropriate to describe magnetic interactions between low-spin ferric heme systems and that a body of literature on redox interactions in multi-heme proteins will be affected by this conclusion.

Analysis of the electrochemistry of hemes with E(m)s spanning 800 mV

The free energy of heme reduction in different proteins is found to vary over more than 18 kcal/mol. It is a challenge to determine how proteins manage to achieve this enormous range of E(m)s with a single type of redox cofactor. Proteins containing 141 unique hemes of a-, b-, and c-type, with bis-His, His-Met, and aquo-His ligation were calculated using Multi-Conformation Continuum Electrostatics (MCCE). The experimental E(m)s range over 800 mV from -350 mV in cytochrome c(3) to 450 mV in cytochrome c peroxidase (vs. SHE). The quantitative analysis of the factors that modulate heme electrochemistry includes the interactions of the heme with its ligands, the solvent, the protein backbone, and sidechains. MCCE calculated E(m)s are in good agreement with measured values. Using no free parameters the slope of the line comparing calculated and experimental E(m)s is 0.73 (R(2) = 0.90), showing the method accounts for 73% of the observed E(m) range. Adding a +160 mV correction to the His-Met c-type hemes yields a slope of 0.97 (R(2) = 0.93). With the correction 65% of the hemes have an absolute error smaller than 60 mV and 92% are within 120 mV. The overview of heme proteins with known structures and E(m)s shows both the lowest and highest potential hemes are c-type, whereas the b-type hemes are found in the middle E(m) range. In solution, bis-His ligation lowers the E(m) by approximately 205 mV relative to hemes with His-Met ligands. The bis-His, aquo-His, and His-Met ligated b-type hemes all cluster about E(m)s which are approximately 200 mV more positive in protein than in water. In contrast, the low potential bis-His c-type hemes are shifted little from in solution, whereas the high potential His-Met c-type hemes are raised by approximately 300 mV from solution. The analysis shows that no single type of interaction can be identified as the most important in setting heme electrochemistry in proteins. For example, the loss of solvation (reaction field) energy, which raises the E(m), has been suggested to be a major factor in tuning in situ E(m)s. However, the calculated solvation energy vs. experimental E(m) shows a slope of 0.2 and R(2) of 0.5 thus correlates weakly with E(m)s. All other individual interactions show even less correlation with E(m). However the sum of these terms does reproduce the range of observed E(m)s. Therefore, different proteins use different aspects of their structures to modulate the in situ heme electrochemistry. This study also shows that the calculated E(m)s are relatively insensitive to different heme partial charges and to the protein dielectric constant used in the simulation.

Thermodynamic and kinetic characterisation of individual haems in multicentre cytochromes c3

The characterisation of individual centres in multihaem proteins is difficult due to the similarities in the redox and spectroscopic properties of the centres. NMR has been used successfully to distinguish redox centres and allow the determination of the microscopic thermodynamic parameters in several multihaem cytochromes c(3) isolated from different sulphate-reducing bacteria. In this article we show that it is also possible to discriminate the kinetic properties of individual centres in multihaem proteins, if the complete microscopic thermodynamic characterisation is available and the system displays fast intramolecular equilibration in the time scale of the kinetic experiment. The deconvolution of the kinetic traces using a model of thermodynamic control provides a reference rate constant for each haem that does not depend on driving force and can be related to structural factors. The thermodynamic characterisation of three tetrahaem cytochromes and their kinetics of reduction by sodium dithionite are reported in this paper. Thermodynamic and kinetic data were fitted simultaneously to a model to obtain microscopic reduction potentials, haem-haem and haem-proton interacting potentials, and reference rate constants for the haems. The kinetic information obtained for these cytochromes and recently published data for other multihaem cytochromes is discussed with respect to the structural factors that determine the reference rates. The accessibility for the reducing agent seems to play an important role in controlling the kinetic rates, although is clearly not the only factor.

On the Use of Different Dielectric Constants for Computing Individual and Pairwise Terms in Poisson−Boltzmann Studies of Protein Ionization Equilibrium

Poisson-Boltzmann (PB) models are a fast and common tool for studying electrostatic processes in proteins, particularly their ionization equilibrium (protonation and/or reduction), often yielding quite good results when compared with more detailed models. Yet, they are conceptually very simple and necessarily approximate, their empirical character being most evident when it comes to the choice of the dielectric constant assigned to the protein region. The present study analyzes several factors affecting the ability of PB-based methods to model protein ionization equilibrium. We give particular attention to a suggestion made by Warshel and co-workers (e.g., Sham et al. J. Phys. Chem. B 1997, 101, 4458) of using different protein dielectric constants for computing the individual (site) and the pairwise (site-site) terms of the ionization free energies. Our prediction of pK(a) values for several proteins indicates that no advantage is obtained by such a procedure, even for sites that are buried and/or display large pK(a) shifts relative to the solution values. In particular, the present methodology gives the best predictions using a dielectric constant around 20, for shifted/buried and nonshifted/exposed sites alike. The similarities and differences between the PB model and Warshel's PDLD/S model are discussed, as well as the reasons behind their apparently discrepant results. The present PB model is shown to predict also good reduction potentials in redox proteins.

Proton-assisted two-electron transfer in natural variants of tetraheme cytochromes from Desulfomicrobium Sp

The tetraheme cytochrome c3 isolated from Desulfomicrobium baculatum (DSM 1743)(Dsmb) was cloned, and the sequence analysis showed that this cytochrome differs in just three amino acid residues from the cytochrome c3 isolated from Desulfomicrobium norvegicum (Dsmn): (DsmnXXDsmb) Thr-37 --> Ser, Val-45 --> Ala, and Phe-88 --> Tyr. X-ray crystallography was used to determine the structure of cytochrome c3 from Dsmb, showing that it is very similar to the published structure of cytochrome c3 from Dsmn. A detailed thermodynamic and kinetic characterization of these two tetraheme cytochromes c3 was performed by using NMR and visible spectroscopy. The results obtained show that the network of cooperativities between the redox and protonic centers is consistent with a synergetic process to stimulate the hydrogen uptake activity of hydrogenase. This is achieved by increasing the affinity of the cytochrome for protons through binding electrons and, reciprocally, by favoring a concerted two-electron transfer assisted by the binding of proton(s). The data were analyzed within the framework of the differences in the primary and tertiary structures of the two proteins, showing that residue 88, close to heme I, is the main cause for the differences in the microscopic thermodynamic parameters obtained for these two cytochromes c3. This comparison reveals how replacement of a single amino acid can tune the functional properties of energy-transducing proteins, so that they can be optimized to suit the bioenergetic constraints of specific habitats.

Redox Characterization of Geobacter sulfurreducens Cytochrome c7: Physiological Relevance of the Conserved Residue F15 Probed by Site-Specific Mutagenesis

The complete genome sequence of the delta-proteobacterium Geobacter sulfurreducens reveals a large abundance of multiheme cytochromes. Cytochrome c(7), isolated from this metal ion-reducing bacterium, is a triheme periplasmic electron-transfer protein with M(r) 9.6 kDa. This protein is involved in metal ion-reducing pathways and shares 56% sequence identity with a triheme cytochrome isolated from the closely related delta-proteobacterium Desulfuromonas acetoxidans (Dac(7)). In this work, two-dimensional NMR was used to monitor the heme core and the general folding in solution of the G. sulfurreducens triheme cytochrome c(7) (PpcA). NMR signals obtained for the three hemes of PpcA at different stages of oxidation were cross-assigned to the crystal structure [Pokkuluri, P. R., Londer, Y. Y., Duke, N. E. C., Long, W. C., and Schiffer, M. (2004) Biochemistry 43, 849-859] using the complete network of chemical exchange connectivities, and the order in which each heme becomes oxidized was determined at pH 6.0 and 8.2. Redox titrations followed by visible spectroscopy were also performed in order to monitor the macroscopic redox behavior of PpcA. The results obtained showed that PpcA and Dac(7) have different redox properties: (i) the order in which each heme becomes oxidized is different; (ii) the reduction potentials of the heme groups and the global redox behavior of PpcA are pH dependent (redox-Bohr effect) in the physiological pH range, which is not observed with Dac(7). The differences observed in the redox behavior of PpcA and Dac(7) may account for the different functions of these proteins and constitute an excellent example of how homologous proteins can perform different physiological functions. The redox titrations followed by visible spectroscopy of PpcA and two mutants of the conserved residue F15 (PpcAF15Y and PpcAF15W) lead to the conclusion that F15 modulates the redox behavior of PpcA, thus having an important physiological role.

Modeling electron transfer thermodynamics in protein complexes: interaction between two cytochromes c(3)

Redox protein complexes between type I and type II tetraheme cytochromes c(3) from Desulfovibrio vulgaris Hildenborough are here analyzed using theoretical methodologies. Various complexes were generated using rigid-body docking techniques, and the two lowest energy complexes (1 and 2) were relaxed using molecular dynamics simulations with explicit solvent and subjected to further characterization. Complex 1 corresponds to an interaction between hemes I from both cytochromes c(3). Complex 2 corresponds to an interaction between the heme IV from type I and the heme I from type II cytochrome c(3). Binding free energy calculations using molecular mechanics, Poisson-Boltzmann, and surface accessibility methods show that complex 2 is more stable than complex 1. Thermodynamic calculations on complex 2 show that complex formation induces changes in the reduction potential of both cytochromes c(3), but the changes are larger in the type I cytochrome c(3) (the largest one occurring on heme IV, of approximately 80 mV). These changes are sufficient to invert the global titration curves of both cytochromes, generating directionally in electron transfer from type I to type II cytochrome c(3), a phenomenon of obvious thermodynamic origin and consequences, but also with kinetic implications. The existence of processes like this occurring at complex formation may constitute a natural design of efficient redox chains.

EPR spectroscopy: a powerful technique for the structural and functional investigation of metalloproteins

Numerous metal centers in proteins can be prepared in a redox state in which their ground state is paramagnetic. Complementary data provided by EPR, Mössbauer, electron nuclear double resonance, magnetic circular dichroism, and NMR spectroscopies have therefore played a major role in the elucidation of the structure and function of these centers. Among those techniques the most commonly used is certainly EPR spectroscopy. In this article various aspects of the current applications of EPR to the structural and functional study of metalloproteins are presented. They are illustrated by recent studies carried out in our laboratory in the field of metalloenzymes and electron transfer systems. The power of numerical simulation techniques is emphasized throughout this work.

Characterization of DorC from Rhodobacter capsulatus, a c-type cytochrome involved in electron transfer to dimethyl sulfoxide reductase

The dorC gene of the dimethyl sulfoxide respiratory (dor) operon of Rhodobacter capsulatus encodes a pentaheme c-type cytochrome that is involved in electron transfer from ubiquinol to periplasmic dimethyl sulfoxide reductase. DorC was expressed as a C-terminal fusion to an 8-amino acid FLAG epitope and was purified from detergent-solubilized membranes by ion exchange chromatography and immunoaffinity chromatography. The DorC protein had a subunit Mr = 46,000, and pyridine hemochrome analysis indicated that it contained 5 mol heme c/mol DorC polypeptide, as predicted from the derived amino acid sequence of the dorC gene. The reduced form of DorC exhibited visible absorption maxima at 551.5 nm (alpha-band), 522 nm (beta-band), and 419 nm (Soret band). Redox potentiometry of the heme centers of DorC identified five components (n = 1) with midpoint potentials of -34, -128, -184, -185, and -276 mV. Despite the low redox potentials of the heme centers, DorC was reduced by duroquinol and was oxidized by dimethyl sulfoxide reductase.

Ionic strength-dependent physicochemical factors in cytochrome c3 regulating the electron transfer rate

The effect of ionic strength on the macroscopic and microscopic redox potentials and the heme environment of cytochrome c3 from Desulfovibrio vulgaris Miyazaki F have been investigated by NMR and electrochemical methods. The redox potentials of this tetraheme protein are found to be ionic strength-dependent. Especially, the microscopic redox potentials of hemes 2 and 3 at the fourth reduction step increase significantly with increasing ionic strength, which is in contraction to the theoretical expectation. The coordinated imidazole proton signals are unaffected by ionic strength. However, the methyl and propionate proton signals of hemes 1 and 4 showed significant ionic strength dependencies that are distinct from those for hemes 2 and 3. This heme classification is the same as that found in the ionic strength dependencies of the microscopic redox potentials at the fourth reduction step. Furthermore, the effect of ionic strength on the electrostatic potentials at the heme irons has been examined on the theoretical basis. The electrostatic potential at heme 4 changes up to 1 M ionic strength, which was not expected from the observations reported on cytochromes so far. These results are discussed in connection with the reported anomalous ionic strength dependency of the reduction rate of cytochrome c3.

Characterization of the reaction center bound tetraheme cytochrome of Rhodocyclus tenuis

Properties of the tetrahemic reaction center bound cytochrome have been investigated by different techniques. The mid-point potentials of the four hemes were determined by redox titration. The best fit of the data was obtained with a (n = 1) Nernst curve by using the following values of the redox parameters: Em = +420 mV for the two high-potential hemes and Em = +110 and +60 mV for the two low-potential hemes. The mid-point potentials of the two high-potential hemes are the highest reported so far. The spectral properties of the four hemes in the alpha-band have been determined by absorption spectroscopy and measurements of light-induced difference spectra in membranes of Rhodocyclus tenuis. The two high potential hemes present very similar spectra centered at 557 nm. The absorption spectra of the two low-potential hemes are very similar, and their alpha-band centered around 551 nm. Spectral properties at 100 K and the linear dichroism of optical transitions allow the determination of the relative orientations of the hemes with respect to the membrane plane. The orientation patterns thus obtained corresponds to none of the arrangements described so far for reaction center bound cytochromes.

Regulation of the redox order of four hemes by pH in cytochrome c3 from D. vulgaris Miyazaki F

The assignment of 1H-NMR signals of the heme methyl and propionate groups of cytochrome c3 of D. vulgaris Miyazaki F was performed. The heme assignment was revised for hemes 2 and 3 (sequential heme numbering). Namely, heme 4 is mainly reduced at first with hemes 1, 2 and 3 following it in this order. The p2H titration of heme methyl signals in four macroscopic oxidation states was performed in the p2H range of 5.2 to 9.0. While the heme methyl resonances in the fully oxidized state showed just small changes with p2H, most resonances in the intermediate oxidation states revealed clear p2H dependence. In particular, the methyl resonances of heme 1 shifted significantly in the acidic region. Then, the chemical shifts of beta-CH2 (next to the carboxyl group) of all propionate groups in the fully oxidized state were observed at various p2H in the range of 4.5 to 9.0. Only the propionate group at C-13 (IUPAC-IUB nomenclature) of heme 1 showed a clear change in this p2H range, its titration curve being similar to those of the methyl resonances of heme 1 in the intermediate oxidation states. pKa of the propionate group was 5.95 +/- 0.05. Analysis of the microscopic formal redox potentials was carried out for the observations at p2H 5.2, 7.1 and 9.0. The redox potentials of heme 1 showed the most remarkable p2H dependence, resulting in the change of the order of the redox potentials of four hemes. A significant change was also found in the interacting potential between hemes 1 and 2. In the light of the p2H-titration experiments, the propionate at C-13 of heme 1 was identified as the most plausible ionizable group responsible for the p2H dependence of microscopic redox potentials of heme 1 in the acidic region.

Control of the redox potential in c-type cytochromes: importance of the entropic contribution

The enthalpic and entropic components of the redox free energy variation of cytochrome c553 from Desulfovibrio vulgaris Hildenborough and its mutant Y64V, flavocytochrome b2 from Saccharomyces cerevisiae, and the different hemes of cytochromes c3 from Desulfovibrio vulgaris Miyazaki and Desulfovibrio desulfuricans Norway have been determined in 0.1 M Tris-HCl pH 7.0 (7.6 for cytochromes c3) at 25 degrees C by using nonisothermal potentiometric titrations. The set of available experimental data demonstrates that the entropic component plays an important role in the control of the redox potential in c-type and b-type cytochromes. The variation of the entropic component within the class of cytochromes characterized by a positive value of E degrees ' is proposed to be mainly determined by the variation of the exposure of the heme propionates to the solvent. In the case of tetraheme cytochromes c3, the thermodynamic characteristics vary largely among the hemes belonging to the same molecule, which reflects the environmental peculiarities of each heme and also the heme-heme redox interactions. This study substantiates the existence of compensatory effects between large and opposite contributions to E degree ' predicted by all the current theoretical models which are based on electrostatic free energy calculations.

Electron transfer and spectral alpha-band properties of the di-heme protein cytochrome c4 from Pseudomonas stutzeri

Cytochrome c4 is a 190-residue protein active in the aerobic and anaerobic respiration of several bacteria. We have isolated Pseudomonas stutzeri (ATCC no. 11607) cytochrome c4 by an optimized growth procedure following factorial design. The ultraviolet/visible spectra of reduced cytochrome c4 have a composite alpha/beta band which can be resolved into six components. One of these seems to be specific for the high-potential heme group. The kinetics for full oxidation and reduction with the two inorganic redox couples, [Co(terpy)2]2+/3+ and [Co(bipy)3]2+/3+, is formally compatible with either bi- or tri-exponential kinetics. The former would be in line with weak interaction between the heme groups, the latter with notable interaction effects. Arguments in favour of the latter and a cooperative two-electron transfer pattern are given. All phases are approximately proportional to the Co-complex concentration, implying that intramolecular electron transfer in this time range is unlikely. The rate constants are in the range (0.7-80) x 10(4) M-1 s-1 at pH = 7.6 (Tris) and 0.1 M NaCl and very little dependent on the ionic strength in the range 0.1-0.3 M. The reduction potentials could be calculated from the forward and reverse rate constant ratios. The values are 241 +/- 5 and 328 +/- 2 mV (Nernst hydrogen electrode) if bi-exponential kinetics is used and interaction between the heme groups disregarded. The intrinsic microscopic reduction potential values are closer when the tri-exponential, cooperative model is used as this model transfers 30-40 mV to electrostatically dominated interaction potentials. The overall electron transfer pattern can be related to the recently determined crystal structure of the P. stutzeri cytochrome c4.

NMR studies and redox titration of the tetraheme cytochrome c3 from Desulfomicrobium baculatum. Identification of the low-potential heme

The tetraheme cytochromes c3 isolated from two strains of Desulfomicrobium baculatum were studied by monitoring the spectral changes undergone during redox titrations followed by 1H NMR. The evolution of the three-protein intensity signals at low field allowed the partial identification of the heme methyl resonances in the spectrum of the fully oxidized state. The chemical shift variation shown by the protons of the aromatic sidechains as well as of the substituents of the higher-potential heme HIII [Coutinho, I. B., Turner, D. L., LeGall, J. & Xavier, A. V. (1993) Biochem. J. 294, 899-908] yielded the assignment of the lower midpoint redox potential to heme HII in the three-dimensional structure. This cross-assignment is achieved by comparing the chemical shifts of the resonances in the spectra obtained at intermediate oxidation levels with the pseudocontact shifts predicted to arise from the three lower-potential hemes. The cross-assignment for the cytochromes from these two strains is different from that of the cytochromes from Desulfovibrio vulgaris and Desulfovibrio gigas.

Crystal structure of cytochrome c3 from Desulfovibrio desulfuricans Norway at 1.7 A resolution

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.

Individual redox characteristics and kinetic properties of the hemes in cytochromes c3: new methods of investigation

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.

Molecular and structural basis of electron transfer in tetra- and octa-heme cytochromes

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.

Characterization of the structure and redox behaviour of cytochrome c3 from Desulfovibrio baculatus by 1H-nuclear-magnetic-resonance spectroscopy

Complete assignment of the aromatic and haem proton resonances in the cytochromes c3 isolated from Desulfovibrio baculatus strains (Norway 4, DSM 1741) and (DSM 1743) was achieved using one- and two-dimensional 1H n.m.r. Nuclear Overhauser enhancements observed between haem and aromatic resonances and between resonances due to different haems, together with the ring-current contributions to the chemical shifts of haem resonances, support the argument that the haem core architecture is conserved in the various cytochromes c3, and that the X-ray structure of the D. baculatus cytochrome c3 is erroneous. The relative orientation of the haems for both cytochromes was determined directly from n.m.r. data. The n.m.r. structures have a resolution of approximately 0.25 nm and are found to be in close agreement with the X-ray structure from D. vulgaris cytochrome c3. The proton assignments were used to relate the highest potential to a specific haem in the three-dimensional structure by monitoring the chemical-shift variation of several haem resonances throughout redox titrations followed by 1H n.m.r. The haem with highest redox potential is not the same as that in other cytochromes c3.

Mössbauer characterization of the tetraheme cytochrome c3 from Desulfovibrio baculatus (DSM 1743). Spectral deconvolution of the heme components

Mössbauer spectroscopy was used to study the tetraheme cytochrome c3 from Desulfovibrio baculatus (DSM 1743). Samples with different degrees of reduction were prepared using a redoxtitration technique. In the reduced cytochrome c3, all four hemes are reduced and exhibit diamagnetic Mössbauer spectra typical for low-spin ferrous hemes (S = 0). In the oxidized protein, the hemes are low-spin ferric (S = 1/2) and exhibit overlapping magnetic Mössbauer spectra. A method of differential spectroscopy was applied to deconvolute the four overlapping heme spectra and a crystal-field model was used for data analysis. Characteristic Mössbauer spectral components for each heme group are obtained. Hyperfine and crystal-field parameters for all four hemes are determined from these deconvoluted spectra.

A thermodynamic model for the cooperative functional properties of the tetraheme cytochrome c3 from Desulfovibrio gigas

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.

Identification of the site of interaction between cytochrome c3 and ferredoxin using peptide mapping of the cross-linked complex

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).

Purification and characterization of the oxidase from the marine bacterium Pseudomonas nautica 617

The aerobic respiratory system of the hydrocarbonoclastic marine bacterium Pseudomonas nautica 617 ends with a single terminal oxidase. It is a heme-containing membranous protein which has been demonstrated only to reduce molecular oxygen to hydrogen peroxide [Denis, M., Arnaud S. & Malatesta, F. (1989) FEBS Lett. 247, 475-479]. The purification of this oxidase was achieved in a single step through by DEAE-Trisacryl chromatography. SDS/PAGE showed the presence of four subunits. The pI was found to be 4.45 and a Mr of 130,000 was determined by gel filtration. The amino acid composition of the purified terminal oxidase has been determined. About 52% of the residues are hydrophobic, strengthening the membranous nature of this bacterial oxidase. Room temperature optical spectra are typical of heme b with a 560-nm band for the reduced form in the alpha range. The prosthetic group is made of two hemes b, one high-spin (S = 5/2, gl = 5.9, g parallel approximately 2.0), the other low-spin (S = 1/2, gz = 2.94, gy = 2.27). No other metal centre was detected by EPR. The two hemes remained unresolved in optical spectra, even at low temperature, and throughout redox titration. They behaved potentiometrically like a one-electron, single redox couple, with Em = 87 +/- 10 mV at pH 7.2 and 293 K. The purified oxidase did not oxidize ferrocytochrome c, but displayed quinol oxidase activity both with the native quinone (2419 nmol O2.min-1.mg protein-1 and commercially available coenzyme (101.74 nmol O2.min-1.mg protein-1). Exposure of the reduced enzyme to CO induced the collapse of alpha and beta bands as occurred during reoxidation. In contrast, NaCN and NaN3 fully inhibited the oxidase activity. Results are discussed with respect to other purified quinol oxidases.

Structural and functional approach toward a classification of the complex cytochrome c system found in sulfate-reducing bacteria

Following the discovery of the tetraheme cytochrome c3 in the strict anaerobic sulfate-reducing bacteria (Postgate, J.R. (1954) Biochem. J. 59, xi; Ishimoto et al. (1954) Bull. Chem. Soc. Japan 27, 564-565), a variety of c-type cytochromes (and others) have been reported, indicating that the array of heme proteins in these bacteria is complex. We are proposing here a tentative classification of sulfate- (and sulfur-) reducing bacteria cytochromes c based on: number of hemes per monomer, heme axial ligation, heme spin state and primary structures (whole or fragmentary). Different and complementary spectroscopic tools have been used to reveal the structural features of the heme sites.

Ferredoxin electron transfer site on cytochrome c3. Structural hypothesis of an intramolecular electron transfer pathway within a tetra-heme cytochrome

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.

Single-crystal electron paramagnetic resonance study of cytochrome c3 from Desulfovibrio desulfuricans Norway Strain. Assignment of the heme midpoint redox potentials

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.

EPR study of the redox interactions in cytochrome c3 from Desulfovibrio vulgaris Miyazaki

We present a new examination of the EPR redox titration data for the tetraheme cytochrome c3 from Desulfovibrio vulgaris Miyazaki. Our analysis includes the contribution of the interaction potentials between the four redox sites and is based on the model previously developed for the study of cytochrome c3 from Desulfovibrio desulfuricans Norway. We observed, as for D. desulfuricans Norway cytochrome c3, that the conformation of the heme with the lowest redox potential, heme 4, is sensitive to the redox state of the heme with the highest potential, heme 1. However in D. vulgaris Miyazaki cytochrome c3 spectral simulations show that heme 4 is present in two conformational states which interconvert partially when heme 1 is reduced. The sets of redox parameters which satisfy the fitting procedure of the titration curves are in the following domain: -250 mV less than or equal to e41 less than or equal to -220 mV, -325 mV less than or equal to e2 less than or equal to -320 mV, -335 mV less than or equal to e3 less than or equal to -330 mV, -360 mV less than or equal to e4 less than or equal to -355 mV, -5 mV less than or equal to I12 less than or equal to 20 mV, -10 mV less than or equal to I13 less than or equal to 5 mV, -15 mV less than or equal to I23 less than or equal to -5 mV, -15 mV less than or equal to I24 less than or equal to -10 mV, -25 mV, less than or equal to I34 less than or equal to -15 mV. As in D. desulfuricans Norway cytochrome c3 the interactions are moderate. Simple electrostatic considerations suggest that these moderate values could be related to the large accessibility of the hemes to the solvent. Our work does not confirm the existence of a cooperative interaction between heme 2 and heme 3 which has been proposed on the basis of electrochemical measurements.