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Ca2+ and the bacterial peroxidases: the cytochrome c peroxidase from Pseudomonas stutzeri, Timoteo, C. G., Tavares P., Goodhew C. F., Duarte L. C., Jumel K., Girio F. M. F., Harding S., Pettigrew G. W., and Moura I. , Journal of Biological Inorganic Chemistry, Jan, Volume 8, Number 1-2, p.29-37, (2003) AbstractWebsite

The production of cytochrome c peroxidase (CCP) from Pseudomonas (Ps.) stutzeri (ATCC 11607) was optimized by adjusting the composition of the growth medium and aeration of the culture. The protein was isolated and characterized biochemically and spectroscopically in the oxidized and mixed valence forms. The activity of Ps. stutzeri CCP was studied using two different ferrocytochromes as electron donors: Ps. stutzeri cytochrome C-551 (the physiological electron donor) and horse heart cytochrome c. These electron donors interact differently with Ps. stutzeri CCP, exhibiting different ionic strength dependence. The CCP from Paracoccus (Pa.) denitrificans was proposed to have two different Ca2+ binding sites: one usually occupied (site I) and the other either empty or partially occupied in the oxidized enzyme (site II). The Ps. stutzeri enzyme was purified in a form with tightly bound Ca2+. The affinity for Ca2+ in the mixed valence enzyme is so high that Ca2+ returns to it from the EGTA which was added to empty the site in the oxidized enzyme. Molecular mass determination by ultracentrifugation and behavior on gel filtration chromatography have revealed that this CCP is isolated as an active dimer, in contrast to the Pa. denitrificans CCP which requires added Ca2+ for formation of the dimer and also for activation of the enzyme. This is consistent with the proposal that Ca2+ in the bacterial peroxidases influences the monomer/dimer equilibrium and the transition to the active form of the enzyme. Additional Ca2+ does affect both the kinetics of oxidation of horse heart cytochrome c (but not cytochrome C-551) and higher aggregation states of the enzyme. This suggests the presence of a superficial Ca2+ binding site of low affinity.

NMR solution structures of two mutants of desulforedoxin, Goodfellow, B. J., Rusnak F., Moura I., Ascenso C. S., and Moura J. J. , J Inorg Biochem, Jan 1, Volume 93, Number 1-2, p.100-8, (2003) AbstractWebsite

The differences in geometry at the metal centres in the two known [Fe-4S] proteins rubredoxin (Rd) and desulforedoxin (Dx) are postulated to be a result of the different spacing of the C-terminal cysteine pair in the two proteins. In order to address this question, two mutants of Desulfovibrio gigas Dx with modified cysteinyl spacing were prepared and their solution structures have been determined by NMR. Mutant 1 of Dx (DxM1) has a single glycine inserted between the adjacent cysteines (C28 and C29) found in the wild type Dx sequence. Mutant 3 (DxM3) has two amino acid residues, -P-V-, inserted between C28 and C29 in order to mimic the primary sequence found in Rd from Desulfovibrio gigas. The solution structure of DxM1 exists, like wild type Dx, as a dimer in solution although the single glycine inserted between the adjacent cysteines disrupts the stability of the dimer resulting in exchange between a dimer state and a small population of another, probably monomeric, state. For DxM3 the two amino acid residues inserted between the adjacent cysteines results in a monomeric protein that has a global fold near the metal centre very similar to that found in Rd.

Electrochemical studies on small electron transfer proteins using membrane electrodes, dos Santos, M. M. C., de Sousa P. M. P., Goncalves M. L. S., Krippahl L., Moura J. J. G., Lojou E., and Bianco P. , Journal of Electroanalytical Chemistry, Jan 16, Volume 541, p.153-162, (2003) AbstractWebsite

Membrane electrodes (ME) were constructed using gold, glassy carbon and pyrolytic graphite supports and a dialysis membrane, and used to study the electrochemical behavior of small size electron transfer proteins: monohemic cytochrome c(522) from Pseudomonas nautica and cytochrome c(533) as well as rubredoxin from Desulfovibrio vulgaris. Different electrochemical techniques were used including cyclic voltammetry (CV), square wave voltammetry (SW) and differential pulse voltammetry (DP). A direct electrochemical response was obtained in all cases except with rubredoxin where a facilitator was added to the protein solution entrapped between the membrane and the electrode surface. Formal potentials and heterogeneous charge transfer rate constants were determined from the voltammetric data. The influence of the ionic strength and the pH of the medium on the electrochemical response at the ME were analyzed. The benefits from the use of the ME in protein electrochemistry and its role in modulating the redox behavior are analyzed. A critical comparison is presented with data obtained at non-MEs. Finally, the interactions that must be established between the proteins and the electrode surfaces are discussed, thereby modeling molecular interactions that occur in biological systems. (C) 2002 Elsevier Science B.V. All rights reserved.

Modeling protein complexes with BiGGER, Krippahl, L., Moura J. J., and Palma P. N. , Proteins, Jul 1, Volume 52, Number 1, p.19-23, (2003) AbstractWebsite

This article describes the method and results of our participation in the Critical Assessment of PRediction of Interactions (CAPRI) experiment, using the protein docking program BiGGER (Bimolecular complex Generation with Global Evaluation and Ranking) (Palma et al., Proteins 2000;39:372-384). Of five target complexes (CAPRI targets 2, 4, 5, 6, and 7), only one was successfully predicted (target 6), but BiGGER generated reasonable models for targets 4, 5, and 7, which could have been identified if additional biochemical information had been available.

Molecular aspects of denitrification/nitrate dissimilation, Moura, I., Cabrito I., Almeida G., Cunha C., Romao M. J., and Moura J. J. G. , Journal of Inorganic Biochemistry, Jul 15, Volume 96, Number 1, p.195-195, (2003) AbstractWebsite
Tauroursodeoxycholic acid prevents Bax-induced membrane perturbation and cytochrome C release in isolated mitochondria, Rodrigues, C. M., Sola S., Sharpe J. C., Moura J. J., and Steer C. J. , Biochemistry, Mar 18, Volume 42, Number 10, p.3070-80, (2003) AbstractWebsite

Bax is a potent pro-apoptotic member of the Bcl-2 protein family that localizes to the mitochondrial membrane during apoptosis. Tauroursodeoxycholic acid (TUDCA) modulates the apoptotic threshold, in part, by preventing Bax translocation both in vitro and in vivo. The mechanisms by which Bax induces and TUDCA inhibits release of cytochrome c are unclear. We show here that recombinant Bax protein induced cytochrome c release in isolated mitochondria without detectable swelling. Co-incubation with TUDCA prevented efflux of mitochondrial factors and proteolytic processing of caspases in cytosolic extracts. Spectroscopic analyses of mitochondria exposed to Bax revealed increased polarity and fluidity of the membrane lipid core as well as altered protein order, indicative of Bax binding, together with loss of spin-label paramagnetism, characteristic of oxidative damage. TUDCA markedly abrogated the Bax-induced membrane perturbation. In conclusion, our results indicate that Bax protein directly induces cytochrome c release from mitochondria through a mechanism that does not require the permeability transition. Rather, it is accompanied by changes in the organization of membrane lipids and proteins. TUDCA is a potent inhibitor of Bax association with mitochondria. Thus, TUDCA modulates apoptosis by suppressing mitochondrial membrane perturbation through pathways that are also independent of the mitochondrial permeability transition.

Isolation and characterisation of metallothionein from the clam Ruditapes decussatus, Simes, D. C., Bebianno M. J., and Moura J. J. , Aquat Toxicol, May 8, Volume 63, Number 3, p.307-18, (2003) AbstractWebsite

Metallothioneins (MT) were obtained after purification from metal-exposed clams (Ruditapes decussatus) using gel-permeation and ion-exchange chromatography. Four cadmium-metallothioneins (CdMTs) were resolved by ion-exchange chromatography and they all had similar molecular weights, high cadmium content and an absorption spectra indicative of the presence of characteristic Cd-S aggregates. The NH(2)-terminal sequence suggests the presence of at least two class I clam MT isoforms. For the other two putative clam CdMTs isolated, the results of the amino acid determination were inconclusive. One was slightly contaminated and the other one had a blocked NH(2)-terminal. These clam metalothioneins contain glycine, which seems to be a common feature of molluscan MT family and exhibited more similarity to oysters than to mussels. Further investigation on the inducibility of these isoforms will be necessary if clams are to be used as biomarkers of metal exposure.

Cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774. The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA), Cunha, C. A., Macieira S., Dias J. M., Almeida G., Goncalves L. L., Costa C., Lampreia J., Huber R., Moura J. J., Moura I., and Romao M. J. , J Biol Chem, May 9, Volume 278, Number 19, p.17455-65, (2003) AbstractWebsite

The gene encoding cytochrome c nitrite reductase (NrfA) from Desulfovibrio desulfuricans ATCC 27774 was sequenced and the crystal structure of the enzyme was determined to 2.3-A resolution. In comparison with homologous structures, it presents structural differences mainly located at the regions surrounding the putative substrate inlet and product outlet, and includes a well defined second calcium site with octahedral geometry, coordinated to propionates of hemes 3 and 4, and caged by a loop non-existent in the previous structures. The highly negative electrostatic potential in the environment around hemes 3 and 4 suggests that the main role of this calcium ion may not be electrostatic but structural, namely in the stabilization of the conformation of the additional loop that cages it and influences the solvent accessibility of heme 4. The NrfA active site is similar to that of peroxidases with a nearby calcium site at the heme distal side nearly in the same location as occurs in the class II and class III peroxidases. This fact suggests that the calcium ion at the distal side of the active site in the NrfA enzymes may have a similar physiological role to that reported for the peroxidases.

The isolation and characterization of cytochrome c nitrite reductase subunits (NrfA and NrfH) from Desulfovibrio desulfuricans ATCC 27774. Re-evaluation of the spectroscopic data and redox properties, Almeida, M. G., Macieira S., Goncalves L. L., Huber R., Cunha C. A., Romao M. J., Costa C., Lampreia J., Moura J. J., and Moura I. , Eur J Biochem, Oct, Volume 270, Number 19, p.3904-15, (2003) AbstractWebsite

The cytochrome c nitrite reductase is isolated from the membranes of the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 as a heterooligomeric complex composed by two subunits (61 kDa and 19 kDa) containing c-type hemes, encoded by the genes nrfA and nrfH, respectively. The extracted complex has in average a 2NrfA:1NrfH composition. The separation of ccNiR subunits from one another is accomplished by gel filtration chromatography in the presence of SDS. The amino-acid sequence and biochemical subunits characterization show that NrfA contains five hemes and NrfH four hemes. These considerations enabled the revision of a vast amount of existing spectroscopic data on the NrfHA complex that was not originally well interpreted due to the lack of knowledge on the heme content and the oligomeric enzyme status. Based on EPR and Mossbauer parameters and their correlation to structural information recently obtained from X-ray crystallography on the NrfA structure [Cunha, C.A., Macieira, S., Dias, J.M., Almeida, M.G., Goncalves, L.M.L., Costa, C., Lampreia, J., Huber, R., Moura, J.J.G., Moura, I. & Romao, M. (2003) J. Biol. Chem. 278, 17455-17465], we propose the full assignment of midpoint reduction potentials values to the individual hemes. NrfA contains the high-spin catalytic site (-80 mV) as well as a quite unusual high reduction potential (+150 mV)/low-spin bis-His coordinated heme, considered to be the site where electrons enter. In addition, the reassessment of the spectroscopic data allowed the first partial spectroscopic characterization of the NrfH subunit. The four NrfH hemes are all in a low-spin state (S = 1/2). One of them has a gmax at 3.55, characteristic of bis-histidinyl iron ligands in a noncoplanar arrangement, and has a positive reduction potential.

Electron transfer complexes of cytochrome c peroxidase from Paracoccus denitrificans containing more than one cytochrome, Pettigrew, G. W., Pauleta S. R., Goodhew C. F., Cooper A., Nutley M., Jumel K., Harding S. E., Costa C., Krippahl L., Moura I., and Moura J. , Biochemistry, Oct 21, Volume 42, Number 41, p.11968-81, (2003) AbstractWebsite

According to the model proposed in previous papers [Pettigrew, G. W., Prazeres, S., Costa, C., Palma, N., Krippahl, L., and Moura, J. J. (1999) The structure of an electron-transfer complex containing a cytochrome c and a peroxidase, J. Biol. Chem. 274, 11383-11389; Pettigrew, G. W., Goodhew, C. F., Cooper, A., Nutley, M., Jumel, K., and Harding, S. E. (2003) Electron transfer complexes of cytochrome c peroxidase from Paracoccus denitrificans, Biochemistry 42, 2046-2055], cytochrome c peroxidase of Paracoccus denitrificans can accommodate horse cytochrome c and Paracoccus cytochrome c(550) at different sites on its molecular surface. Here we use (1)H NMR spectroscopy, analytical ultracentrifugation, molecular docking simulation, and microcalorimetry to investigate whether these small cytochromes can be accommodated simultaneously in the formation of a ternary complex. The pattern of perturbation of heme methyl and methionine methyl resonances in binary and ternary solutions shows that a ternary complex can be formed, and this is confirmed by the increase in the sedimentation coefficient upon addition of horse cytochrome c to a solution in which cytochrome c(550) fully occupies its binding site on cytochrome c peroxidase. Docking experiments in which favored binary solutions of cytochrome c(550) bound to cytochrome c peroxidase act as targets for horse cytochrome c and the reciprocal experiments in which favored binary solutions of horse cytochrome c bound to cytochrome c peroxidase act as targets for cytochrome c(550) show that the enzyme can accommodate both cytochromes at the same time on adjacent sites. Microcalorimetric titrations are difficult to interpret but are consistent with a weakened binding of horse cytochrome c to a binary complex of cytochrome c peroxidase and cytochrome c(550) and binding of cytochrome c(550) to the cytochrome c peroxidase that is affected little by the presence of horse cytochrome c in the other site. The presence of a substantial capture surface for small cytochromes on the cytochrome c peroxidase has implications for rate enhancement mechanisms which ensure that the two electrons required for re-reduction of the enzyme after reaction with hydrogen peroxide are delivered efficiently.

A further investigation of the cytochrome b5-cytochrome c complex, Banci, L., Bertini I., Felli I. C., Krippahl L., Kubicek K., Moura J. J., and Rosato A. , J Biol Inorg Chem, Sep, Volume 8, Number 7, p.777-86, (2003) AbstractWebsite

The interaction of reduced rabbit cytochrome b(5) with reduced yeast iso-1 cytochrome c has been studied through the analysis of (1)H-(15)N HSQC spectra, of (15)N longitudinal ( R(1)) and transverse ( R(2)) relaxation rates, and of the solvent exchange rates of protein backbone amides. For the first time, the adduct has been investigated also from the cytochrome c side. The analysis of the NMR data was integrated with docking calculations. The result is that cytochrome b(5) has two negative patches capable of interacting with a single positive surface area of cytochrome c. At low protein concentrations and in equimolar mixture, two different 1:1 adducts are formed. At high concentration and/or with excess cytochrome c, a 2:1 adduct is formed. All the species are in fast exchange on the scale of differences in chemical shift. By comparison with literature data, it appears that the structure of one 1:1 adduct changes with the origin or primary sequence of cytochrome b(5).

Broad-temperature range spectroscopy of the two-centre modular redox metalloprotein Desulfovibrio desulfuricans desulfoferrodoxin, Andersen, N. H., Harnung S. E., Trabjerg I., Moura I., Moura J. J. G., and Ulstrup J. , Dalton Transactions, Sep 7, Number 17, p.3328-3338, (2003) AbstractWebsite

The electronic-vibrational couplings of the two-centre non-heme iron protein Desulfovibrio desulfuricans desulfoferrodoxin (DFx) in three oxidation states, i.e. fully oxidised (grey), half-oxidised (pink), and fully reduced (colourless), have been investigated by variable temperature (VT) UV/VIS, MCD, CD, and EPR spectroscopy. The UV/VIS spectra of grey DFx at room temperature is characterised by broad charge transfer (CT) transitions associated with oxidised centre 1 (495 and 368 nm) and II (335 and 635 nm). The transitions are resolved at 78 K, substantiated by VT-MCD and -CD. The data offer novel information about the electronic-vibrational couplings of the transitions. Multiphonon bandshape analysis discloses strong contributions from both local Fe-S and S-C stretching and solvent/protein modes. A number of transitions are blue- or red-shifted compared with monomeric desulforedoxin, superoxide reductase or dismutase, and cloned Desulfovibrio vulgaris DFx fragments. Conversion from grey to pink DFx is accompanied by drastic electronic-vibrational changes of both centres. The data suggest that electron transfer and optical CT-transitions of DFx are controlled by environmental reorganization in the whole region between the metal centres.

Biossensores: Modernas Ferramentas para Monitorização e Controlo Analítico, Almeida, M. G. , Bol. Biotecnol. , Volume 79, p.12-23, (2004) Abstract
Direct electrochemistry of the Desulfovibrio gigas aldehyde oxidoreductase, Correia dos Santos, M. M., Sousa P. M., Goncalves M. L., Romao M. J., Moura I., and Moura J. J. , Eur J Biochem, Apr, Volume 271, Number 7, p.1329-38, (2004) AbstractWebsite

This work reports on the direct electrochemistry of the Desulfovibrio gigas aldehyde oxidoreductase (DgAOR), a molybdenum enzyme of the xanthine oxidase family that contains three redox-active cofactors: two [2Fe-2S] centers and a molybdopterin cytosine dinucleotide cofactor. The voltammetric behavior of the enzyme was analyzed at gold and carbon (pyrolytic graphite and glassy carbon) electrodes. Two different strategies were used: one with the molecules confined to the electrode surface and a second with DgAOR in solution. In all of the cases studied, electron transfer took place, although different redox reactions were responsible for the voltammetric signal. From a thorough analysis of the voltammetric responses and the structural properties of the molecular surface of DgAOR, the redox reaction at the carbon electrodes could be assigned to the reduction of the more exposed iron cluster, [2Fe-2S] II, whereas reduction of the molybdopterin cofactor occurs at the gold electrode. Voltammetric results in the presence of aldehydes are also reported and discussed.

An efficient poly(pyrrole-viologen)-nitrite reductase biosensor for the mediated detection of nitrite, Da Silva, S., Cosnier S., Almeida M. G., and Moura J. J. G. , Electrochemistry Communications, Apr, Volume 6, Number 4, p.404-408, (2004) AbstractWebsite

A biosensor for nitrite analytical determination was developed using a cytochrome c nitrite reductase (ccNiR) from Desulfovibrio desufuricans ATCC 27774 immobilized and electrically connected on a glassy carbon electrode by entrapment in an electrogencrated poly(pyrrole-viologen) matrix. The modified bioelectrode was studied by cyclic voltammetry and a catalytic current was observed in presence of nitrite. The linear range of the electrode response was 5.4-43.4 muM. The detection limit and the sensitivity were 5.4 muM and 1721 mA M-1 cm(-2), respectively. The K-M(app) value determined from the Lineweaver-Burk plot was 86 muM. The biosensor fully maintained its electroenzymatic activity towards nitrite after four days.. No catalytic response was observed in the presence of nitrate ions while interference from sulfites was considered negligible. Finally, the biosensor composition was optimized in term of monomer-enzyme ratio. (C) 2004 Elsevier B.V. All rights reserved.

Ligand K-edge X-ray absorption spectroscopy and DFT calculations on [Fe3S4]0,+ clusters: delocalization, redox, and effect of the protein environment, Dey, A., Glaser T., Moura J. J., Holm R. H., Hedman B., Hodgson K. O., and Solomon E. I. , J Am Chem Soc, Dec 29, Volume 126, Number 51, p.16868-78, (2004) AbstractWebsite

Ligand K-edge XAS of an [Fe3S4]0 model complex is reported. The pre-edge can be resolved into contributions from the mu(2)S(sulfide), mu(3)S(sulfide), and S(thiolate) ligands. The average ligand-metal bond covalencies obtained from these pre-edges are further distributed between Fe(3+) and Fe(2.5+) components using DFT calculations. The bridging ligand covalency in the [Fe2S2]+ subsite of the [Fe3S4]0 cluster is found to be significantly lower than its value in a reduced [Fe2S2] cluster (38% vs 61%, respectively). This lowered bridging ligand covalency reduces the superexchange coupling parameter J relative to its value in a reduced [Fe2S2]+ site (-146 cm(-1) vs -360 cm(-1), respectively). This decrease in J, along with estimates of the double exchange parameter B and vibronic coupling parameter lambda2/k(-), leads to an S = 2 delocalized ground state in the [Fe3S4]0 cluster. The S K-edge XAS of the protein ferredoxin II (Fd II) from the D. gigas active site shows a decrease in covalency compared to the model complex, in the same oxidation state, which correlates with the number of H-bonding interactions to specific sulfur ligands present in the active site. The changes in ligand-metal bond covalencies upon redox compared with DFT calculations indicate that the redox reaction involves a two-electron change (one-electron ionization plus a spin change of a second electron) with significant electronic relaxation. The presence of the redox inactive Fe(3+) center is found to decrease the barrier of the redox process in the [Fe3S4] cluster due to its strong antiferromagnetic coupling with the redox active Fe2S2 subsite.

Two azurins with unusual redox and spectroscopic properties isolated from the Pseudomonas chlororaphis strains DSM 50083(T) and DSM 50135, Pinho, D., Besson S., Brondino C. D., Pereira E., de Castro B., and Moura I. , Journal of Inorganic Biochemistry, Feb, Volume 98, Number 2, p.276-286, (2004) AbstractWebsite

Two azurins (Az624 and Az626) were isolated from the soluble extract of two strains of Pseudomonas chlororaphis, DSM 50083(T) and DSM 50135, respectively, grown under microaerobic conditions with nitrate as final electron acceptor. The azurins, purified to electrophoretic homogeneity in three chromatographic steps, exhibit several peculiar properties. They have high reduction potentials and lower pI than most azurins described in the literature. As previously observed for Pseudomonas aeruginosa azurin, their reduction potentials are pH-dependent, but the pK values of their oxidized forms are lower, which suggests that deeper structural changes are associated with the oxidation process of these novel azurins. A hitherto undescribed pH-dependence of the diffusion coefficient was observed in Az624, that could be caused either by conformational changes, or by the formation of supramolecular aggregates associated with a protonation process. Both azurins exhibit axial X-band electron paramagnetic resonance spectra in frozen solution showing a typical hyperfine with the copper nucleus (I = 3/2) and a well-resolved superhyperfine structure with two equivalent N-14 nucleus (I = 1), which is not usually observed for azurins from other species. (C) 2003 Elsevier Inc. All rights reserved.

Structural stability of adenylate kinase from the sulfate-reducing bacteria Desulfovibrio gigas, Gavel, O. Y., Bursakov S. A., Pina D. G., Zhadan G. G., Moura J. J., Moura I., and Shnyrov V. L. , Biophys Chem, Jul 1, Volume 110, Number 1-2, p.83-92, (2004) AbstractWebsite

A novel adenylate kinase (AK) has recently been purified from Desulfovibrio gigas and characterized as a Co(2+)/Zn(2+)-containing enzyme: this is an unusual characteristic for AKs from Gram-negative bacteria, in which these enzymes are normally devoid of metals. Here, we studied the conformational stability of holo- and apo-AK as a function of temperature by differential scanning calorimetry (DSC), circular dichroism (CD), and intrinsic fluorescence spectroscopy. The thermal unfolding of AK is a cooperative two-state process, and is sufficiently reversible in the 9-11 pH range, that can be correctly interpreted in terms of a simple two-state thermodynamic model. The spectral parameters as monitored by ellipticity changes in the CD spectra of the enzyme as well as the decrease in tryptophan intensity emission upon heating were seen to be good complements to the highly sensitive but integral DSC-method.

X-ray crystal structure and EPR spectra of "arsenite-inhibited" Desulfovibriogigas aldehyde dehydrogenase: a member of the xanthine oxidase family, Boer, D. R., Thapper A., Brondino C. D., Romao M. J., and Moura J. J. , J Am Chem Soc, Jul 21, Volume 126, Number 28, p.8614-5, (2004) AbstractWebsite

X-ray crystallography has been used to determine the structure of arsenite-inhibited aldehyde dehydrogenase from Desulfovibrio gigas, a member of the xanthine oxidase family of mononuclear molybdenum enzymes. The structure shows an AsO3 moiety bound to the molybdenum atom of the active site through one of the oxygen atoms. A reduced sample of arsenite-inhibited aldehyde dehydrogenase has a Mo(V) signal that shows anisotropic hyperfine and quadrupole coupling to one arsenic atom. This signal has a strong resemblance with a previously reported signal for arsenite-inhibited xanthine oxidase.

Copper-containing nitrite reductase from Pseudomonas chlororaphis DSM 50135 - Evidence for modulation of the rate of intramolecular electron transfer through nitrite binding to the type 2 copper center, Pinho, D., Besson S., Brondino C. D., de Castro B., and Moura I. , European Journal of Biochemistry, Jun, Volume 271, Number 12, p.2361-2369, (2004) AbstractWebsite

The nitrite reductase (Nir) isolated from Pseudomonas chlororaphis DSM 50135 is a blue enzyme, with type 1 and type 2 copper centers, as in all copper-containing Nirs described so far. For the first time, a direct determination of the reduction potentials of both copper centers in a Cu-Nir was performed: type 2 copper (T2Cu), 172 mV and type 1 copper (T1Cu), 298 mV at pH 7.6. Although the obtained values seem to be inconsistent with the established electron-transfer mechanism, EPR data indicate that the binding of nitrite to the T2Cu center increases its potential, favoring the electron-transfer process. Analysis of the EPR spectrum of the turnover form of the enzyme also suggests that the electron-transfer process between T1Cu and T2Cu is the fastest of the three redox processes involved in the catalysis: (a) reduction of T1Cu; (b) oxidation of T1Cu by T2Cu; and (c) reoxidation of T2Cu by NO2-. Electrochemical experiments show that azurin from the same organism can donate electrons to this enzyme.

Structural basis for the mechanism of Ca2+ activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617, Dias, J. M., Alves T., Bonifacio C., Pereira A. S., Trincao J., Bourgeois D., Moura I., and Romao M. J. , Structure, Jun, Volume 12, Number 6, p.961-973, (2004) AbstractWebsite

Cytochrome c peroxidase (CCP) catalyses the reduction of H2O2 to H2O, an important step in the cellular detoxification process. The crystal structure of the di-heme CCP from Pseudomonas nautica 617 was obtained in two different conformations in a redox state with the electron transfer heme reduced. Form IN, obtained at pH 4.0, does not contain Ca2+ and was refined at 2.2 Angstrom resolution. This inactive form presents a closed conformation where the peroxidatic heme adopts a six-ligand coordination, hindering the peroxidatic reaction from taking place. Form OUT is Ca2+ dependent and was crystallized at pH 5.3 and refined at 2.4 Angstrom resolution. This active form shows an open conformation, with release of the distal histidine (His71) ligand, providing peroxide access to the active site. This is the first time that the active and inactive states are reported for a di-heme peroxidase.

Incorporation of either molybdenum or tungsten into formate dehydrogenase from Desulfovibrio alaskensis NCIMB 13491; EPR assignment of the proximal iron-sulfur cluster to the pterin cofactor in formate dehydrogenases from sulfate-reducing bacteria, Brondino, C. D., Passeggi M. C., Caldeira J., Almendra M. J., Feio M. J., Moura J. J., and Moura I. , J Biol Inorg Chem, Mar, Volume 9, Number 2, p.145-51, (2004) AbstractWebsite

We report the characterization of the molecular properties and EPR studies of a new formate dehydrogenase (FDH) from the sulfate-reducing organism Desulfovibrio alaskensis NCIMB 13491. FDHs are enzymes that catalyze the two-electron oxidation of formate to carbon dioxide in several aerobic and anaerobic organisms. D. alaskensis FDH is a heterodimeric protein with a molecular weight of 126+/-2 kDa composed of two subunits, alpha=93+/-3 kDa and beta=32+/-2 kDa, which contains 6+/-1 Fe/molecule, 0.4+/-0.1 Mo/molecule, 0.3+/-0.1 W/molecule, and 1.3+/-0.1 guanine monophosphate nucleotides. The UV-vis absorption spectrum of D. alaskensis FDH is typical of an iron-sulfur protein with a broad band around 400 nm. Variable-temperature EPR studies performed on reduced samples of D. alaskensis FDH showed the presence of signals associated with the different paramagnetic centers of D. alaskensis FDH. Three rhombic signals having g-values and relaxation behavior characteristic of [4Fe-4S] clusters were observed in the 5-40 K temperature range. Two EPR signals with all the g-values less than two, which accounted for less than 0.1 spin/protein, typical of mononuclear Mo(V) and W(V), respectively, were observed. The signal associated with the W(V) ion has a larger deviation from the free electron g-value, as expected for tungsten in a d(1) configuration, albeit with an unusual relaxation behavior. The EPR parameters of the Mo(V) signal are within the range of values typically found for the slow-type signal observed in several Mo-containing proteins belonging to the xanthine oxidase family of enzymes. Mo(V) resonances are split at temperatures below 50 K by magnetic coupling with one of the Fe/S clusters. The analysis of the inter-center magnetic interaction allowed us to assign the EPR-distinguishable iron-sulfur clusters with those seen in the crystal structure of a homologous enzyme.

Antagonists Mo and Cu in a heterometallic cluster present on a novel protein (orange protein) isolated from Desulfovibrio gigas, Bursakov, S. A., Gavel O. Y., Di Rocco G., Lampreia J., Calvete J., Pereira A. S., Moura J. J., and Moura I. , J Inorg Biochem, May, Volume 98, Number 5, p.833-40, (2004) AbstractWebsite

An orange-coloured protein (ORP) isolated from Desulfovibrio gigas, a sulphate reducer, has been previously shown by extended X-ray absorption fine structure (EXAFS) to contain a novel mixed-metal sulphide cluster of the type [S(2)MoS(2)CuS(2)MoS(2)] [J. Am. Chem. Soc. 122 (2000) 8321]. We report here the purification and the biochemical/spectroscopic characterisation of this novel protein. ORP is a soluble monomeric protein (11.8 kDa). The cluster is non-covalently bound to the polypeptide chain. The presence of a MoS(4)(2-) moiety in the structure of the cofactor contributes with a quite characteristic UV-Vis spectra, exhibiting an orange colour, with intense absorption peaks at 480 and 338 nm. Pure ORP reveals an Abs(480)/Abs(338) ratio of 0.535. The gene sequence coding for ORP as well as the amino acid sequence was determined. The putative biological function of ORP is discussed.

Crystallization and preliminary X-ray diffraction analysis of the 16-haem cytochrome of Desulfovibrio gigas, Santos-Silva, T., Diasa J. M., Bourenkov G., Bartunik H., Moura I., and Romao M. J. , Acta Crystallographica Section D-Biological Crystallography, May, Volume 60, p.968-970, (2004) AbstractWebsite

High-molecular-weight cytochromes (Hmcs) belong to a large family of multihaem cytochromes in sulfate-reducing bacteria. HmcA is the first cytochrome reported to have 16 c-type haems arranged in its polypeptide chain. The function of this cytochrome is still unknown, although it is clear that it belongs to a membrane-bound complex involved in electron transfer from the periplasm to the membrane. HmcA from Desulfovibrio gigas has been purified and successfully crystallized using the hanging-drop vapour-diffusion method. The crystals grew using PEG and zinc acetate as precipitants to maximum dimensions of 0.2 x 0.2 x 0.2 mm in an orthorhombic space group, with unit-cell parameters a = 88.9, b = 90.9, c = 83.7 Angstrom. The crystals diffracted to beyond 2.07 Angstrom and a MAD data set was collected.

Decavanadate as a biochemical tool in the elucidation of muscle contraction regulation, Tiago, T., Aureliano M., and Moura J. J. , J Inorg Biochem, Nov, Volume 98, Number 11, p.1902-10, (2004) AbstractWebsite

Recently reported decameric vanadate (V(10)) high affinity binding site in myosin S1, suggests that it can be used as a tool in the muscle contraction regulation. In the present article, it is shown that V(10) species induces myosin S1 cleavage, upon irradiation, at the 23 and 74 kDa sites, the latter being prevented by actin and the former blocked by the presence of ATP. Identical cleavage patterns were found for meta- and decavanadate solutions, indicating that V(10) and tetrameric vanadate (V(4)) have the same binding sites in myosin S1. Concentrations as low as 50 muM decavanadate (5 muM V(10) species) induces 30% of protein cleavage, whereas 500 muM metavanadate is needed to attain the same extent of cleavage. After irradiation, V(10) species is rapidly decomposed, upon protein addition, forming vanadyl (V(4+)) species during the process. It was also observed by NMR line broadening experiments that, V(10) competes with V(4) for the myosin S1 binding sites, having a higher affinity. In addition, V(4) interaction with myosin S1 is highly affected by the products release during ATP hydrolysis in the presence or absence of actin, whereas V(10) appears to be affected at a much lower extent. From these results it is proposed that the binding of vanadate oligomers to myosin S1 at the phosphate loop (23 kDa site) is probably the cause of the actin stimulated myosin ATPase inhibition by the prevention of ATP/ADP exchange, and that this interaction is favoured for higher vanadate anions, such as V(10).