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2004
Hettmann, T, Siddiqui RA, Frey C, Santos-Silva T, Romao MJ, Diekmann S.  2004.  Mutagenesis study on amino acids around the molybdenum centre of the periplasmic nitrate reductase from Ralstonia eutropha. Biochemical and Biophysical Research Communications. 320:1211-1219., Number 4 AbstractWebsite
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Pauleta, SR, Guerlesquin F, Goodhew CF, Devreese B, Van Beeumen J, Pereira AS, Moura I, Pettigrew GW.  2004.  Paracoccus pantotrophus pseudoazurin is an electron donor to cytochrome c peroxidase. Biochemistry. {43}:{11214-11225}., Number {35}, 1155 16TH ST, NW, WASHINGTON, DC 20036 USA: AMER CHEMICAL SOC Abstract

The gene for pseudoazurin was isolated from Paracoccus pantotrophus LMD 52.44 and expressed in a heterologous system with a yield of 54.3 mg of pure protein per liter of culture. The gene and protein were shown to be identical to those from P. pantotrophus LMD 82.5. The extinction coefficient of the protein was re-evaluated and was found to be 3.00 mM(-1) cm(-1) at 590 nm. It was confirmed that the oxidized protein is in a weak monomer/dimer equilibrium that is ionic- strength-dependent. The pseudoazurin was shown to be a highly active electron donor to cytochrome c peroxidase, and activity showed an ionic strength dependence consistent with an electrostatic interaction. The pseudoazurin has a very large dipole moment, the vector of which is positioned at the putative electron-transfer site, His81, and is conserved in this position across a wide range of blue copper proteins. Binding of the peroxidase to pseudoazurin causes perturbation of a set of NMR resonances associated with residues on the His81 face, including a ring of lysine residues. These lysines are associated with acidic residues just back from the rim, the resonances of which are also affected by binding to the peroxidase. We propose that these acidic residues moderate the electrostatic influence of the lysines and so ensure that specific charge interactions do not form across the interface with the peroxidase.

Dias, JM, Alves T, Bonifacio C, Pereira AS, Trincao J, Bourgeois D, Moura I, Romao MJ.  2004.  Structural basis for the mechanism of Ca2+ activation of the di-heme cytochrome c peroxidase from Pseudomonas nautica 617. Structure. 12:961-973., Number 6 AbstractWebsite
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Helberger, N, Kerényi K, Krings B, Lambers R, Orwat C, Riehm U, van Gompel S, Dufft N.  2004.  {Digital Rights Management and Consumer Acceptability: A Multi-Disciplinary Discussion of Consumer Concerns and Expectations}. , Number 6641: University Library of Munich, Germany Abstract

The INDICARE project – the Informed Dialogue about Consumer Acceptability of DRM Solutions in Europe – has been set up to raise awareness about consumer and user issues of Digital Rights Management (DRM) solutions. One of the main goals of the INDICARE project is to contribute to the consensus-building among multiple players with heterogeneous interests in the digital environment. To promote this process and to contribute to the creation of a common level of understanding is the aim of the present report. It provides an overview of consumer concerns and expectations regarding DRMs, and discusses the findings from a social, legal, technical and business perspective. A general overview of the existing EC initiatives shows that questions of consumer acceptability of DRM have only recently begun to draw wider attention. A review of the relevant statements, studies and reports confirms that awareness of consumer concerns is still at a low level. Five major categories of concerns have been distinguished so far: (1) fair conditions of use and access to digital content, (2) privacy, (3) interoperability, (4) transparency and (5) various aspects of consumer friendliness. From the legal point of view, many of the identified issues go beyond the scope of copyright law, i.e. the field of law where DRM was traditionally discussed. Often they are a matter of general or sector-specific consumer protection law. Furthermore, it is still unclear to what extent technology and an appropriate design of technical solutions can provide an answer to some of the concerns of consumers. One goal of the technical chapter was exactly to highlight some of these technical possibilities. Finally, it is shown that consumer acceptability of DRM is important for the economic success of different business models based on DRM. Fair and responsive DRM design can be a profitable strategy, however DRM-free alternatives do exist too.

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

Timoteo, CG, Tavares P, Goodhew CF, Duarte LC, Jumel K, Girio FMF, Harding S, Pettigrew GW, Moura I.  2003.  Ca2+ and the bacterial peroxidases: the cytochrome c peroxidase from Pseudomonas stutzeri, Jan. Journal of Biological Inorganic Chemistry. 8:29-37., Number 1-2 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.

Timóteo, CG, Tavares P, Goodhew CF, Duarte LC, Jumel K, Girio FMF, Harding S, Pettigrew GW, Moura I.  2003.  Ca2+ and the bacterial peroxidases: the cytochrome c peroxidase from Pseudomonas stutzeri, Feb. JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY. {8}:{29-37}., Number {1-2} Abstract

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.

Carvalho, AL, Dias FMV, Prates JAM, Nagy T, Gilbert HJ, Davies GJ, Ferreira LMA, Romao MJ, Fontes C.  2003.  Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proceedings of the National Academy of Sciences of the United States of America. 100:13809-13814., Number 24 AbstractWebsite
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Bonifácio, C, Cunha CA, Müller A, Timóteo CG, Dias JM, Moura I, Romão MJ.  2003.  Crystallization and preliminary X-ray diffraction analysis of the di-haem cytochrome c peroxidase from Pseudomonas stutzeri. Acta Crystallographica Section D. 59:345-347., Number 2: Munksgaard International Publishers AbstractWebsite
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Bonifacio, C, Cunha CA, Muller A, Timoteo CG, Dias JM, Moura I, Romao MJ.  2003.  Crystallization and preliminary X-ray diffraction analysis of the di-haem cytochrome c peroxidase from Pseudomonas stutzeri. Acta Crystallographica Section D-Biological Crystallography. 59:345-347. AbstractWebsite
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Cunha, CA, Macieira S, Dias JM, Almeida G, Goncalves LL, Costa C, Lampreia J, Huber R, Moura JJG, Moura I, Romao MJ.  2003.  Cytochrome c nitrite reductase from Desulfovibrio desulfuricans ATCC 27774 - The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA). Journal of Biological Chemistry. 278:17455-17465., Number 19 AbstractWebsite
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Roque, A, Lodeiro C, Pina F, Maestri M, Dumas S, Passaniti P, Balzani V.  2003.  Multistate/multifunctional systems. A thermodynamic, kinetic, and photochemical investigation of the 4 '-dimethylaminoflavylium compound. Journal of the American Chemical Society. 125:987-994., Number 4 AbstractWebsite
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Hettmann, T, Siddiqui RA, van Langen J, Frey C, Romao MJ, Diekmann S.  2003.  Mutagenesis study on the role of a lysine residue highly conserved in formate dehydrogenases and periplasmic nitrate reductases. Biochemical and Biophysical Research Communications. 310:40-47., Number 1 AbstractWebsite
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Albelda, MT, Aguilar J, Alves S, Aucejo R, Diaz P, Lodeiro C, Lima JC, Garcia-Espana E, Pina F, Soriano C.  2003.  Potentiometric, NMR, and fluorescence-emission studies on the binding of adenosine 5 '-triphosphate (ATP) by open-chain polyamine receptors containing naphthylmethyl and/or anthrylmethyl groups. Helvetica Chimica Acta. 86:3118-3135., Number 9 Abstract
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2002
Raaijmakers, H, Macieira S, Dias JM, Teixeira S, Bursakov S, Huber R, Moura JJ, Moura I, Romao MJ.  2002.  Gene sequence and the 1.8 A crystal structure of the tungsten-containing formate dehydrogenase from Desulfovibrio gigas, Sep. Structure. 10:1261-72., Number 9 AbstractWebsite

Desulfovibrio gigas formate dehydrogenase is the first representative of a tungsten-containing enzyme from a mesophile that has been structurally characterized. It is a heterodimer of 110 and 24 kDa subunits. The large subunit, homologous to E. coli FDH-H and to D. desulfuricans nitrate reductase, harbors the W site and one [4Fe-4S] center. No small subunit ortholog containing three [4Fe-4S] clusters has been reported. The structural homology with E. coli FDH-H shows that the essential residues (SeCys158, His159, and Arg407) at the active site are conserved. The active site is accessible via a positively charged tunnel, while product release may be facilitated, for H(+) by buried waters and protonable amino acids and for CO(2) through a hydrophobic channel.

Tiago, T, Aureliano M, Duarte RO, Moura JJG.  2002.  Vanadate oligomers interaction with phosphorylated myosin, Nov 15. Inorganica Chimica Acta. 339:317-321. AbstractWebsite

Using a myosin preparation containing endogenous myosin light-chain (LC2) kinase and phosphatase and calmodulin, i.e. near physiological ones, the interaction of vanadate oligomers with phosphorylated myosin was evaluated. Decavanadate or metavanadate solutions (2-15 mM total vanadate) did not prevent the phosphorylation state of the regulatory myosin lightchain, as observed by urea-polyacrylamide gel electrophoresis. The relative order of line broadening upon protein addition, reflecting the interaction of the vanadate oligomers with phosphorylated myosin, was V10 > V-4 > V-1 = 1 whereas, no changes were observed for monomeric vanadate. In the presence of ATP, V-1 signal was shifted upfield 2 ppm and became broadened, while V4 signal became narrowed. Moreover, a significant increase in myosin ATPase inhibition (60%) was observed when decameric vanadate species were present (1.4 mM). It is concluded that, under conditions near physiological ones, decameric vanadate differs from vanadate oligomers present in metavanadate solutions due to its strong interaction with the phosphorylated enzyme and myosin ATPase inhibition. Besides, ATP decreases the affinity of myosin for tetravanadate, induces the interaction with monomeric vanadate, whereas it does not affect decameric vanadate interaction. (C) 2002 Elsevier Science B.V. All rights reserved.

Chen, P, DeBeer George S, Cabrito I, Antholine WE, Moura JJ, Moura I, Hedman B, Hodgson KO, Solomon EI.  2002.  Electronic structure description of the mu(4)-sulfide bridged tetranuclear Cu(Z) center in N(2)O reductase, Feb 6. J Am Chem Soc. 124:744-5., Number 5 AbstractWebsite

Spectroscopy coupled with density functional calculations has been used to define the spin state, oxidation states, spin distribution, and ground state wave function of the mu4-sulfide bridged tetranuclear CuZ cluster of nitrous oxide reductase. Initial insight into the electronic contribution to N2O reduction is developed, which involves a sigma superexchange pathway through the bridging sulfide.

Albelda, MT, Diaz P, Garcia-Espana E, Lima JC, Lodeiro C, de Melo JS, Parola AJ, Pina F, Soriano C.  2002.  Switching from intramolecular energy transfer to intramolecular electron transfer by the action of pH and Zn2+ co-ordination, 2002. Chemical Physics Letters. 353:63-68. AbstractWebsite

Intramolecular electron (eT) and energy transfer (ET) have shown to occur in a covalently linked donor-acceptor (CLDA) system consisting of a naphthalene donor covalently linked through a polyamine chain connector to an anthracene acceptor; the connector has been chosen in order to switch ON or OFF the energy flux as a function of its protonation state as well as by co-ordination to Zn2+. The largest energy transfer efficiency (eta = 0.61) occurs for the fully protonated form (pH < 2), while at pH > 9 (eT) from the lone pairs of the nitrogens to the excited fluorophore takes place, leading to complete quenching of the emission. On the other hand at neutral and basic pH values. coordination of Zn2+ prevents the eT quenching allowing the ET process to occur. (C) 2002 Elsevier Science B.V. All rights reserved.

Viciosa, MT, Nunes AM, Fernandes A, Almeida PL, Godinho MH, Dionísio MD.  2002.  Dielectric studies of the nematic mixture E7 on a hydroxypropylcellulose substrate. Liquid Crystals. 29(3):429-441.Website
Dias, JM, Bonifácio C, Alves T, Moura JJG, Moura I, Romão MJ.  2002.  Crystallization and preliminary X-ray diffraction analysis of two pH-dependent forms of a di-haem cytochrome c peroxidase from Pseudomonas nautica. Acta Crystallographica Section D. 58:697-699., Number 4: Munksgaard International Publishers AbstractWebsite
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Dias, JM, Bonifacio C, Alves T, Moura JJG, Moura I, Romao MJ.  2002.  Crystallization and preliminary X-ray diffraction analysis of two pH-dependent forms of a di-haem cytochrome c peroxidase from Pseudomonas nautica. Acta Crystallographica Section D-Biological Crystallography. 58:697-699. AbstractWebsite
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Raaijmakers, H, Macieira S, Dias JM, Teixeira S, Bursakov S, Huber R, Moura JJG, Moura I, Romao MJ.  2002.  Gene sequence and the 1.8 angstrom crystal structure of the tungsten-containing formate dehydrogenase from Desulfolvibrio gigas. Structure. 10:1261-1272., Number 9 AbstractWebsite
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de Melo, JS, Albelda MT, Diaz P, Garcia-Espana E, Lodeiro C, Alves S, Lima JC, Pina F, Soriano C.  2002.  Ground and excited state properties of polyamine chains bearing two terminal naphthalene units. Journal of the Chemical Society-Perkin Transactions 2. :991-998., Number 5 Abstract
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Pina, F, Lima JC, Lodeiro C, de Melo JS, Diaz P, Albelda MT, Garcia-Espana E.  2002.  Long range electron transfer quenching in polyamine chains bearing a terminal naphthalene unit. Journal of Physical Chemistry a. 106:8207-8212., Number 35 Abstract
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