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2012
Safari, L, Amaro P, Fritzsche S, Santos JP, Tashenov S, Fratini F.  2012.  Relativistic polarization analysis of Rayleigh scattering by atomic hydrogen, Oct. Physical Review A. 86:043405. AbstractWebsite

A relativistic analysis of the polarization properties of light elastically scattered by atomic hydrogen is performed, based on the Dirac equation and second-order perturbation theory. The relativistic atomic states used for the calculations are obtained by making use of the finite basis set method and are expressed in terms of B splines and B polynomials. We introduce two experimental scenarios in which the light is circularly and linearly polarized, respectively. For each of these scenarios, the polarization-dependent angular distribution and the degrees of circular and linear polarization of the scattered light are investigated as a function of scattering angle and photon energy. Analytical expressions are derived for the polarization-dependent angular distribution which can be used for scattering by both hydrogenic as well as many-electron systems. Detailed computations are performed for Rayleigh scattering by atomic hydrogen within the incident photon energy range 0.5 to 5 keV. Particular attention is paid to the effects that arise from higher (nondipole) terms in the expansion of the electron-photon interaction.

Sanz, V, Conde J, Ambrosone A, Hernandez Y, Marchesasno V, Estrada {GG }, Ibarra {MR }, Baptista {PV}, Tian F, Tortiglione C, {de la Fuente} {JM }.  2012.  Multifunctional gold nanoparticles for gene silencing, mar. Abstracts Of Papers Of The American Chemical Society. 243: ACS - American Chemical Society Abstract
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Amaro, P, Schlesser S, Guerra M, Le Bigot E-O, Isac J-M, Travers P, Santos JP, Szabo C, Gumberidze A, Indelicato P.  2012.  Absolute Measurement of the Relativistic Magnetic Dipole Transition Energy in Heliumlike Argon, Jul. Physical Review Letters. 109:043005. AbstractWebsite

The 1s2s 3S1 - 1s2 1S0 relativistic magnetic dipole transition in heliumlike argon, emitted by the plasma of an electron-cyclotron resonance ion source, has been measured using a double-flat crystal x-ray spectrometer. Such a spectrometer, used for the first time on a highly charged ion transition, provides absolute (reference-free) measurements in the x-ray domain. We find a transition energy of 3104.1605(77) eV (2.5 ppm accuracy). This value is the most accurate, reference-free measurement done for such a transition and is in good agreement with recent QED predictions.

Trindade, AC, Canejo JP, Patrício P, Brogueira P, Teixeira PI, Godinho MH.  2012.  Hierarchical wrinkling on elastomeric Janus spheres, 2012. Journal of Materials Chemistry. 22(41):22044-22049.: The Royal Society of Chemistry AbstractWebsite

Hierarchical wrinkling on elastomeric Janus spheres is permanently imprinted by swelling, for different lengths of time, followed by drying the particles in an appropriate solvent. First-order buckling with a spatial periodicity (λ11) of the order of a few microns and hierarchical structures comprising of 2nd order buckling with a spatial periodicity (λ12) of the order of hundreds of nanometers have been obtained. The 2nd order buckling features result from a Grinfeld surface instability due to the diffusion of the solvent and the presence of sol molecules.

Kanudia, A, Boavida D, van den Broek M, Cabal H, Gargiulo M, Gouveia JP, Labriet M, Seixas J, Tosato GC.  2012.  CCS infrastructure development scenarios for the integrated Iberian Peninsula and Morocco energy system, 18-22 November. GHGT_11, Conference session #9 on “CCS technology assessment and system integration”. , Kyoto International Conference Center, Japan
van den Broek, M, Mesquita P, Carneiro J, Silva J, Berghout N, Ramirez A, Gouveia JP, Seixas J, Cabal H, Martinez R, Rimi A, Boavida D, Tosato GC.  2012.  Region specific challenges of a CO2 pipeline infrastructure in the West Mediterranean area - Model results versus stakeholder views., 18-22 November. GHGT_11, on “CCS technology assessment and system integration”. , Kyoto International Conference Center, Japan.
Tana, M, Bianchi A, Sclocco R, Franchin T, Cerutti S, Leal A.  2012.  . Parcel-Based Connectivity Analysis of fMRI Data for the Study of Epileptic Seizure Propagation.. Brain Topography . (DOI:10.1007/s10548-012-0225-2)
Bahubalindruni, Ganga, Tavares, Vitor Grade, Barquinha, Duarte, Candido, Martins, Fortunato, de Oliveira PG.  2012.  Basic analog circuits with a-GIZO thin-film transistors: Modeling and simulation. 2012 International Conference on Synthesis, Modeling, Analysis and Simulation Methods and Applications to Circuit Design (SMACD).
Kuz, S, Heinicke A, Schwichtenhövel D, Mayer MP, Schlick C.  2012.  The Effect of Anthropomorphic Movements of Assembly Robots on Human Prediction. Advances in Ergonomics in Manufacturing. (Karwowski, W., Trzcielinski, S., Eds.).:263-271., Boca Raton, FL: CRC Press Abstract

From a user centered point of view an important basic requirement to enable human-robot cooperation is to achieve conformity with operator's expectations of robot behavior. Therefore, this study focuses on the question, whether anthropomorphic robot movement trajectories can lead to an improved anticipation of the robot's behavior. Based on a virtual simulation environment a robotized assembly cell consisting of the assembly robot and the actual workplace was considered. In order to be able to simulate anthropomorphic movements, the human wrist trajectories of defined pick and place movements were obtained using an infrared motion capture system. The captured data were used to navigate the virtual assembly robot. Within the experiment anthropomorphic and robotic trajectories were distinguished. During the experiment, the main task of the participants was to predict the movement's destination as quickly as possible. Thus, the corresponding reaction value was analyzed to investigate the influence of anthropomorphic robot movements on human prediction in industrial environments.

SCUTARU, G, SANDU F, COCORADA E, PAVALACHE M, Gomes L, Coito F, MÖRSKY-LINDQUIST AK, TALABA D, NEUNDORF V, FEDAK V, Others.  2012.  Konsoliderad rapport ang{\aa}ende användning av VR och fjärrexperiment i utbildning. Abstract

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Bahubalindruni, Ganga, Duarte, Candido, Tavares, Vitor Grade, Barquinha, Martins, Fortunato, de Oliveira PG.  2012.  Multipliers with transparent a-GIZO TFTs using a neural model. 20th Telecommunications Forum (TELFOR). , Belgrade
Tana, M, Bianchi A, Sclocco R, Franchin T, Cerutti S, Leal A.  2012.  Parcel-Based Connectivity Analysis of fMRI Data for the Study of Epileptic Seizure Propagation. Brain Topography (DOI:10.1007/s10548-012-0225-2).
Palma, AS, Liu Y, Zhang Y, Zhang H, Luis AS, Carvalho AL, Gilbert HJ, Boraston A, Fontes CMGA, Chai W, Ten F.  2012.  Designer-oligosaccharide microarrays to decipher ligands in mammalian and prokaryotic glucan-recognition systems. Glycobiology. 22:1612-1613., Number 11 AbstractWebsite
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Timoteo, CG, Guilherme M, Penas D, Folgosa F, Tavares P, Pereira AS.  2012.  Desulfovibrio vulgaris bacterioferritin uses H2O2 as a co-substrate for iron oxidation and reveals DPS-like DNA protection and binding activities. BIOCHEMICAL JOURNAL. {446}:{125-133}., Number {1} Abstract

A gene encoding Bfr (bacterioferritin) was identified and isolated from the genome of Desulfovibrio vulgaris cells, and overexpressed in Escherichia coli. In vitro, H2O2 oxidizes Fe2+ ions at much higher reaction rates than O-2. The H2O2 oxidation of two Fe2+ ions was proven by Mossbauer spectroscopy of rapid freeze-quenched samples. On the basis of the Mossbauer parameters of the intermediate species we propose that D. vulgaris Bfr follows a mineralization mechanism similar to the one reported for vertebrate H-type ferritins subunits, in which a diferrous centre at the ferroxidase site is oxidized to diferric intermediate species, that are subsequently translocated into the inner nanocavity. D. vulgaris recombinant Bfr oxidizes and stores up to 600 iron atoms per protein. This Bfr is able to bind DNA and protect it against hydroxyl radical and DNase deleterious effects. The use of H2O2 as an oxidant, combined with the DNA binding and protection activities, seems to indicate a DPS (DNA-binding protein from starved cells)-like role for D. vulgaris Bfr.

Gawande, MB, Velhinho A, Nogueira ID, Ghumman CAA, Teodoro OMND, Branco PS.  2012.  A facile synthesis of cysteine-ferrite magnetic nanoparticles for application in multicomponent reactions-a sustainable protocol. RSC ADVANCES. 2:6144-6149., Number 15 Abstract
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Coelho, C, Mahro M, Trincao J, Carvalho ATP, Ramos MJ, Terao M, Garattini E, Leimkuehler S, Romao MJ.  2012.  The First Mammalian Aldehyde Oxidase Crystal Structure INSIGHTS INTO SUBSTRATE SPECIFICITY. Journal of Biological Chemistry. 287:40690-40702., Number 48 AbstractWebsite
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Pereira, AS, Timoteo CG, Guilherme M, Folgosa F, Naik SG, Duarte AG, Huynh BH, Tavares P.  2012.  Spectroscopic Evidence for and Characterization of a Trinuclear Ferroxidase Center in Bacterial Ferritin from Desulfovibrio vulgaris Hildenborough. Journal Of The American Chemical Society. {134}:{10822-10832}., Number {26} Abstract

Ferritins are ubiquitous and can be found in practically all organisms that utilize Fe. They are composed of 24 subunits forming a hollow sphere with an inner cavity of similar to 80 angstrom in diameter. The main function of ferritin is to oxidize the cytotoxic Fe2+ ions and store the oxidized Fe in the inner cavity. It has been established that the initial step of rapid oxidation of Fe2+ (ferroxidation) by H-type ferritins, found in vertebrates, occurs at a diiron binding center, termed the ferroxidase center. In bacterial ferritins, however, X-ray crystallographic evidence and amino acid sequence analysis revealed a trinuclear Fe binding center comprising a binuclear Fe binding center (sites A and B), homologous to the ferroxidase center of H-type ferritin, and an adjacent mononuclear Fe binding site (site C). In an effort to obtain further evidence supporting the presence of a trinuclear Fe binding center in bacterial ferritins and to gain information on the states of the iron bound to the trinuclear center, bacterial ferritin from Desulfovibrio vulgaris (DvFtn) and its E130A variant was loaded with substoichiometric amounts of Fe2+, and the products were characterized by Mossbauer and EPR spectroscopy. Four distinct Fe species were identified: a paramagnetic diferrous species, a diamagnetic diferrous species, a mixed valence Fe2+Fe3+ species, and a mononuclear Fe2+ species. The latter three species were detected in the wild-type DvFtn, while the paramagnetic diferrous species was detected in the E130A variant. These observations can be rationally explained by the presence of a trinuclear Fe binding center, and the four Fe species can be properly assigned to the three Fe binding sites. Further, our spectroscopic data suggest that (1) the fully occupied trinuclear center supports an all ferrous state, (2) sites B and C are bridged by a mu-OH group forming a diiron subcenter within the trinuclear center, and (3) this subcenter can afford both a mixed valence Fe2+Fe3+ state and a diferrous state. Mechanistic insights provided by these new findings are discussed and a minimal mechanistic scheme involving O-O bond cleavage is proposed.

2011
Folgosa, F, Cordas CM, Santos JA, Pereira AS, Moura JJ, Tavares P, Moura I.  2011.  New spectroscopic and electrochemical insights on a class I superoxide reductase: evidence for an intramolecular electron-transfer pathway, Sep 15. Biochem J. 438:485-94., Number 3 AbstractWebsite

SORs (superoxide reductases) are enzymes involved in bacterial resistance to reactive oxygen species, catalysing the reduction of superoxide anions to hydrogen peroxide. So far three structural classes have been identified. Class I enzymes have two iron-centre-containing domains. Most studies have focused on the catalytic iron site (centre II), yet the role of centre I is poorly understood. The possible roles of this iron site were approached by an integrated study using both classical and fast kinetic measurements, as well as direct electrochemistry. A new heterometallic form of the protein with a zinc-substituted centre I, maintaining the iron active-site centre II, was obtained, resulting in a stable derivative useful for comparison with the native all-iron from. Second-order rate constants for the electron transfer between reduced rubredoxin and the different SOR forms were determined to be 2.8 x 10 M(1) . s(1) and 1.3 x 10 M(1) . s(1) for SORFe(IIII)-Fe(II) and for SORFe(IIII)-Fe(III) forms respectively, and 3.2 x 10 M(1) . s(1) for the SORZn(II)-Fe(III) form. The results obtained seem to indicate that centre I transfers electrons from the putative physiological donor rubredoxin to the catalytic active iron site (intramolecular process). In addition, electrochemical results show that conformational changes are associated with the redox state of centre I, which may enable a faster catalytic response towards superoxide anion. The apparent rate constants calculated for the SOR-mediated electron transfer also support this observation.

Timoteo, CG, Pereira AS, Martins CE, Naik SG, Duarte AG, Moura JJ, Tavares P, Huynh BH, Moura I.  2011.  Low-spin heme b(3) in the catalytic center of nitric oxide reductase from Pseudomonas nautica, May 24. Biochemistry. 50:4251-62., Number 20 AbstractWebsite

Respiratory nitric oxide reductase (NOR) was purified from membrane extract of Pseudomonas (Ps.) nautica cells to homogeneity as judged by polyacrylamide gel electrophoresis. The purified protein is a heterodimer with subunits of molecular masses of 54 and 18 kDa. The gene encoding both subunits was cloned and sequenced. The amino acid sequence shows strong homology with enzymes of the cNOR class. Iron/heme determinations show that one heme c is present in the small subunit (NORC) and that approximately two heme b and one non-heme iron are associated with the large subunit (NORB), in agreement with the available data for enzymes of the cNOR class. Mossbauer characterization of the as-purified, ascorbate-reduced, and dithionite-reduced enzyme confirms the presence of three heme groups (the catalytic heme b(3) and the electron transfer heme b and heme c) and one redox-active non-heme Fe (Fe(B)). Consistent with results obtained for other cNORs, heme c and heme b in Ps. nautica cNOR were found to be low-spin while Fe(B) was found to be high-spin. Unexpectedly, as opposed to the presumed high-spin state for heme b(3), the Mossbauer data demonstrate unambiguously that heme b(3) is, in fact, low-spin in both ferric and ferrous states, suggesting that heme b(3) is six-coordinated regardless of its oxidation state. EPR spectroscopic measurements of the as-purified enzyme show resonances at the g approximately 6 and g approximately 2-3 regions very similar to those reported previously for other cNORs. The signals at g = 3.60, 2.99, 2.26, and 1.43 are attributed to the two charge-transfer low-spin ferric heme c and heme b. Previously, resonances at the g approximately 6 region were assigned to a small quantity of uncoupled high-spin Fe(III) heme b(3). This assignment is now questionable because heme b(3) is low-spin. On the basis of our spectroscopic data, we argue that the g = 6.34 signal is likely arising from a spin-spin coupled binuclear center comprising the low-spin Fe(III) heme b(3) and the high-spin Fe(B)(III). Activity assays performed under various reducing conditions indicate that heme b(3) has to be reduced for the enzyme to be active. But, from an energetic point of view, the formation of a ferrous heme-NO as an initial reaction intermediate for NO reduction is disfavored because heme [FeNO](7) is a stable product. We suspect that the presence of a sixth ligand in the Fe(II)-heme b(3) may weaken its affinity for NO and thus promotes, in the first catalytic step, binding of NO at the Fe(B)(II) site. The function of heme b(3) would then be to orient the Fe(B)-bound NO molecules for the formation of the N-N bond and to provide reducing equivalents for NO reduction.

Coelho, C, Gonzalez PJ, Moura JG, Moura I, Trincao J, Joao Romao M.  2011.  The crystal structure of Cupriavidus necator nitrate reductase in oxidized and partially reduced states, May 20. J Mol Biol. 408:932-48., Number 5 AbstractWebsite

The periplasmic nitrate reductase (NapAB) from Cupriavidus necator is a heterodimeric protein that belongs to the dimethyl sulfoxide reductase family of mononuclear Mo-containing enzymes and catalyzes the reduction of nitrate to nitrite. The protein comprises a large catalytic subunit (NapA, 91 kDa) containing the molybdenum active site plus one [4Fe-4S] cluster, as well as a small subunit (NapB, 17 kDa), which is a diheme c-type cytochrome involved in electron transfer. Crystals of the oxidized form of the enzyme diffracted beyond 1.5 A at the European Synchrotron Radiation Facility. This is the highest resolution reported to date for a nitrate reductase, providing true atomic details of the protein active center, and this showed further evidence on the molybdenum coordination sphere, corroborating previous data on the related Desulfovibrio desulfuricans NapA. The molybdenum atom is bound to a total of six sulfur atoms, with no oxygen ligands or water molecules in the vicinity. In the present work, we were also able to prepare partially reduced crystals that revealed two alternate conformations of the Mo-coordinating cysteine. This crystal form was obtained by soaking dithionite into crystals grown in the presence of the ionic liquid [C(4)mim]Cl(-). In addition, UV-Vis and EPR spectroscopy studies showed that the periplasmic nitrate reductase from C. necator might work at unexpectedly high redox potentials when compared to all periplasmic nitrate reductases studied to date.

Mukhopadhyay, A, Kladova AV, Bursakov SA, Gavel OY, Calvete JJ, Shnyrov VL, Moura I, Moura JJ, Romao MJ, Trincao J.  2011.  Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria, Jan. J Biol Inorg Chem. 16:51-61., Number 1 AbstractWebsite

Adenylate kinases (AK) from Gram-negative bacteria are generally devoid of metal ions in their LID domain. However, three metal ions, zinc, cobalt, and iron, have been found in AK from Gram-negative bacteria. Crystal structures of substrate-free AK from Desulfovibrio gigas with three different metal ions (Zn(2+), Zn-AK; Co(2+), Co-AK; and Fe(2+), Fe-AK) bound in its LID domain have been determined by X-ray crystallography to resolutions 1.8, 2.0, and 3.0 A, respectively. The zinc and iron forms of the enzyme were crystallized in space group I222, whereas the cobalt-form crystals were C2. The presence of the metals was confirmed by calculation of anomalous difference maps and by X-ray fluorescence scans. The work presented here is the first report of a structure of a metal-containing AK from a Gram-negative bacterium. The native enzyme was crystallized, and only zinc was detected in the LID domain. Co-AK and Fe-AK were obtained by overexpressing the protein in Escherichia coli. Zn-AK and Fe-AK crystallized as monomers in the asymmetric unit, whereas Co-AK crystallized as a dimer. Nevertheless, all three crystal structures are very similar to each other, with the same LID domain topology, the only change being the presence of the different metal atoms. In the absence of any substrate, the LID domain of all holoforms of AK was present in a fully open conformational state. Normal mode analysis was performed to predict fluctuations of the LID domain along the catalytic pathway.

Paes de Sousa, PM, Rodrigues D, Timoteo CG, Simoes Goncalves ML, Pettigrew GW, Moura I, Moura JJ, Correia dos Santos MM.  2011.  Analysis of the activation mechanism of Pseudomonas stutzeri cytochrome c peroxidase through an electron transfer chain, Aug. J Biol Inorg Chem. 16:881-8., Number 6 AbstractWebsite

The activation mechanism of Pseudomonas stutzeri cytochrome c peroxidase (CCP) was probed through the mediated electrochemical catalysis by its physiological electron donor, P. stutzeri cytochrome c-551. A comparative study was carried out, by performing assays with the enzyme in the resting oxidized state as well as in the mixed-valence activated form, using cyclic voltammetry and a pyrolytic graphite membrane electrode. In the presence of both the enzyme and hydrogen peroxide, the peak-like signal of cytochrome c-551 is converted into a sigmoidal wave form characteristic of an E(r)C'(i) catalytic mechanism. An intermolecular electron transfer rate constant of (4 +/- 1) x 10(5) M(-1) s(-1) was estimated for both forms of the enzyme, as well as a similar Michaelis-Menten constant. These results show that neither the intermolecular electron transfer nor the catalytic activity is kinetically controlled by the activation mechanism of CCP in the case of the P. stutzeri enzyme. Direct enzyme catalysis using protein film voltammetry was unsuccessful for the analysis of the activation mechanism, since P. stutzeri CCP undergoes an undesirable interaction with the pyrolytic graphite surface. This interaction, previously reported for the Paracoccus pantotrophus CCP, induces the formation of a non-native conformation state of the electron-transferring haem, which has a redox potential 200 mV lower than that of the native state and maintains peroxidatic activity.

Cordas, CM, Wilton J, Cardoso T, Folgosa F, Pereira AS, Tavares P.  2011.  Electrochemical behaviour of Dps-a mini-ferritin, Aug. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS. {40}:{181}., Number {1} Abstract
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Oliveira, J, Petrov V, Parola AJ, Pina F, Azevedo J, Teixeira N, Bras NF, Fernandes PA, Mateus N, Ramos MJ, de Freitas V.  2011.  Chemical Behavior of Methylpyranomalvidin-3-O-glucoside in Aqueous Solution Studied by NMR and UV-Visible Spectroscopy, 2011. Journal of Physical Chemistry B. 115:1538-1545. AbstractWebsite

In the present work, the proton-transfer reactions of the methylpyranomalvidin-3-O-glucoside pigment in water with different pH values was studied by NMR and UV-visible spectroscopies. The results showed four equilibrium forms: the methylpyranomalvidin-3-O-glucoside cation, the neutral quinoidal base, the respective anionic quinoidal base, and a dianionic base unprotonated at the methyl group. According to the NMR data, it seems that for methylpyranomalvidin-3-O-glucoside besides the acid base equilibrium between the pyranoflavylium cation and the neutral quinoidal base, a new species is formed at pD 4.88-6.10. This is corroborated by the appearance of a new set of signals in the NMR spectrum that may be assigned to the formation of hemiketal/cis-chalcone species to a small extent. The two ionization constants (pK(a1) and pK(a2)) obtained by both methods (NMR and UV-visible) for methylpyranomalvidin-3-O-glucoside are in agreement (pK(a1) = 5.17 +/- 0.03; pK(a2) = 8.85 +/- 0.08; and pK(a1) = 4.57 +/- 0.07; pK(a2) = 8.23 +/- 0.04 obtained by NMR and UV-visible spectroscopies, respectively). Moreover, the fully dianionic unprotonated form (at the methyl group) of the methylpyranomalvidin-3-O-glucoside is converted slowly into a new structure that displays a yellow color at basic pH. On the basis of the results obtained through LC-MS and NMR, the proposed structure was found to correspond to the flavonol syringetin-3-glucoside.

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