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2012
Barquinha P., R. M, Fortunato E..  2012.  N-Type Oxide Semiconductor Thin-Film Transistors. GaN and ZnO-based Materials and Devices. :435-476., Berlin: Springer
Batalha, IL, Lowe CR, Roque ACA.  2012.  Platforms for enrichment of phosphorylated proteins and peptides in proteomics. Trends in Biotechnology. 30(2):100-110. AbstractWebsite

Protein phosphorylation is a complex and highly dynamic process involved in numerous biological events. Abnormal phosphorylation is one of the underlying mechanisms for the development of cancer and metabolic disorders. The identification and absolute quantification of specific phospho-signatures can help elucidate protein functions in signaling pathways and facilitate the development of new and personalized diagnostic and therapeutic tools. This review presents a variety of strategies currently utilized for the enrichment of phosphorylated proteins and peptides before mass spectrometry analysis during proteomic studies. The investigation of specific affinity reagents, allied to the integration of different enrichment processes, is triggering the development of more selective, rapid and cost-effective high-throughput automated platforms.

Gomes, PJ, Coelho M, Dionísio M, Ribeiro PA, Raposo M.  2012.  Probing radiation damage by alternated current conductivity as a method to characterize electron hopping conduction in DNA molecules. Applied Physics Letters. 101(12):123702-1-4.Website
Ramos, S, Moura JJG, Aureliano M.  2012.  Recent advances into vanadyl, vanadate and decavanadate interactions with actin. Metallomics. 4(1):16-22., Number 1: The Royal Society of Chemistry
Carvalho, T, Augusto V, Brás AR, Lourenço NMT, Afonso CAM, Barreiros S, Correia NT, Vidinha P, Cabrita EJ, Dias CJ, Dionísio M, Roling B.  2012.  Understanding the Ion Jelly Conductivity Mechanism. The Journal of Physical Chemistry B. 116(9):2664-2676.Website
Branco, RJF, Dias AMGC, Roque ACA.  2012.  Understanding the molecular recognition between antibody fragments and protein A biomimetic ligand. Journal of Chromatography A. 1244:106-115. AbstractWebsite

Affinity chromatography with protein A from Staphylococcus aureus (SpA) is the most widespread and
accepted methodology for antibody capture during the downstream process of antibody manufacturing.
A triazine based ligand (ligand 22/8) was previously developed as an inexpensive and robust alternative
to SpA chromatography (Li et al. [12] and Teng et al. [11]). Despite the experimental success, there is no
structural information on the binding modes of ligand 22/8 to antibodies, namely to Immunoglobulin G
(IgG) molecules and fragments. In this work, we addressed this issue by a molecular docking approach
allied to molecular dynamics simulations. Theoretical results confirmed the preference of the synthetic
ligand to bind IgG through the binding site found in the crystallographic structure of the natural complex
between SpA and the Fc fragment of IgG. Our studies also suggested other unknown “hot-spots” for
specific binding of the affinity ligand at the hinge between VH and CH1 domains of Fab fragment. The best
docking poses were further analysed by molecular dynamics studies at three different protonation states
(pH 3, 7 and 11). The main interactions between ligand 22/8 and the IgG fragments found at pH 7 were
weaker at pH 3 and pH 11 and in these conditions the ligand start losing tight contact with the binding
site, corroborating the experimental evidence for protein elution from the chromatographic adsorbents
at these pH conditions.

Rodriguez, L, Lima JC, Ferrer M, Rossell O, Engeser M.  2012.  3D Au-Ag heterometallic supramolecular cage: Triplet capture by heavy atom effect. Inorganica Chimica Acta. 381:195-202. Abstract
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Rodriguez, L, Ferrer M, Crehuet R, Anglada J, Lima JC.  2012.  Correlation between Photophysical Parameters and Gold-Gold Distances in Gold(I) (4-Pyridyl)ethynyl Complexes. Inorganic Chemistry. 51:7636-7641., Number 14 Abstract
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Ferraz, R, Branco LC, Marrucho IM, Araujo JMM, Rebelo LPN, da Ponte MN, Prudencio C, Noronha JP, Petrovski Z.  2012.  Development of novel ionic liquids based on ampicillin. Medchemcomm. 3:494-497., Number 4 AbstractWebsite
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Bras, JLA, Carvalho AL, Viegas A, Najmudin S, Alves VD, Prates JAM, Ferreira LMA, Romao MJ, Gilbert HJ, Fontes CMGA.  2012.  ESCHERICHIA COLI EXPRESSION, PURIFICATION, CRYSTALLIZATION, AND STRUCTURE DETERMINATION OF BACTERIAL COHESIN-DOCKERIN COMPLEXES. Cellulases. 510(Gilbert, H. J., Ed.).:395-415. 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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Rosa, J, Conde J, de la Fuente JM, Lima JC, Baptista PV.  2012.  Gold-nanobeacons for real-time monitoring of RNA synthesis. Biosensors & Bioelectronics. 36:161-167., Number 1 Abstract
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Kowacz, M, Mukhopadhyay A, Carvalho AL, Esperanca J, Romao MJ, Rebelo LPN.  2012.  Hofmeister effects of ionic liquids in protein crystallization: Direct and water-mediated interactions. Crystengcomm. 14:4912-4921., Number 15 AbstractWebsite

We have performed experiments on the crystallization of two low molecular weight, positively charged proteins, lysozyme and ribonuclease A, using ionic liquids as either crystallization additives or, in particular cases, as precipitating agents. The ionic liquids (ILs) have been ordered according to their salting-in/out ability and the relative position of these ionic liquids in this ranking has been rationalized by considering their hydration properties (positive-negative, hydrophobic-hydrophilic). The ability to screen the effective charge of cationic proteins and aid protein nucleation (salting-out) has been shown to be superior for large polarizable anions with low charge density, negatively hydrated-Cl-, Br-, [SCN](-), methane-[C1SO3](-) and ethanesulfonates [C2SO3](-), than for anions with a relatively stable hydration shell, positively hydrated-lactate [Lac](-), butylsulfonate [C4SO3](-) and acetate [Ac](-). Upon increasing the background salt concentration, where electrostatic interactions are already effectively screened, the ability of the IL ions to stabilize proteins in solution (salting-in) has been shown to increase as the ions are likely to migrate to the non-polar protein surface and lower protein-water interfacial tension. This tendency is enhanced as the focus moves from those ions with positively hydrated hydrophilic compartments (e. g. [Ac](-)) to those with negatively hydrated groups (e. g. [C1SO3](-)) and the prevailing hydrophobic hydration (e. g. [C4SO3](-)). The observed inversion in the relative effect of ILs on protein crystallization with increasing ionic strength of the aqueous media has been interpreted as the differing effects of ion adsorption: charge screening and interfacial tension modification. Moreover, this work can further help in our understanding of the influence of ionic liquids on conformational changes of biomacromolecules in solution. Identification of the specific incorporation sites for choline and acetate ions, localized in two lysozyme crystals grown in pure IL solutions without any buffer or inorganic precipitant, can give us some insight into the role of the ionic liquid ions in protein structure development.

Conde, J, Rosa J, Lima JC, Baptista PV.  2012.  Nanophotonics for Molecular Diagnostics and Therapy Applications. International Journal of Photoenergy. Abstract
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Conde, J, Rosa J, Lima {JC }, Baptista {PV}.  2012.  Nanophotonics for molecular diagnostics and therapy applications. International Journal Of Photoenergy. 2012: Photoenergy Center / Hindawi Publishing Corporation Abstract

Light has always fascinated mankind and since the beginning of recorded history it has been both a subject of research and a tool for investigation of other phenomena. Today, with the advent of nanotechnology, the use of light has reached its own dimension where light-matter interactions take place at wavelength and subwavelength scales and where the physical/chemical nature of nanostructures controls the interactions. This is the field of nanophotonics which allows for the exploration and manipulation of light in and around nanostructures, single molecules, and molecular complexes. What is more is the use of nanophotonics in biomolecular interactionsnanobiophotonicshas prompt for a plethora of molecular diagnostics and therapeutics making use of the remarkable nanoscale properties. In this paper, we shall focus on the uses of nanobiophotonics for molecular diagnostics involving specific sequence characterization of nucleic acids and for gene delivery systems of relevance for therapy strategies. The use of nanobiophotonics for the combined diagnostics/therapeutics (theranostics) will also be addressed, with particular focus on those systems enabling the development of safer, more efficient, and specific platforms. Finally, the translation of nanophotonics for theranostics into the clinical setting will be discussed.

Santos, MFA, Seixas JD, Coelho AC, Mukhopadhyay A, Reis PM, Romao MJ, Romao CC, Santos-Silva T.  2012.  New insights into the chemistry of fac- Ru(CO)(3) (2+) fragments in biologically relevant conditions: The CO releasing activity of Ru(CO)(3)Cl-2(1,3-thiazole) , and the X-ray crystal structure of its adduct with lysozyme. Journal of Inorganic Biochemistry. 117:285-291. AbstractWebsite
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Bras, JLA, Alves VD, Carvalho AL, Najmudin S, Prates JAM, Ferreira LMA, Bolam DN, Romao MJ, Gilbert HJ, Fontes CMGA.  2012.  Novel Clostridium thermocellum Type I Cohesin-Dockerin Complexes Reveal a Single Binding Mode. Journal of Biological Chemistry. 287:44394-44405., Number 53 AbstractWebsite
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Roldao, A, Mellado MCM, Lima JC, Carrondo MJT, Alves PM, Oliveira R.  2012.  On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP. Plos Computational Biology. 8, Number 2 Abstract
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Aveiro, SS, Freire F, Clayton J, Cameloc M, Carvalho AL, Ferreira GC, Romao MJ, Macedo AL, Goodfellow BJ.  2012.  Structural studies of the p22HBP/SOUL family of heme-binding proteins. Febs Journal. 279:458-458. AbstractWebsite
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Carvalho, T, Augusto V, Brás AR, c}o L{\cNMT, Afonso CAM, Barreiros S, Correia NT, Vidinha P, Cabrita EJ, Dion{\'ısio M, Roling B.  2012.  Understanding the Ion Jelly Conductivity Mechanism. Journal of Physical Chemistry B. 116:2664-2676. Abstract

The properties of the light flexible device, ion jelly, which combines gelatin with an ionic liquid (IL) were recently reported being promising to develop safe and highly conductive electrolytes. This article aims for the understanding of the ion jelly conductive mechanism using dielectric relaxation spectroscopy (DRS) in the frequency range 10-1-106 Hz; the study was complemented with differential scanning calorimetry (DSC) and pulse field gradient nuclear magnetic resonance (PFG NMR) spectroscopy. The room temperature ionic liquid 1-butyl-3-methylimmidazolium dicyanamide (BMIMDCA) used as received (1.9% w/w water content) and with 6.6% (w/w) of water content and two ion jellies with two different ratios BMIMDCA/gelatin/water % (w/w), IJ1 (41.1/46.7/12.2) and IJ3 (67.8/25.6/6.6), have been characterized. A glass transition was detected by DSC for all materials allowing for classifying them as glass formers. For the ionic liquid, it was observed that the glass transition temperature decreases with the increase of water content. While in subsequent calorimetric runs crystallization was observed for BMIMDCA with negligible water content, no crystallization was detected for any of the ion jelly materials upon themal cycling. To the dielectric spectra of all tested materials, both dipolar relaxation and conductivity contribute; at the lowest frequencies, electrode and interfacial polarization highly dominate. Conductivity, which manifests much more intensity relative to dipolar reorientations, strongly evidences subdiffusive ion dynamics at high frequencies. From dielectric measures, transport properties as mobility and diffusion coefficients were extracted. Data treatment was carried out in order to deconvolute the average diffusion coefficients estimated from dielectric data in its individual contributions of cations (D+) and anions (D-). The D+ values thus obtained for IJ3, the ion jelly with the highest IL/gelatin ratio, cover a large temperature range up to room temperature and revealed excellent agreement with direct measurements from PFG NMR, obeying to the same VFT equation. For BMIMDCA6.6%water, which has the same water amount as IJ3, the diffusion coefficients were only estimated from DRS measurements over a limited temperature range; however, a single VFT equation describes both DRS and PFG NMR data. Moreover, it was found that the diffusion coefficients and mobility are similar for the ionic liquid and IJ3, which points to a role of both water and gelatin weakening the contact ion pair, facilitating the translational motion of ions and promoting its dissociation; nevertheless, it is conceivable that a critical composition of gelatin that leads to those properties. The VFT temperature dependence observed for the conductivity was found to be determined by a similar dependence of the mobility. Both conductivity and segmental motion revealed to be correlated as inferred by the relatively low values of the decoupling indexes. The obtained results show that ion jelly could be in fact a very promising material to design novel electrolytes for different electrochemical devices, having a performance close to the IL but presenting an additional stability regarding electrical measurements and resistance against crystallization relative to the bulk ionic liquid.

Cândido, AC, Rosa IM.  2012.  {Políticas de Financiamento de I&D em Portugal [R&D financing policies in Portugal]}. , Number 11/2012: Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology Abstract

This paper aims to present the main events over the years on public policies for financing R & D in Portugal, with special focus on the QREN (National Strategic Reference Framework). Between 2007 and 2013, is the QREN which provides the framework to be applied to economic policy in Portugal. The Incentives System for Companies Investment is one of the key instruments of economic promotion policies, particularly in terms of promoting innovation and regional development. The review made shows us that there is not still a systemic and integrated policy innovation in Portugal, but there is a set of instruments that can play a role in this policy and also has missed coherence and coordination between them.

2011
Oliveira, J, Mateus N, Rodriguez-borges JE, Cabrita EJ, Silva AMS, de Freitas V.  2011.  Synthesis of a new pyranoanthocyanin dimer linked through a methyl-methine bridge, JUN 8 2011. Tetrahedron Letters. 52:2957-2960., Number 23 Abstract

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Mota, CS, Valette O, Gonzalez PJ, Brondino CD, Moura JJ, Moura I, Dolla A, Rivas MG.  2011.  Effects of molybdate and tungstate on expression levels and biochemical characteristics of formate dehydrogenases produced by Desulfovibrio alaskensis NCIMB 13491, Jun. J Bacteriol. 193:2917-23., Number 12 AbstractWebsite

Formate dehydrogenases (FDHs) are enzymes that catalyze the formate oxidation to carbon dioxide and that contain either Mo or W in a mononuclear form in the active site. In the present work, the influence of Mo and W salts on the production of FDH by Desulfovibrio alaskensis NCIMB 13491 was studied. Two different FDHs, one containing W (W-FDH) and a second incorporating either Mo or W (Mo/W-FDH), were purified. Both enzymes were isolated from cells grown in a medium supplemented with 1 muM molybdate, whereas only the W-FDH was purified from cells cultured in medium supplemented with 10 muM tungstate. We demonstrated that the genes encoding the Mo/W-FDH are strongly downregulated by W and slightly upregulated by Mo. Metal effects on the expression level of the genes encoding the W-FDH were less significant. Furthermore, the expression levels of the genes encoding proteins involved in molybdate and tungstate transport are downregulated under the experimental conditions evaluated in this work. The molecular and biochemical properties of these enzymes and the selective incorporation of either Mo or W are discussed.

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.

Ivanova, G, Simeonova M, Cabrita EJ, Rangel M.  2011.  NMR Insight into the Supramolecular Structure of Daunorubicin Loaded Polymer Nanoparticles, FEB 10 2011. Journal of Physical Chemistry B. 115:902-909., Number 5 Abstract

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