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2011
Rodriguez, L, Lima JC, Pina F, Cacciapaglia R, Di Stefano S, Ruggi A.  2011.  Photophysical Study of Naphthalenophanes: Evidence of Adduct Formation with Molecular Oxygen. Journal of Physical Chemistry a. 115:123-127., Number 2 Abstract
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Bras, JLA, Correia MAS, Romao MJ, Prates JAM, Fontes CMGA, Najmudin S.  2011.  Purification, crystallization and preliminary X-ray characterization of the pentamodular arabinoxylanase CtXyl5A from Clostridium thermocellum. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 67:833-836. AbstractWebsite
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2010
Barroso, T, Temtem M, Hussain A, Aguiar-Ricardo A, Roque ACA.  2010.  Preparation and characterization of a cellulose affinity membrane for human immunoglobulin G (IgG) purification, feb. Journal of Membrane Science. 348:224–230., Number 1-2 AbstractWebsite

This paper reports the design, preparation and characterization of cellulose affinity membranes for antibody purification using a new methodology. Cellulose membranes were prepared from polymer-ionic liquid solutions, namely 1-butyl-3-methylimidazolium chloride {([BMIM][Cl])}, by the water induced phase inversion process. After functionalization with a synthetic ligand 2-(3-aminophenol)-6-(4-amino-1-naphthol)-4-chloro-s-triazine (ligand 22/8), these were evaluated as affinity supports for human immunoglobulin G {(IgG).} Membranes were characterized in terms of morphology {(SEM)}, porosity (mercury porosimetry), hydrophilicity (contact angle measurement), transport properties (permeability) and mechanical performance {(DMA).} Membranes prepared with varying cellulose contents (5 and 10&\#xa0;wt.% cellulose in ionic liquid solutions) lead to films with different properties. The 10&\#xa0;wt.% cellulose membrane presented enhanced morphological and mechanical properties, however, the morphology of this membrane was significantly altered after ligand coupling. Adsorption isotherms for human {IgG} onto 10&\#xa0;wt.% matrix activated with ligand 22/8 were obtained. Preliminary results showed that the bovine serum albumin {(BSA)}, a model impurity, did not adsorb onto the membrane while up to 6&\#xa0;mg {IgG/g} was bound and 2&\#xa0;mg {IgG/g} recovered.

Pinheiro, {AV}, Parola J}{A, Baptista {PV}, Lima {JC }.  2010.  PH effect on the photochemistry of 4-methylcoumarin phosphate esters: caged-phosphate case study, dec. Journal of Physical Chemistry A. 114:12795–12803., Number 49: ACS - American Chemical Society Abstract

There are numerous reports of coumarin ester derivatives, in particular phosphate esters, as photocleavable cages in biological systems. Despite the comprehensive analysis of the photocleavage mechanism, studies of 4-methylcoumarin caged phosphates and/or nucleotides were always performed at constant pH. In this work, we present the study of the pH effect on the photochemistry of (7-diethylaminocoumarin-4-yl)methyl phosphate (DEACM-P). Fluorescence and photocleavage quantum yields, as well as the fluorescence decay times were measured as a function of the pH. It was found that the pH produces significant changes in the overall photochemical quantum yield of DEACM-P, and the observed changes are complementary to those obtained from the fluorescence quantum yield. Deprotonation of DEACM-HPO4 - to yield DEACM-PO4 2-, produces a decrease in the photochemical quantum yield (from 0.0045 to 0.0003) and an increase in the fluorescence quantum yield (from 0.072 to 0.092). Moreover, from the analysis of the decay times, we have also found that hydroxyl ion is not only relevant, but it is mechanistically involved in the photoreaction of DEACM-HPO4 -.

Pinheiro, AV, Parola AJ, Baptista PV, Lima JC.  2010.  pH Effect on the Photochemistry of 4-Methylcoumarin Phosphate Esters: Caged-Phosphate Case Study, 2010. Journal of Physical Chemistry A. 114:12795-12803. AbstractWebsite

There are numerous reports of coumarin ester derivatives, in particular phosphate esters, as photocleavable cages in biological systems. Despite the comprehensive analysis of the photocleavage mechanism, studies of 4-methylcoumarin caged phosphates and/or nucleotides were always performed at constant pH. In this work. we present the study of the pH effect on the photochemistry of (7-diethylaminocoumarin-4-yl)methyl phosphate (DEACM-P). Fluorescence and photocleavage quantum yields, as well as the fluorescence decay times were measured as a function of the pH. It was found that the pH produces significant changes in the overall photochemical quantum yield of DEACM-P, and the observed changes are complementary to those obtained from the fluorescence quantum yield. Deprotonation of DEACM-HPO(4)(-) to yield DEACM -PO(4)(2-), produces a decrease in the photochemical quantum yield (from 0.0045 to 0.0003) and an increase in the fluorescence quantum yield (from 0.072 to 0.092). Moreover, from the analysis of the decay times, we have also found that hydroxyl ion is not only relevant, but it is mechanistically involved in the photoreaction of DEACM-HPO(4)(-).

Martins, F.  2010.  Princípios Bio-climáticos para o Desenho Urbano no Algarve – Estratégias para as Cidades. Universidade Lusíada. (Amado, Miguel, Ed.)., Lisboa
Catarino, T, Pessanha M, Candia ADG, Gouveia Z, Fernandes AP, Pokkuluri PR, Murgida D, Marti MA, Todorovic S, Salgueiro CA.  2010.  Probing the Chemotaxis Periplasmic Sensor Domains from Geobacter sulfurreducens by Combined Resonance Raman and Molecular Dynamic Approaches: NO and CO Sensing. The Journal of Physical Chemistry B. 114 (34):11251-11260. AbstractWebsite

The periplasmic sensor domains encoded by genes gsu0582 and gsu0935 are part of methyl accepting chemotaxis proteins in the bacterium Geobacter sulfurreducens (Gs). The sensor domains of these proteins contain a heme-c prosthetic group and a PAS-like fold as revealed by their crystal structures. Biophysical studies of the two domains showed that nitric oxide (NO) binds to the heme in both the ferric and ferrous forms, whereas carbon monoxide (CO) binds only to the reduced form. In order to address these exogenous molecules as possible physiological ligands, binding studies and resonance Raman (RR) spectroscopic characterization of the respective CO and NO adducts were performed in this work. In the absence of exogenous ligands, typical RR frequencies of five-coordinated (5c) high-spin and six-coordinated (6c) low-spin species were observed in the oxidized form. In the reduced state, only frequencies corresponding to the latter were detected. In both sensors, CO binding yields 6c low-spin adducts by replacing the endogenous distal ligand. The binding of NO by the two proteins causes partial disruption of the proximal Fe-His bond, as revealed by the RR fingerprint features of 5cFe-NO and 6cNO-Fe-His species. The measured CO and NO dissociation constants of ferrous GSU0582 and GSU0935 sensors reveal that both proteins have high and similar affinity toward these molecules (Kd ≈ 0.04−0.08 μM). On the contrary, in the ferric form, sensor GSU0582 showed a much higher affinity for NO (Kd ≈ 0.3 μM for GSU0582 versus 17 μM for GSU0935). Molecular dynamics calculations revealed a more open heme pocket in GSU0935, which could account for the different affinities for NO. Taken together, spectroscopic data and MD calculations revealed subtle differences in the binding properties and structural features of formed CO and NO adducts, but also indicated a possibility that a (5c) high-spin/(6c) low-spin redox-linked equilibrium could drive the physiological sensing of Gs cells.

Espírito Santo, H.  2010.  Procedimentos para uma certificação da construção sustentável. Faculdade de Ciências e Tecnologia. (Amado, Miguel, Ed.)., Lisbon Abstract

Increasing levels of environmental pollution and destruction of the planet, as
well as the future of societies, have been prominent themes in our time.
Concern about the sustainable future of ecosystems and future generations
brings to each sector of activity the need to define a process of sustainable development
and measures that ought to be implemented.
In the construction sector this is a major issue, since it consumes a great part of
natural resources, and leads to high emissions of pollutants. Likewise, this sector
determines the mode of living of human beings, as well as their comfort and health.
The work herein presented has the purpose to study how, and what systems and
procedures should be implemented to ensure techniques for sustainable construction,
and consequently achieve the principles of sustainable development into its
components: environment, society and economy.
The national reality of professionals will also be referred to, thus contributing to
a practice of sustainable construction, complementary to what currently exists both
national and internationally.
Thus, this study aims to reflect on the importance of certification, systems and
procedures, to ensure compliance of construction with the sustainability goals.

BRITO PALMA, L, VIEIRA COITO F, Sousa Gil P, Neves-Silva R.  2010.  Process control based on PCA models. Emerging Technologies and Factory Automation (ETFA), 2010 IEEE Conference on. :1–4.: IEEE. Abstract

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Szefczyk, B, Cordeiro NM, Franco R, Gomes JANF.  2010.  Properties of the interface between water and self-assembled > monolayers of neutral, anionic and cationic alkane thiols. J. Mol. Struct. THEOCHEM. 946:83-87.
Amado, M, Silva V, Santos C, Moura E.  2010.  Public Participation In Sustainable Urban Planning. International Journal of Human and Social Sciences. 5(2)public_participation_in_sustainable_urban_planning.pdf
Inoue, K, Qian X, Morgado L, Kim B-C, Mester T, Izallalen M, Salgueiro CA, Lovley DR.  2010.  Purification and Characterization of OmcZ, an Outer-Surface, Octaheme c-Type Cytochrome Essential for Optimal Current Production by Geobacter sulfurreducens. Applied and Environmental Microbiology. 76(12):3999-4007. AbstractWebsite

Previous studies have demonstrated that Geobacter sulfurreducens requires the c-type cytochrome OmcZ, which is present in large (OmcZL; 50-kDa) and small (OmcZS; 30-kDa) forms, for optimal current production in microbial fuel cells. This protein was further characterized to aid in understanding its role in current production. Subcellular-localization studies suggested that OmcZS was the predominant extracellular form of OmcZ. N- and C-terminal amino acid sequence analysis of purified OmcZS and molecular weight measurements indicated that OmcZS is a cleaved product of OmcZL retaining all 8 hemes, including 1 heme with the unusual c-type heme-binding motif CX14CH. The purified OmcZS was remarkably thermally stable (thermal-denaturing temperature, 94.2°C). Redox titration analysis revealed that the midpoint reduction potential of OmcZS is approximately −220 mV (versus the standard hydrogen electrode [SHE]) with nonequivalent heme groups that cover a large reduction potential range (−420 to −60 mV). OmcZS transferred electrons in vitro to a diversity of potential extracellular electron acceptors, such as Fe(III) citrate, U(VI), Cr(VI), Au(III), Mn(IV) oxide, and the humic substance analogue anthraquinone-2,6-disulfonate, but not Fe(III) oxide. The biochemical properties and extracellular localization of OmcZ suggest that it is well suited for promoting electron transfer in current-producing biofilms of G. sulfurreducens.

Costa, T, Sergio Seixas de Melo J, Castro CS, Gago S, Pillinger M, Goncalves IS.  2010.  Picosecond Dynamics of Dimer Formation in a Pyrene Labeled Polymer. Journal of Physical Chemistry B. 114:12439-12447., Number 39 AbstractWebsite
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Ferreira, JL, Melo MJ, Ramos AM.  2010.  Poly(vinyl acetate) paints in works of art: A photochemical approach. Part 1. Polymer Degradation and Stability. 95:453-461., Number 4 AbstractWebsite
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BRITO PALMA, L, VIEIRA COITO F, Sousa Gil P, Neves-Silva R.  2010.  Process control based on PCA models. Emerging Technologies and Factory Automation (ETFA), 2010 IEEE Conference on. :1–4.: IEEE Abstract

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Najmudin, S, Pinheiro BA, Prates JAM, Gilbert HJ, Romao MJ, Fontes CMGA.  2010.  Putting an N-terminal end to the Clostridium thermocellum xylanase Xyn10B story: Crystal structure of the CBM22-1-GH10 modules complexed with xylohexaose. Journal of Structural Biology. 172:353-362., Number 3 AbstractWebsite
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2009
Cale, R, Aragao I, Martins H, Cardoso G, Ferreira LM, Branco PS, Bastos LM, de Pinho PG.  2009.  Propofol and metabolites monitoring in serum of patients with induced sedation, SEP 13. TOXICOLOGY LETTERS. 189:S113-S114.: European Soc Toxicol Abstract
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Baía, P.  2009.  Processamento de sinais ECG: Variabilidade da frequência cardíaca, June. (Manuel Ortigueira, Ed.).: FCT-UNL Abstract

Neste trabalho pretende-se estudar a variabilidade da frequência cardíaca através da implementação de vários métodos de análise de electrocardiogramas. Na primeira parte descrevem-se os métodos de análise espectral, bem como a representação tempo-frequência. A decomposição de sinais para detectar e isolar os batimentos cardíacos do electrocardiograma é implementada. Descrevem-se algoritmos de isolamento para detecção dos eventos interessantes e pontos fiduciais que os constituem. Na segunda parte estima-se a variação da frequência cardíaca e estabelece-se a sua relação com as variações temporais e espectrais das características encontradas pelos métodos implementados na primeira parte do trabalho.

Diniz, AM, Gomes R, Parola AJ, Laia CAT, Pina F.  2009.  Photochemistry of 7-Hydroxy-2-(4-hydroxystyryl)-1-benzopyrylium and Related Compounds, 2009. Journal of Physical Chemistry B. 113:719-727. AbstractWebsite

2-Styryl-1-benzopyrylium derivatives exhibit deeper hues and absorption spectra that are substantially red-shifted when compared with their 2-phenyl-1-benzopyrylium analogues. They follow the same pH and light-dependent network of chemical reactions previously described for 2-phenyl-1-benzopyrylium compounds. In this work, the photochromic properties of 7-hydroxy-2-(4-hydroxystyryl)-1-benzopyrylium chloride are reported. This compound was fully characterized by UV-vis absorption, fluorescence emission, pH jumps, and flash photolysis, and its properties were compared with the analogue 7,4'-dihydroxyflavylium (7-hydroxy-2-(4-hydroxyphenyl)-1- benzopyrylium). The trans-chalcones of both compounds lacking the hydroxyl in position 2 were synthesized and used as model compounds since they exhibit cis-trans isomerization but cannot be involved in the other processes resulting from the ring closure. The transient absorption of two triplets attributed to the chalcones Ct/Ct(-), and a tautomer was detected by nanosecond flash photolysis, independent of the existence of the 2-hydroxyl substituent. The experimental results are compatible with the main formation of cis-chalcone from the singlet state. In the case of the styryl derivatives, the fraction of triplet formed from excitation of Ct is much higher, and the fraction of isomerization is much smaller. For this reason, the photochemistry of 7-hydroxy-2-(4-hydroxystyryl)-1-benzopyrylium in water is much less efficient than that of its parent 7,4'-dihydroxyflavylium; however, in the presence of CTAB micelles, intense red colors can be obtained upon irradiation, confirming the usefulness of this family of compounds as photochromic systems.

Boscolo, B, Leal SS, Salgueiro CA, Ghibaudi EM, Gomes CM.  2009.  The prominent conformational plasticity of lactoperoxidase: A chemical and pH stability analysis. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1794(7):1041-1048. AbstractWebsite

Lactoperoxidase (LPO) is a structurally complex and stable mammalian redox enzyme. Here we aim at evaluating the influence of ionic interactions and how these intertwine with the structural dynamics, stability and activity of LPO. In this respect, we have compared LPO guanidinium hydrochloride (GdmCl) and urea denaturation pathways and performed a detailed investigation on the effects of pH on the LPO conformational dynamics and stability. Our experimental findings using far-UV CD, Trp fluorescence emission and ESR spectroscopies clearly indicate that LPO charged-denaturation with GdmCl induced a sharp two-step process versus a three-step unfolding mechanism induced by urea. This differential effect between GdmCl and urea suggests that ionic interactions must play a rather prominent role in the stabilization of LPO. With both denaturants, the protein core was shown to retain activity up to near the respective Cm values. Moreover, a pH titration of LPO evidenced no significant conformational alterations or perturbation of heme activity within the 4 to 11 pH interval. In contrast, alterations of ionic interactions by poising LPO at pH 3, 2 and 12 resulted in a loss of secondary structure, loosening of tertiary contacts and loss of activity, which appear to be associated with the perturbation of the hydrophobic core, as evidenced by ANS binding, as well as disruption of the heme pocket demonstrated by optical and EPR spectroscopies. Overall, LPO is characterised by a high degree of peripheral structural plasticity without perturbation of the core heme moiety. The possible physiological meaning of such features is discussed.

Petrov, V, Laia CAT, Pina F.  2009.  Photochromism of 7,4 '-Dihydroxyflavylium in an AOT Reversed Micelle System. Langmuir. 25:594-601., Number 1 AbstractWebsite
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Freire, F, Romao MJ, Macedo AL, Aveiro SS, Goodfellow BJ, Carvalho AL.  2009.  Preliminary structural characterization of human SOUL, a haem-binding protein. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 65:723-726. AbstractWebsite
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2008
Najmudin, S, Gonzalez PJ, Trincao J, Coelho C, Mukhopadhyay A, Cerqueira NM, Romao CC, Moura I, Moura JJ, Brondino CD, Romao MJ.  2008.  Periplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum, Jun. J Biol Inorg Chem. 13:737-53., Number 5 AbstractWebsite

Nitrate reductase from Desulfovibrio desulfuricans ATCC 27774 (DdNapA) is a monomeric protein of 80 kDa harboring a bis(molybdopterin guanine dinucleotide) active site and a [4Fe-4S] cluster. Previous electron paramagnetic resonance (EPR) studies in both catalytic and inhibiting conditions showed that the molybdenum center has high coordination flexibility when reacted with reducing agents, substrates or inhibitors. As-prepared DdNapA samples, as well as those reacted with substrates and inhibitors, were crystallized and the corresponding structures were solved at resolutions ranging from 1.99 to 2.45 A. The good quality of the diffraction data allowed us to perform a detailed structural study of the active site and, on that basis, the sixth molybdenum ligand, originally proposed to be an OH/OH(2) ligand, was assigned as a sulfur atom after refinement and analysis of the B factors of all the structures. This unexpected result was confirmed by a single-wavelength anomalous diffraction experiment below the iron edge (lambda = 1.77 A) of the as-purified enzyme. Furthermore, for six of the seven datasets, the S-S distance between the sulfur ligand and the Sgamma atom of the molybdenum ligand Cys(A140) was substantially shorter than the van der Waals contact distance and varies between 2.2 and 2.85 A, indicating a partial disulfide bond. Preliminary EPR studies under catalytic conditions showed an EPR signal designated as a turnover signal (g values 1.999, 1.990, 1.982) showing hyperfine structure originating from a nucleus of unknown nature. Spectropotentiometric studies show that reduced methyl viologen, the electron donor used in the catalytic reaction, does not interact directly with the redox cofactors. The turnover signal can be obtained only in the presence of the reaction substrates. With use of the optimized conditions determined by spectropotentiometric titration, the turnover signal was developed with (15)N-labeled nitrate and in D(2)O-exchanged DdNapA samples. These studies indicate that this signal is not associated with a Mo(V)-nitrate adduct and that the hyperfine structure originates from two equivalent solvent-exchangeable protons. The new coordination sphere of molybdenum proposed on the basis of our studies led us to revise the currently accepted reaction mechanism for periplasmic nitrate reductases. Proposals for a new mechanism are discussed taking into account a molybdenum and ligand-based redox chemistry, rather than the currently accepted redox chemistry based solely on the molybdenum atom.

Gavel, OY, Kladova AV, Bursakov SA, Dias JM, Texeira S, Shnyrov VL, Moura JJ, Moura I, Romao MJ, Trincao J.  2008.  Purification, crystallization and preliminary X-ray diffraction analysis of adenosine triphosphate sulfurylase (ATPS) from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774, Jul 1. Acta Crystallogr Sect F Struct Biol Cryst Commun. 64:593-5., Number Pt 7 AbstractWebsite

Native zinc/cobalt-containing ATP sulfurylase (ATPS; EC 2.7.7.4; MgATP:sulfate adenylyltransferase) from Desulfovibrio desulfuricans ATCC 27774 was purified to homogeneity and crystallized. The orthorhombic crystals diffracted to beyond 2.5 A resolution and the X-ray data collected should allow the determination of the structure of the zinc-bound form of this ATPS. Although previous biochemical studies of this protein indicated the presence of a homotrimer in solution, a dimer was found in the asymmetric unit. Elucidation of this structure will permit a better understanding of the role of the metal in the activity and stability of this family of enzymes.

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