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2015
Barquinha, P, Pereira S, Pereira LÍ, Wojcik P, Grey P, Martins R, Fortunato E.  2015.  {Flexible and Transparent WO 3 Transistor with Electrical and Optical Modulation}, may. Advanced Electronic Materials. 1:n/a–n/a., Number 5 AbstractWebsite
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Rodrigues, J, Mata D, Pimentel A, Nunes D, Martins R, Fortunato E, Neves AJ, Monteiro T, Costa FM.  2015.  {One-step synthesis of ZnO decorated CNT buckypaper composites and their optical and electrical properties}, may. Materials Science and Engineering: B. 195:38–44. AbstractWebsite
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Bernacka-Wojcik, I, Águas H, Carlos {FF}, Lopes P, Wojcik {PJ}, Costa {MN}, Veigas B, Igreja R, Fortunato E, Baptista P, Martins R.  2015.  Single Nucleotide Polymorphism Detection Using Gold Nanoprobes and Bio-Microfluidic Platform With Embedded Microlenses, jun. Biotechnology and Bioengineering. 112:1210–1219., Number 6: Wiley-Blackwell Abstract

The use of microfluidics platforms combined with the optimal optical properties of gold nanopartides has found plenty of application in molecular biosensing. This paper describes a biotnicrofluidic platform coupled to a non-cross-linking colorimetric gold nanoprobe assay to detect a single nucleotide polymorphism associated with increased risk of obesity fat-mass and obesity-associated (FTO) rs9939609 (Carlos et al., 2014). The system enabled significant discrimination between positive and negative assays using a target DNA concentration of 5 ng/mu l below the limit of detection of the conventionally used microplate reader (i.e., 15 ng/mu l) with 10 times lower solution volume (i.e., 3 mu l.). A set of optimization of our previously reported bio-microfluidic platform (Bemacka-Wojcik et al., 2013) resulted in a 160% improvement of colorimetric analysis results. Incorporation of planar microlenses increased 6 times signal-to-loss ratio reaching the output optical fiber improving by 34% the colorimetric analysis of gold nanopartides, while the implementation of an optoelectronic acquisition system yielded increased accuracy and reduced noise. The microfluidic chip was also integrated with a miniature fiber spectrometer to analyze the assays' cobrimetric changes and also the LEDs transmission spectra when illuminating through various solutions. Furthermore, by coupling an optical micmscope to a digital camera with a long exposure time (30s), we could visualise the different scatter intensities of gold nanoparticles within channels following salt addition. These intensities correlate well to the expected difference in aggregation between FTO positive (none to small aggregates) and negative samples (large aggregates). (C) 2015 Wiley Periodicals, Inc.

Kiazadeh, A, Salgueiro D, Branquinho R, Pinto J, Gomes HL, Barquinha P, Martins R, Fortunato E.  2015.  {Operational stability of solution based zinc tin oxide/SiO2 thin film transistors under gate bias stress}, jun. APL Materials. 3:062804., Number 6 AbstractWebsite

In this study, we report solution-processed amorphous zinc tin oxide transistors exhibiting high operational stability under positive gate bias stress, translated by a recoverable threshold voltage shift of about 20{%} of total applied stress voltage. Under vacuum condition, the threshold voltage shift saturates showing that the gate-bias stress is limited by trap exhaustion or balance between trap filling and emptying mechanism. In ambient atmosphere, the threshold voltage shift no longer saturates, stability is degraded and the recovering process is impeded. We suggest that the trapping time during the stress and detrapping time in recovering are affected by oxygen adsorption/desorption processes. The time constants extracted from stretched exponential fitting curves are ≈106 s and 105 s in vacuum and air, respectively.

Bernacka-Wojcik, I, Aguas H, Carlos FF, Lopes P, Wojcik PJ, Costa MN, Veigas B, Igreja R, Fortunato E, Baptista PV, Martins R.  2015.  {Single Nucleotide Polymorphism Detection Using Gold Nanoprobes and Bio-Microfluidic Platform With Embedded Micro lenses}, jun. BIOTECHNOLOGY AND BIOENGINEERING. 112:1210–1219., Number 6 Abstract
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G-Berasategui, E, Zubizarreta C, Bayón R, Barriga J, Barros R, Martins R, Fortunato E.  2015.  {Study of the optical, electrical and corrosion resistance properties of AZO layers deposited by DC pulsed magnetron sputtering}, jun. Surface and Coatings Technology. 271:141–147. AbstractWebsite

Aluminium-doped zinc oxide (AZO) is a common material used as a front contact layer on chalcopyrite CuInGaSe2 (CIGS)-based thin-film solar cells since it combines optimum optical and electrical properties with low cost and abundant elemental availability. Low-resistivity and high-transmission front contacts are required to develop high-performance CIGS solar cells. However, the durability of the cells is highly influenced by the corrosion resistance behaviour of the AZO layers. In this work, an exhaustive study of the aluminium-doped zinc oxide layers (AZO) deposited by pulsed DC magnetron sputtering (MS) has been performed. The optical, electrical and electrochemical corrosion resistance properties of the AZO layers have been evaluated as a function of the deposition pressure. The results show that adjusting the deposition pressure could develop AZO layers with very high electrochemical corrosion resistance in chlorinated aqueous media combined with optimum electrical and optical properties. Layers grown at 3×10−3mbar pressure present very high corrosion resistance values (in the order of 106 {\$}Ømega{\$}) and very high electrochemical stability, indicating no tendency for electrochemical corrosion degradation. Besides, these layers are highly transparent with an average transmittance in the visible range above 90{%} and with a low resistivity of 6.8×10−4 {\$}Ømega{\$}cm for a 1000nm films thickness, making them optimum candidate front contact for high-performance and high durability CIGS solar cells.

Aguas, H, Mateus T, Vicente A, Gaspar D, Mendes MJ, Schmidt WA, Pereira L, Fortunato E, Martins R.  2015.  {Thin Film Silicon Photovoltaic Cells on Paper for Flexible Indoor Applications}, jun. ADVANCED FUNCTIONAL MATERIALS. 25:3592–3598., Number 23 Abstract
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Moniz, A.  2015.  Assessing Technologies: Global Patterns of Trust and Distrust. Report on one session at the XVIII World Congress of Sociology, jan. Technikfolgenabschätzung –{} Theorie und Praxis. 24, Number 1 119-121, Karlsruhe: Karlsruhe Institute of Technology AbstractWebsite

Technology assessment (TA) had never been treated as a relevant topic within the International Sociological Association (ISA) before. The first steps towards establishing this association were taken in 1948, at the initiative of the Social Science Department of UNESCO. Its formal foundation was in 1949. The World Congress of Sociology in Japan was hopefully the beginning of continuous integration of TA into the thematic sessions within the ISA.

Veigas, B, Fortunato E, Baptista {PV }.  2015.  Mobile based gold nanoprobe TB diagnostics for point-of-need, jan. Mobile Health Technologies: Methods and Protocols. Part 1(Rasooly, {Avraham }, Herold, {Keith E. }, Eds.).:41–56., United States: Humana Press Abstract

Nanotechnology based diagnostics has provided improved tools for pathogen detection and sensitive and specific characterization of antibiotic resistance signatures. Tuberculosis (TB) is caused by members of the Mycobacterium tuberculosis Complex (MTBC) and, according to the World Health Organization, is one of the most serious infectious diseases in the world. Recent advances in molecular diagnostics of TB have improved both the detection time and sensitivity but they still require specialized technical personnel and cumbersome laboratory equipment. Diagnostics at point-of-need is crucial to TB control as it may provide rapid identification of pathogen together with the resistance profile of TB strains, originated from single nucleotide polymorphisms (SNPs) in different loci , allowing for a more accurate indication of the adequate therapy.Gold nanoparticles have been widely used in molecular diagnostics platforms. Here, we describe the use of gold nanoprobes (oligonucleotide functionalized gold nanoparticles) to be used in a non-crosslinking colorimetric method for the direct detection of specific DNA targets. Due to the remarkable optical properties of gold nanoparticles, this detection system provides colorimetric detection of the pathogen together with the potential of identification of several single nucleotide polymorphisms (SNPs) involved in TB resistance to antibiotics. For point-of-need use, we adapted this strategy to a low-cost mobile scheme using a paper based revelation platform and where the spectral signature is transposed to RGB data via a smartphone device. This way, identification of pathogen and characterization of resistance signatures is achieved at point-of-need.

Veigas, B, Fortunato E, Baptista PV.  2015.  {Field Effect Sensors for Nucleic Acid Detection: Recent Advances and Future Perspectives}, jan. Sensors. 15:10380–10398., Number 5: Multidisciplinary Digital Publishing Institute AbstractWebsite

In the last decade the use of field-effect-based devices has become a basic structural element in a new generation of biosensors that allow label-free DNA analysis. In particular, ion sensitive field effect transistors (FET) are the basis for the development of radical new approaches for the specific detection and characterization of DNA due to FETs' greater signal-to-noise ratio, fast measurement capabilities, and possibility to be included in portable instrumentation. Reliable molecular characterization of DNA and/or RNA is vital for disease diagnostics and to follow up alterations in gene expression profiles. FET biosensors may become a relevant tool for molecular diagnostics and at point-of-care. The development of these devices and strategies should be carefully designed, as biomolecular recognition and detection events must occur within the Debye length. This limitation is sometimes considered to be fundamental for FET devices and considerable efforts have been made to develop better architectures. Herein we review the use of field effect sensors for nucleic acid detection strategies—from production and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics lab.

Marques, AC, Santos L, Costa MN, Dantas JM, Duarte P, Gonçalves A, Martins R, Salgueiro CA, Fortunato E.  2015.  {Office paper platform for bioelectrochromic detection of electrochemically active bacteria using tungsten trioxide nanoprobes.}, jan. Scientific reports. 5:9910. AbstractWebsite

Electrochemically active bacteria (EAB) have the capability to transfer electrons to cell exterior, a feature that is currently explored for important applications in bioremediation and biotechnology fields. However, the number of isolated and characterized EAB species is still very limited regarding their abundance in nature. Colorimetric detection has emerged recently as an attractive mean for fast identification and characterization of analytes based on the use of electrochromic materials. In this work, WO3 nanoparticles were synthesized by microwave assisted hydrothermal synthesis and used to impregnate non-treated regular office paper substrates. This allowed the production of a paper-based colorimetric sensor able to detect EAB in a simple, rapid, reliable, inexpensive and eco-friendly method. The developed platform was then tested with Geobacter sulfurreducens, as a proof of concept. G. sulfurreducens cells were detected at latent phase with an RGB ratio of 1.10 ± 0.04, and a response time of two hours.

Santos, L, Nunes D, Calmeiro T, Branquinho R, Salgueiro D, Barquinha P, Pereira LÍ, Martins R, Fortunato E.  2015.  {Solvothermal synthesis of gallium-indium-zinc-oxide nanoparticles for electrolyte-gated transistors.}, jan. ACS applied materials {&} interfaces. 7:638–46., Number 1 AbstractWebsite

Solution-processed field-effect transistors are strategic building blocks when considering low-cost sustainable flexible electronics. Nevertheless, some challenges (e.g., processing temperature, reliability, reproducibility in large areas, and cost effectiveness) are requirements that must be surpassed in order to achieve high-performance transistors. The present work reports electrolyte-gated transistors using as channel layer gallium-indium-zinc-oxide nanoparticles produced by solvothermal synthesis combined with a solid-state electrolyte based on aqueous dispersions of vinyl acetate stabilized with cellulose derivatives, acrylic acid ester in styrene and lithium perchlorate. The devices fabricated using this approach display a ION/IOFF up to 1 × 10(6), threshold voltage (VTh) of 0.3-1.9 V, and mobility up to 1 cm(2)/(V s), as a function of gallium-indium-zinc-oxide ink formulation and two different annealing temperatures. These results validates the usage of electrolyte-gated transistors as a viable and promising alternative for nanoparticle based semiconductor devices as the electrolyte improves the interface and promotes a more efficient step coverage of the channel layer, reducing the operating voltage when compared with conventional dielectrics gating. Moreover, it is shown that by controlling the applied gate potential, the operation mechanism of the electrolyte-gated transistors can be modified from electric double layer to electrochemical doping.

Pavan, M, Rühle S, Ginsburg A, Keller DA, Barad H-N, Sberna PM, Nunes D, Martins R, Anderson AY, Zaban A, Fortunato E.  2015.  {TiO2/Cu2O all-oxide heterojunction solar cells produced by spray pyrolysis}, jan. Solar Energy Materials and Solar Cells. 132:549–556. AbstractWebsite

Here we present for the first time a TiO2/Cu2O all-oxide heterojunction solar cell entirely produced by spray pyrolysis onto fluorine doped tin oxide (FTO) covered glass substrates, using silver as a back contact. A combinatorial approach was chosen to investigate the impact of the TiO2 window layer and the Cu2O light absorber thicknesses. We observe an open circuit voltage up to 350mV and a short circuit current density which is strongly dependent of the Cu2O thickness, reaching a maximum of {\~{}}0.4mA/cm2. Optical investigation reveals that a thickness of 300nm spray pyrolysis deposited Cu2O is sufficient to absorb most photons with an energy above the symmetry allowed optical transition of 2.5eV, indicating that the low current densities are caused by strong recombination in the absorber that consists of small Cu2O grains.

Nunes, D, Santos L, Duarte P, Pimentel A, Pinto JV, Barquinha P, Carvalho PA, Fortunato E, Martins R.  2015.  {Room temperature synthesis of Cu₂O nanospheres: optical properties and thermal behavior.}, feb. Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. 21:108–19., Number 1 AbstractWebsite

The present work reports a simple and easy wet chemistry synthesis of cuprous oxide (Cu2O) nanospheres at room temperature without surfactants and using different precursors. Structural characterization was carried out by X-ray diffraction, transmission electron microscopy, and scanning electron microscopy coupled with focused ion beam and energy-dispersive X-ray spectroscopy. The optical band gaps were determined from diffuse reflectance spectroscopy. The photoluminescence behavior of the as-synthesized nanospheres showed significant differences depending on the precursors used. The Cu2O nanospheres were constituted by aggregates of nanocrystals, in which an on/off emission behavior of each individual nanocrystal was identified during transmission electron microscopy observations. The thermal behavior of the Cu2O nanospheres was investigated with in situ X-ray diffraction and differential scanning calorimetry experiments. Remarkable structural differences were observed for the nanospheres annealed in air, which turned into hollow spherical structures surrounded by outsized nanocrystals.

Santos, L, Wojcik P, Pinto JV, Elangovan E, Viegas J, Pereira LÍ, Martins R, Fortunato E.  2015.  {Structure and Morphologic Influence of WO 3 Nanoparticles on the Electrochromic Performance of Dual-Phase a -WO 3 /WO 3 Inkjet Printed Films}, feb. Advanced Electronic Materials. 1:n/a–n/a., Number 1-2 AbstractWebsite
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Pedrosa, P, Vinhas R, de Fernandes {MANCR}, Baptista {PMRV}.  2015.  Gold Nanotheranostics: Proof-of-Concept or Clinical Tool?, dec Nanomaterials. 5:1853–1879., Number 4: MDPI AG Abstract

Nanoparticles have been making their way in biomedical applications and personalized medicine, allowing for the coupling of diagnostics and therapeutics into a single nanomaterial-nanotheranostics. Gold nanoparticles, in particular, have unique features that make them excellent nanomaterials for theranostics, enabling the integration of targeting, imaging and therapeutics in a single platform, with proven applicability in the management of heterogeneous diseases, such as cancer. In this review, we focus on gold nanoparticle-based theranostics at the lab bench, through pre-clinical and clinical stages. With few products facing clinical trials, much remains to be done to effectively assess the real benefits of nanotheranostics at the clinical level. Hence, we also discuss the efforts currently being made to translate nanotheranostics into the market, as well as their commercial impact.

Conde, J, Ambrosone A, Hernandez Y, Tian F, McCully M, Berry {CC }, Baptista {PMRV}, Tortiglione C, {de la Fuente} {JM }.  2015.  15 years on siRNA delivery: Beyond the State-of-the-Art on inorganic nanoparticles for RNAi therapeutics, aug. Nano today. 10:421–450., Number 4: ELSEVIER SCI LTD Abstract

RNAi has always captivated scientists due to its tremendous power to modulate the phenotype of living organisms. This natural and powerful biological mechanism can now be harnessed to downregulate specific gene expression in diseased cells, opening up endless opportunities. Since most of the conventional siRNA delivery methods are limited by a narrow therapeutic index and significant side and off-target effects, we are now in the dawn of a new age in gene therapy driven by nanotechnology vehicles for RNAi therapeutics. Here, we outlook the {"}do's and dont's{"} of the inorganic RNAi nanomaterials developed in the last 15 years and the different strategies employed are compared and scrutinized, offering important suggestions for the next 15. (C) 2015 Elsevier Ltd. All rights reserved.

Veigas, B, Pedrosa P, Carlos {FF }, Mancio-Silva L, Grosso {AR}, Fortunato E, Mota {MM }, Baptista P.  2015.  One nanoprobe, two pathogens: gold nanoprobes multiplexing for point-of-care, aug. Journal of Nanobiotechnology. 13, Number 1: BioMed Central (BMC) Abstract

Background: Gold nanoparticles have been widely employed for biosensing purposes with remarkable efficacy for DNA detection. Amongst the proposed systems, colorimetric strategies based on the remarkable optical properties have provided for simple yet effective sequence discrimination with potential for molecular diagnostics at point of need. These systems may also been used for parallel detection of several targets to provide additional information on diagnostics of pathogens.Results: For the first time, we demonstrate that a single Au-nanoprobe may provide for detection of two distinct targets (pathogens) allowing colorimetric multi-target detection. We demonstrate this concept by using one single gold-nanoprobe capable to detect members of the Mycobacterium tuberculosis complex and Plasmodium sp., the etiologic agents of tuberculosis and malaria, respectively. Following characterisation, the developed gold-nanoprobe allowed detection of either target in individual samples or in samples containing both DNA species with the same efficacy.Conclusions: Using one single probe via the non-cross-linking colorimetric methodology it is possible to identify multiple targets in one sample in one reaction. This proof-of-concept approach may easily be integrated into sensing platforms allowing for fast and simple multiplexing of Au-nanoprobe based detection at point-of-need.

Restani, {RB }, Conde J, Pires {RF }, Martins P, Fernandes {AR}, Baptista {PV}, Bonifacio {VDB }, Aguiar-Ricardo A.  2015.  POxylated Polyurea Dendrimers: Smart Core-Shell Vectors with IC50 Lowering Capacity, aug. Macromolecular Bioscience. 15:1045–1051., Number 8: WILEY-V C H VERLAG GMBH Abstract

The design and preparation of highly efficient drug delivery platforms using green methodologies is at the forefront of nanotherapeutics research. POxylated polyurea dendrimers are efficiently synthesized using a supercritical-assisted polymerization in carbon dioxide. These fluorescent, pH-responsive and water-soluble core-shell smart nanocarriers show low toxicity in terms of cell viability and absence of glutathione depletion, two of the major side effect limitations of current vectors. The materials are also found to act as good transfection agents, through a mechanism involving an endosomal pathway, being able to reduce 100-fold the IC50 of paclitaxel.

Larguinho, M, Santos S, Almeida J, Baptista P.  2015.  DNA adduct identification using gold-aptamer nanoprobes, apr. Iet Nanobiotechnology. 9:95–101., Number 2: INST ENGINEERING TECHNOLOGY-IET Abstract

The optical and physico-chemical properties of gold nanoparticles (AuNPs) have prompted new and improved approaches which have greatly evolved the fields of biosensing and molecular detection. In this study, the authors took advantage of AuNPs' ease of modification and functionalised it with selected DNA aptamers using a salt aging method to produce gold-aptamer nanoprobes. After characterisation, these nanoprobes were subsequently used for biomolecular detection of glycidamide (GA)-guanine (Gua) adducts generated in vitro. The results are based on differences in nanoprobe stabilisation against salt-induced aggregation, similar to the non-cross-linking method developed by Baptista for discrimination of specific sequences. Alkylated Guas were efficiently discriminated from deoxyguanosine and GA in solution. Despite this, a clear identification of DNA adducts derived from genomic DNA alkylation has proven to be a more challenging task.

Vinhas, R, Correia C, Ribeiro P, Lourenco A, Sousa A, Fernandes A, Baptista P.  2015.  GOLD NANOPROBES IN THE DIAGNOSTIC OF CHRONIC MYELOID LEUKEMIA: DETECTION OF THE E14A2 BCR-ABL TRANSCRIPT DIRECTLY IN RNA SAMPLES, apr. Leukemia research. 39:S90–S90.: PERGAMON-ELSEVIER SCIENCE LTD Abstract
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Pedrosa, P, Vinhas R, Fernandes A, Baptista PV.  2015.  Gold Nanotheranostics: Proof-of-Concept or Clinical Tool?, 2015/10/27/accep Nanomaterials. 5(4)(Selvan, Subramanian Tamil, Ed.).:1853-1879.: MDPI AbstractWebsite

Nanoparticles have been making their way in biomedical applications and personalized medicine, allowing for the coupling of diagnostics and therapeutics into a single nanomaterial—nanotheranostics. Gold nanoparticles, in particular, have unique features that make them excellent nanomaterials for theranostics, enabling the integration of targeting, imaging and therapeutics in a single platform, with proven applicability in the management of heterogeneous diseases, such as cancer. In this review, we focus on gold nanoparticle-based theranostics at the lab bench, through pre-clinical and clinical stages. With few products facing clinical trials, much remains to be done to effectively assess the real benefits of nanotheranostics at the clinical level. Hence, we also discuss the efforts currently being made to translate nanotheranostics into the market, as well as their commercial impact.

Pessoa, JC, Garribba E, Santos MFA, Santos-Silva T.  2015.  Vanadium and proteins: Uptake, transport, structure, activity and function, 2015/10/15/. The Ninth International Symposium on the Chemistry and Biological Chemistry of Vanadium. 301–302:49-86. AbstractWebsite

AbstractVanadium is an element ubiquitously present in our planet's crust and thus there are several organisms that use vanadium for activity or function of proteins. Examples are the vanadium-dependent haloperoxidases and the vanadium-containing nitrogenases. Some organisms that use vanadium have extremely efficient and selective protein-dependent systems for uptake and transport of vanadium and are able to accumulate high levels of vanadium from seawater, vanabins being a unique family of vanadium binding proteins found in ascidians involved in this process. For all of the systems a discussion regarding the role of the V-containing proteins is provided, mostly centered on structural aspects of the vanadium site and, when possible or relevant, relating this to the mechanisms operating. Phosphate is very important in biological systems and is involved in an extensive number of biological recognition and bio-catalytic systems. Vanadate(V) is able to inhibit many of the enzymes involved in these processes, such as ATPases, phosphatases, ribonucleases, phosphodiesterases, phosphoglucomutase and glucose-6-phosphatase, and it appears clear that this is closely related to the analogous physicochemical properties of vanadate and phosphate. The ability of vanadium to interfere with the metabolic processes involving Ca2+ and Mg2+, connected with its versatility to undergo changes in coordination geometry, allow V to influence the function of a large variety of phosphate-metabolizing enzymes and vanadate(V) salts and compounds have been frequently used either as inhibitors of these enzymes, or as probes to study the mechanisms of their reactions and catalytic cycle. In this review we give an overview of the many examples so far reported, also disclosing that vanadate(IV) may also have an equally efficient inhibiting effect. The prospective application of vanadium compounds as therapeutics has also been an important topic of research. How vanadium may be transported in blood and up-taken by cells are particularly relevant issues, this being mainly dependent on transferrin (and albumin) present in blood plasma. The thousands of studies reported on the effects of vanadium compounds reflect the complexity of the interactions occurring. Although it is not easy to anticipate/determine if a particular effect observed in a test tube or in vitro is also going to take place in vivo, it is clear that vanadium ions may interfere with many metabolic processes at many distinct levels. Emphasis is given on structural and functional aspects of vanadium–protein interactions relevant for vanadium binding and/or for clarification of role of the metal center in the reaction mechanisms. The additional knowledge that the presence of vanadium can change the action of a protein, other than simply inhibiting it, may also be important to understand how vanadium affects biological systems. This possibility, together with the vanadate–phosphate analogy further potentiates the belief that vanadium probably has relevant functions in living beings, which may involve interaction or incorporation of the metal ion and/or its compounds with several proteins.

Carvalho, HF, Roque ACA, Iranzo O, Branco RJF.  2015.  Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution, 2015/09/23. PLoS ONE. 10(9):e0138118-.: Public Library of Science AbstractWebsite

Metalloproteases have evolved in a vast number of biological systems, being one of the most diverse types of proteases and presenting a wide range of folds and catalytic metal ions. Given the increasing understanding of protein internal dynamics and its role in enzyme function, we are interested in assessing how the structural heterogeneity of metalloproteases translates into their dynamics. Therefore, the dynamical profile of the clan MA type protein thermolysin, derived from an Elastic Network Model of protein structure, was evaluated against those obtained from a set of experimental structures and molecular dynamics simulation trajectories. A close correspondence was obtained between modes derived from the coarse-grained model and the subspace of functionally-relevant motions observed experimentally, the later being shown to be encoded in the internal dynamics of the protein. This prompted the use of dynamics-based comparison methods that employ such coarse-grained models in a representative set of clan members, allowing for its quantitative description in terms of structural and dynamical variability. Although members show structural similarity, they nonetheless present distinct dynamical profiles, with no apparent correlation between structural and dynamical relatedness. However, previously unnoticed dynamical similarity was found between the relevant members Carboxypeptidase Pfu, Leishmanolysin, and Botulinum Neurotoxin Type A, despite sharing no structural similarity. Inspection of the respective alignments shows that dynamical similarity has a functional basis, namely the need for maintaining proper intermolecular interactions with the respective substrates. These results suggest that distinct selective pressure mechanisms act on metalloproteases at structural and dynamical levels through the course of their evolution. This work shows how new insights on metalloprotease function and evolution can be assessed with comparison schemes that incorporate information on protein dynamics. The integration of these newly developed tools, if applied to other protein families, can lead to more accurate and descriptive protein classification systems.

Pina, F, Oliveira J, de Freitas V.  2015.  Anthocyanins and derivatives are more than flavylium cations, 2015. Tetrahedron. 71(20):3107-3114. AbstractWebsite
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