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Centre of Physics and Technological Research
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The Conformation of the N-Terminal Tails of Deinococcus grandis Dps Is Modulated by the Ionic Strength
Publication . Guerra, João P. L.; Blanchet, Clement E.; Vieira, Bruno J. C.; Almeida, Ana V.; Waerenborgh, João C.; Jones, Nykola C.; Hoffmann, Søren V.; Tavares, Pedro; Pereira, Alice S.; DQ - Departamento de Química; UCIBIO - Applied Molecular Biosciences Unit; MDPI - Multidisciplinary Digital Publishing Institute
DNA-binding proteins from starved cells (Dps) are homododecameric nanocages, with N-and C-terminal tail extensions of variable length and amino acid composition. They accumulate iron in the form of a ferrihydrite mineral core and are capable of binding to and compacting DNA, forming low-and high-order condensates. This dual activity is designed to protect DNA from oxidative stress, resulting from Fenton chemistry or radiation exposure. In most Dps proteins, the DNA-binding properties stem from the N-terminal tail extensions. We explored the structural characteristics of a Dps from Deinococcus grandis that exhibits an atypically long N-terminal tail composed of 52 residues and probed the impact of the ionic strength on protein conformation using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism and small-angle X-ray scattering. A novel high-spin ferrous iron-binding site was identified in the N-terminal tails, using Mössbauer spectroscopy. Our data reveals that the N-terminal tails are structurally dynamic and alter between compact and extended conformations, depending on the ionic strength of the buffer. This prompts the search for other physiologically relevant modulators of tail conformation and hints that the DNA-binding properties of Dps proteins may be affected by external factors.
Sensing the ortho Positions in C6Cl6 and C6H4Cl2 from Cl2− Formation upon Molecular Reduction
Publication . Kumar, Sarvesh; Romero, José; Probst, Michael; Maihom, Thana; García, Gustavo; Limão-Vieira, Paulo; DF – Departamento de Física; CeFITec – Centro de Física e Investigação Tecnológica; MDPI - Multidisciplinary Digital Publishing Institute
The geometrical effect of chlorine atom positions in polyatomic molecules after capturing a low-energy electron is shown to be a prevalent mechanism yielding Cl2−. In this work, we investigated hexachlorobenzene reduction in electron transfer experiments to determine the role of chlorine atom positions around the aromatic ring, and compared our results with those using ortho-, meta- and para-dichlorobenzene molecules. This was achieved by combining gas-phase experiments to determine the reaction threshold by means of mass spectrometry together with quantum chemical calculations. We also observed that Cl2− formation can only occur in 1,2-C6H4Cl2, where the two closest C–Cl bonds are cleaved while the chlorine atoms are brought together within the ring framework due to excess energy dissipation. These results show that a strong coupling between electronic and C–Cl bending motion is responsible for a positional isomeric effect, where molecular recognition is a determining factor in chlorine anion formation.
The Role of Hydrogen Incorporation into Amorphous Carbon Films in the Change of the Secondary Electron Yield
Publication . Bundaleski, Nenad; Adame, Carolina F.; Alves, Eduardo; Barradas, Nuno P.; Cerqueira, Maria F.; Deuermeier, Jonas; Delaup, Yorick; Ferraria, Ana M.; Ferreira, Isabel M. M.; Neupert, Holger; Himmerlich, Marcel; Rego, Ana Maria M. B. do; Rimoldi, Martino; Teodoro, Orlando M. N. D.; Vasilevskiy, Mikhail; Costa Pinto, Pedro; DF – Departamento de Física; CeFITec – Centro de Física e Investigação Tecnológica; DCM - Departamento de Ciência dos Materiais; CENIMAT-i3N - Centro de Investigação de Materiais (Lab. Associado I3N); MDPI - Multidisciplinary Digital Publishing Institute
Over the last few years, there has been increasing interest in the use of amorphous carbon thin films with low secondary electron yield (SEY) to mitigate electron multipacting in particle accelerators and RF devices. Previous works found that the SEY increases with the amount of incorporated hydrogen and correlates with the Tauc gap. In this work, we analyse films produced by magnetron sputtering with different contents of hydrogen and deuterium incorporated via the target poisoning and sputtering of CxDy molecules. XPS was implemented to estimate the phase composition of the films. The maximal SEY was found to decrease linearly with the fraction of the graphitic phase in the films. These results are supported by Raman scattering and UPS measurements. The graphitic phase decreases almost linearly for hydrogen and deuterium concentrations between 12% and 46% (at.), but abruptly decreases when the concentration reaches 53%. This vanishing of the graphitic phase is accompanied by a strong increase of SEY and the Tauc gap. These results suggest that the SEY is not dictated directly by the concentration of H/D, but by the fraction of the graphitic phase in the film. The results are supported by an original model used to calculate the SEY of films consisting of a mixture of graphitic and polymeric phases.
Machine learning prediction of UV–Vis spectra features of organic compounds related to photoreactive potential
Publication . Mamede, Rafael; Pereira, Florbela; Aires-de-Sousa, João; DQ - Departamento de Química; LAQV@REQUIMTE; Nature Publishing Group
Machine learning (ML) algorithms were explored for the classification of the UV–Vis absorption spectrum of organic molecules based on molecular descriptors and fingerprints generated from 2D chemical structures. Training and test data (~ 75 k molecules and associated UV–Vis data) were assembled from a database with lists of experimental absorption maxima. They were labeled with positive class (related to photoreactive potential) if an absorption maximum is reported in the range between 290 and 700 nm (UV/Vis) with molar extinction coefficient (MEC) above 1000 Lmol−1 cm−1, and as negative if no such a peak is in the list. Random forests were selected among several algorithms. The models were validated with two external test sets comprising 998 organic molecules, obtaining a global accuracy up to 0.89, sensitivity of 0.90 and specificity of 0.88. The ML output (UV–Vis spectrum class) was explored as a predictor of the 3T3 NRU phototoxicity in vitro assay for a set of 43 molecules. Comparable results were observed with the classification directly based on experimental UV–Vis data in the same format.
Controlled modulation of the dynamics of the Deinococcus grandis Dps N-terminal tails by divalent metals
Publication . Guerra, João P. L.; Blanchet, Clement E.; Vieira, Bruno J. C.; Waerenborgh, João C.; Jones, Nykola C.; Hoffmann, Søren Vrønning; Pereira, Alice S.; Tavares, Pedro; DQ - Departamento de Química; UCIBIO - Applied Molecular Biosciences Unit; Wiley-Blackwell
DNA-binding proteins from starved cells (Dps) are small multifunctional nanocages expressed by prokaryotes in acute oxidative stress conditions or during the starvation-induced stationary phase, as a bacterial defense mechanism. Dps proteins protect bacterial DNA from damage by either direct binding or by removing precursors of reactive oxygen species from solution. The DNA-binding properties of most Dps proteins studied so far are related to their unordered, flexible, N- and C-terminal extensions. In a previous work, we revealed that the N-terminal tails of Deinoccocus grandis Dps shift from an extended to a compact conformation depending on the ionic strength of the buffer and detected a novel high-spin ferrous iron center in the proximal ends of those tails. In this work, we further explore the conformational dynamics of the protein by probing the effect of divalent metals binding to the tail by comparing the metal-binding properties of the wild-type protein with a binding site-impaired D34A variant using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism, and small-angle X-ray scattering. The N-terminal ferrous species was also characterized by Mössbauer spectroscopy. The results herein presented reveal that the conformation of the N-terminal tails is altered upon metal binding in a gradual, reversible, and specific manner. These observations may point towards the existence of a regulatory process for the DNA-binding properties of Dps proteins through metal binding to their N- and/or C-terminal extensions.
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Entidade financiadora
Fundação para a Ciência e a Tecnologia
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6817 - DCRRNI ID
Número da atribuição
UIDB/00068/2020