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Your search keyword '"Moreira, Irina S."' showing total 210 results
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210 results on '"Moreira, Irina S."'

2. MENSADB: A Thorough Structural Analysis of Membrane Protein Dimers

Author

Matos-Filipe, Pedro, Preto, António J., Koukos, Panagiotis I., Mourão, Joana, Bonvin, Alexandre M. J. J., and Moreira, Irina S.

Subjects
Quantitative Biology - Biomolecules
Abstract

Membrane Proteins (MPs) account for around 15-39% of the human proteome and assume a critical role in a vast set of cellular and physiological mechanisms, including molecular transport, nutrient uptake, toxin and waste product clearance, respiration, and signaling. While roughly 60% of all FDA-approved drugs target MPs, there is a shortage of structural and biochemical data on them mainly hindered by their localization in the lipid bilayer. We present here MEmbrane protein dimer Novel Structure Analyser database (MENSAdb), a real time web-application exposing a broad array of fundamental features about MPs surface and their interfacial regions. In particular, we present conservation, four distinctive Accessible Solvent Area (ASA) descriptors, average and environment-specific B-factors, intermolecular contacts at 2.5 and 4.0 angstroms distance cutoffs, salt-bridges, hydrogen-bonds, hydrophobic, pi-pi interactions, t-stacking and cation-pi interactions. Additionally, users can closely inspect differences in values between three distinctive residues classes: i) non-surface, ii) surface and non-interfacial and iii) interfacial. The database is freely available at www.moreiralab.com/resources/mensadb.

Published
2019

11. Designer high-density lipoprotein particles enhance endothelial barrier function and suppress inflammation

Author

Lin, Yueh-Chien, primary, Swendeman, Steven, additional, Moreira, Irina S., additional, Ghosh, Avishek, additional, Kuo, Andrew, additional, Rosário-Ferreira, Nícia, additional, Guo, Shihui, additional, Culbertson, Alan, additional, Levesque, Michel V., additional, Cartier, Andreane, additional, Seno, Takahiro, additional, Schmaier, Alec, additional, Galvani, Sylvain, additional, Inoue, Asuka, additional, Parikh, Samir M., additional, FitzGerald, Garret A., additional, Zurakowski, David, additional, Liao, Maofu, additional, Flaumenhaft, Robert, additional, Gümüş, Zeynep H., additional, and Hla, Timothy, additional

Published
2024
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26. Arrestin and G Protein Interactions with GPCRs: A Structural Perspective

Author

Barreto, Carlos A.V., primary, Baptista, Salete J., additional, Bueschbell, Beatriz, additional, Magalhães, Pedro R., additional, Preto, António J., additional, Lemos, Agostinho, additional, Rosário‐Ferreira, Nícia, additional, Schiedel, Anke C., additional, Machuqueiro, Miguel, additional, Melo, Rita, additional, and Moreira, Irina S., additional

Published
2022
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27. Enhanced neuronal differentiation by dynamic piezoelectric stimulation

Author

Pinho, Tiffany S., primary, Silva, Deolinda, additional, Ribeiro, Jorge Cibrão, additional, Marote, Ana, additional, Lima, Rui, additional, Batista, Salete J., additional, Melo, Rita, additional, Ribeiro, Clarisse, additional, Cunha, Cristiana B., additional, Moreira, Irina S., additional, Lanceros‐Mendez, Senentxu, additional, and Salgado, António J., additional

Published
2022
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29. Using machine-learning-driven approaches to boost hot-spot's knowledge

Author

Rosário-Ferreira, Nícia, Bonvin, Alexandre M.J.J., Moreira, Irina S., Sub NMR Spectroscopy, and NMR Spectroscopy

Subjects
computational alanine scanning mutagenesis, Computational Mathematics, binding hot-spots, Taverne, Materials Chemistry, interaction energetics, protein–protein interactions, Physical and Theoretical Chemistry, Biochemistry, machine-learning algorithms, Computer Science Applications
Abstract

Understanding protein–protein interactions (PPIs) is fundamental to describe and to characterize the formation of biomolecular assemblies, and to establish the energetic principles underlying biological networks. One key aspect of these interfaces is the existence and prevalence of hot-spots (HS) residues that, upon mutation to alanine, negatively impact the formation of such protein–protein complexes. HS have been widely considered in research, both in case studies and in a few large-scale predictive approaches. This review aims to present the current knowledge on PPIs, providing a detailed understanding of the microspecifications of the residues involved in those interactions and the characteristics of those defined as HS through a thorough assessment of related field-specific methodologies. We explore recent accurate artificial intelligence-based techniques, which are progressively replacing well-established classical energy-based methodologies. This article is categorized under: Data Science > Databases and Expert Systems Structure and Mechanism > Computational Biochemistry and Biophysics Molecular and Statistical Mechanics > Molecular Interactions.

Published
2022

31. Aerobic Granular Sludge

Author

Amorim, Catarina L., primary, Moreira, Irina S., additional, Duque, Anouk F., additional, van Loosdrecht, Mark C. M., additional, and Castro, Paula M. L., additional

Published
2017
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32. Biodegradation and Metabolic Pathway of 17 beta-Estradiol by Rhodococcus sp. ED55

Author

Moreira, Irina S., Murgolo, Sapia, Mascolo, Giuseppe, Castro, Paula M. L., and Veritati - Repositório Institucional da Universidade Católica Portuguesa

Subjects
Bioaugmentation, Rhodococcus sp. ED55, Endocrine disrupting chemicals, Wastewater, 17 beta-estradiol
Abstract

Endocrine disrupting compounds (EDCs) in the environment are considered a motif of concern, due to the widespread occurrence and potential adverse ecological and human health effects. The natural estrogen, 17 beta-estradiol (E2), is frequently detected in receiving water bodies after not being efficiently removed in conventional wastewater treatment plants (WWTPs), promoting a negative impact for both the aquatic ecosystem and human health. In this study, the biodegradation of E2 by Rhodococcus sp. ED55, a bacterial strain isolated from sediments of a discharge point of WWTP in Coloane, Macau, was investigated. Rhodococcus sp. ED55 was able to completely degrade 5 mg/L of E2 in 4 h in a synthetic medium. A similar degradation pattern was observed when the bacterial strain was used in wastewater collected from a WWTP, where a significant improvement in the degradation of the compound occurred. The detection and identification of 17 metabolites was achieved by means of UPLC/ESI/HRMS, which proposed a degradation pathway of E2. The acute test with luminescent marine bacterium Aliivibrio fischeri revealed the elimination of the toxicity of the treated effluent and the standardized yeast estrogenic (S-YES) assay with the recombinant strain of Saccharomyces cerevisiae revealed a decrease in the estrogenic activity of wastewater samples after biodegradation.

Published
2022

36. Enhanced neuronal differentiation by dynamic piezoelectric stimulation.

Author

Pinho, Tiffany S., Silva, Deolinda, Ribeiro, Jorge Cibrão, Marote, Ana, Lima, Rui, Batista, Salete J., Melo, Rita, Ribeiro, Clarisse, Cunha, Cristiana B., Moreira, Irina S., Lanceros‐Mendez, Senentxu, and Salgado, António J.

Abstract

Electroactive smart materials play an important role for tissue regenerative applications. Poly(vinylidene fluoride) (PVDF) is a specific subtype of piezoelectric electroactive material that generates electrical potential upon mechanical stimulation. This work focuses on the application of piezoelectric PVDF films for neural differentiation. Human neural precursor cells (hNPCs) are cultured on piezoelectric poled and non‐poled β‐PVDF films with or without a pre‐coating step of poly‐d‐lysine and laminin (PDL/L). Subsequently, hNPCs differentiation into the neuronal lineage is assessed (MAP2+ and DCX+) under static or dynamic (piezoelectric stimulation) culture conditions. The results demonstrate that poled and coated β‐PVDF films induce neuronal differentiation under static culture conditions which is further enhanced with mechanical stimulation. In silico calculations of the electrostatic potential of different domains of laminin, highlight the high polarity of those domains, which shows a clear preference to interact with the varying surface electric field of the piezoelectric material under mechanical stimulation. These interactions might explain the higher neuronal differentiation induced by poled β‐PVDF films pre‐coated with PDL/L under dynamic conditions. Our results suggest that electromechanical stimuli, such as the ones induced by piezoelectric β‐PVDF films, are suitable to promote neuronal differentiation and hold great promise for the development of neuroregenerative therapies. [ABSTRACT FROM AUTHOR]

Published
2023
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39. In Silico End-to-End Protein–Ligand Interaction Characterization Pipeline: The Case of SARS-CoV-2

Author

Rosário-Ferreira, Nícia, primary, Baptista, Salete J., additional, Barreto, Carlos A. V., additional, Rodrigues, Filipe E. P., additional, Silva, Tomás F. D., additional, Ferreira, Sara G. F., additional, Vitorino, João N. M., additional, Melo, Rita, additional, Victor, Bruno L., additional, Machuqueiro, Miguel, additional, and Moreira, Irina S., additional

Published
2021
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41. Biological removal processes in aerobic granular sludge exposed to diclofenac.

Author

Bessa, Vânia S., Moreira, Irina S., Van Loosdrecht, Mark C. M., and Castro, Paula M. L.

Subjects
MICROPOLLUTANTS, DICLOFENAC, WATER management, CHEMICAL oxygen demand, BATCH reactors, WASTEWATER treatment
Abstract

Diclofenac is a worldwide consumed drug included in the watch list of substances to be monitored according to the European Union Water Framework Directive (Directive 2013/39/EU). Aerobic granular sludge sequencing batch reactors (AGS-SBR) are increasingly used for wastewater treatment but there is scant information on the fate and effect of micropollutants to nutrient removal processes. An AGS-SBR fed with synthetic wastewater containing diclofenac was bioaugmented with a diclofenac degrading bacterial strain and performance and microbial community dynamics was analysed. Chemical oxygen demand, phosphate and ammonia removal were not affected by the micropollutant at 0.03 mM (9.54 mg L–1). The AGS was able to retain the degrading strain, which was detected in the sludge throughout after augmentation. Nevertheless, besides some adsorption to the biomass, diclofenac was not degraded by the augmented sludge given the short operating cycles and even if batch degradation assays confirmed that the bioaugmented AGS was able to biodegrade the compound. The exposure to the pharmaceutical affected the microbial community of the sludge, separating the two first phases of reactor operation (acclimatization and granulation) from subsequent phases. The AGS was able to keep the bioaugmented strain and to maintain the main functions of nutrient removal even through the long exposure to the pharmaceutical, but combined strategies are needed to reduce the spread of micropollutants in the environment. [ABSTRACT FROM AUTHOR]

Published
2022
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43. MENSAdb: a thorough structural analysis of membrane protein dimers

Author

Matos-Filipe, Pedro, Preto, António J, Koukos, Panagiotis I, Mourão, Joana, Bonvin, Alexandre M J J, Moreira, Irina S, Sub NMR Spectroscopy, NMR Spectroscopy, Sub NMR Spectroscopy, and NMR Spectroscopy

Subjects
Computer science, 030303 biophysics, Lipid Bilayers, Stacking, Computational biology, Biochemistry, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Lipid bilayer, Databases, Protein, 030304 developmental biology, 0303 health sciences, Agricultural and Biological Sciences(all), Biochemistry, Genetics and Molecular Biology(all), Membrane Proteins, Biomolecules (q-bio.BM), Hydrogen Bonding, Database Tool, Quantitative Biology - Biomolecules, Membrane protein, FOS: Biological sciences, AcademicSubjects/SCI00960, General Agricultural and Biological Sciences, Genetics and Molecular Biology(all), Information Systems
Abstract

Membrane proteins (MPs) are key players in a variety of different cellular processes and constitute the target of around 60% of all Food and Drug Administration–approved drugs. Despite their importance, there is still a massive lack of relevant structural, biochemical and mechanistic information mainly due to their localization within the lipid bilayer. To help fulfil this gap, we developed the MEmbrane protein dimer Novel Structure Analyser database (MENSAdb). This interactive web application summarizes the evolutionary and physicochemical properties of dimeric MPs to expand the available knowledge on the fundamental principles underlying their formation. Currently, MENSAdb contains features of 167 unique MPs (63% homo- and 37% heterodimers) and brings insights into the conservation of residues, accessible solvent area descriptors, average B-factors, intermolecular contacts at 2.5 Å and 4.0 Å distance cut-offs, hydrophobic contacts, hydrogen bonds, salt bridges, π–π stacking, T-stacking and cation–π interactions. The regular update and organization of all these data into a unique platform will allow a broad community of researchers to collect and analyse a large number of features efficiently, thus facilitating their use in the development of prediction models associated with MPs. Database URL: http://www.moreiralab.com/resources/mensadb.

Published
2021

47. Understanding the Binding Specificity of G-Protein Coupled Receptors toward G-Proteins and Arrestins: Application to the Dopamine Receptor Family

Author

Preto, A. J., primary, Barreto, Carlos A. V., additional, Baptista, Salete J., additional, Almeida, José Guilherme de, additional, Lemos, Agostinho, additional, Melo, André, additional, Cordeiro, M. Nátalia D. S., additional, Kurkcuoglu, Zeynep, additional, Melo, Rita, additional, and Moreira, Irina S., additional

Published
2020
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