Evaluación de las propiedades tribológicas y mecánicas de recubrimientos de CrC depositados por pulverización catódica magnetrón R.F.

Este artículo presenta los resultados obtenidos con el depósito de una serie de recubrimientos de CrC mediante pulverización catódica por magnetrón r.f., la cual presentó contenidos de carbono en el rango de 2558 % acorde a los análisis EDS. Los valores de dureza de estos recubrimientos estuvieron entre 15 y 24 GPa, hallándose los valores de mayor dureza en las muestras con contenido de carbono en el rango de 3953 %. Se encontró una correlación entre el contenido de carbono y los valores de los coeficientes de fricción, los cuales están en el rango de 0,70 a 0,15, obteniendo estos últimos valores para recubrimientos con exceso de carbono. El comportamiento al desgaste bajo pruebas de deslizamiento en seco mostró también una marcada dependencia con el contenido de carbono. Los mejores resultados de desgaste fueron obtenidos para los recubrimientos con el más alto contenido de carbono

Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases

Hydrogenases are efficient biocatalysts for H2 production and oxidation with various potential biotechnological applications.[NiFe]-class hydrogenases are highly active in both production and oxidation processes—albeit primarily biased to the latter—but suffer from being sensitive to O2.[NiFeSe] hydrogenases are a subclass of [NiFe] hydrogenases with, usually, an increased insensitivity to aerobic environments. In this study we aim to understand the structural causes of the low sensitivity of a [NiFeSe]-hydrogenase, when compared with a [NiFe] class enzyme, by studying the diffusion of O2. To unravel the differences between the two enzymes, we used computational methods comprising Molecular Dynamics simulations with explicit O2 and Implicit Ligand Sampling methodologies. With the latter, we were able to map the free energy landscapes for O2 permeation in both enzymes. We derived pathways from these energy landscapes and selected the kinetically more relevant ones with reactive flux analysis using transition path theory. These studies evidence the existence of quite different pathways in both enzymes and predict a lower permeation efficiency for O2 in the case of the [NiFeSe]-hydrogenase when compared with the [NiFe] enzyme. These differences can explain the experimentally observed lower inhibition by O2 on [NiFeSe]-hydrogenases, when compared with [NiFe]-hydrogenases. A comprehensive map of the residues lining the most important O2 pathways in both enzymes is also presented.publishersversionpublishe

Characterization of the multiheme cytochromes involved in the extracellular electron transfer pathway of Thermincola ferriacetica

Bioelectrochemical systems (BES) are emerging as a suite of versatile sustainable technologies to produce electricity and added‐value compounds from renewable and carbon‐neutral sources using electroactive organisms. The incomplete knowledge on the molecular processes that allow electroactive organisms to exchange electrons with electrodes has prevented their real‐world implementation. In this manuscript we investigate the extracellular electron transfer processes performed by the thermophilic Gram‐positive bacteria belonging to the Thermincola genus, which were found to produce higher levels of current and tolerate higher temperatures in BES than mesophilic Gram‐negative bacteria. In our study, three multiheme c‐type cytochromes, Tfer_0070, Tfer_0075, and Tfer_1887, proposed to be involved in the extracellular electron transfer pathway of T. ferri-acetica, were cloned and over‐expressed in E. coli. Tfer_0070 (ImdcA) and Tfer_1887 (PdcA) were purified and biochemically characterized. The electrochemical characterization of these proteins supports a pathway of extracellular electron transfer via these two proteins. By contrast, Tfer_0075 (CwcA) could not be stabilized in solution, in agreement with its proposed insertion in the pepti-doglycan wall. However, based on the homology with the outer‐membrane cytochrome OmcS, a structural model for CwcA was developed, providing a molecular perspective into the mechanisms of electron transfer across the peptidoglycan layer in Thermincola.publishersversionpublishe

The importance of lipid conjugation on anti-fusion peptides against Nipah virus

© 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).Nipah virus (NiV) is a recently emerging zoonotic virus that belongs to the Paramyxoviridae family and the Henipavirus genus. It causes a range of conditions, from asymptomatic infection to acute respiratory illness and fatal encephalitis. The high mortality rate of 40 to 90% ranks these viruses among the deadliest viruses known to infect humans. Currently, there is no antiviral drug available for Nipah virus disease and treatment is only supportive. Thus, there is an urgent demand for efficient antiviral therapies. NiV F protein, which catalyzes fusion between the viral and host membranes, is a potential target for antiviral drugs, as it is a key protein in the initial stages of infection. Fusion inhibitor peptides derived from the HRC-domain of the F protein are known to bind to their complementary domain in the protein's transient intermediate state, preventing the formation of a six-helix bundle (6HB) thought to be responsible for driving the fusion of the viral and cell membranes. Here, we evaluated the biophysical and structural properties of four different C-terminal lipid-tagged peptides. Different compositions of the lipid tags were tested to search for properties that might promote efficacy and broad-spectrum activity. Fluorescence spectroscopy was used to study the interaction of the peptides with biomembrane model systems and human blood cells. In order to understand the structural properties of the peptides, circular dichroism measurements and molecular dynamics simulations were performed. Our results indicate a peptide preference for cholesterol-enriched membranes and a lipid conjugation-driven stabilization of the peptide α-helical secondary structure. This work may contribute for the development of highly effective viral fusion against NiV inhibitors.This work was financially supported by Fundação para a Ciência e a Tecnologia—Ministério da Ciência, Tecnologia e Ensino Superior (FCT-MCTES, Portugal), through projects PTDC/BBB-BQB/3494/2014, PTDC/QUI-BIQ/114774/2009, PTDC/CCI-BIO/28200/2017 and Pest-OE/EQB/LA0004/2011, and by National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), project R01AI114736, lead by Anne Moscona (Columbia University Medical Center, NY, USA). This work was also financially supported by Project LISBOA-01-0145-FEDER-007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020-Programa Operacional Competitividade e Internacionalização (POCI) and by national funds through FCT-MCTES. MCM, PMS and DL were supported by FCT-MCTES fellowships SFRH/BPD/118731/2016, SFRH/BD/118413/2016 and SFRH/BPD/92537/2013, respectively.info:eu-repo/semantics/publishedVersio

The NBDs that wouldn't die: A cautionary tale of the use of isolated nucleotide binding domains of ABC transporters

COMATOSE (CTS), the plant homologue of Adrenoleukodystrophy protein, is a full length ABC transporter localised in peroxisomes. In a recent article, we reported that the two nucleotide binding domains of CTS are not functionally equivalent in vivo. Mutations in conserved residues in the Walker A (K487A) and B (D606N) motifs of NBD1 resulted in a null phenotype, whereas identical mutations in the equivalent residues in NBD2 (K1136A and D1276N) had no detectable effect.1 In order to study the effect of these mutations on the ATPase activity of the nucleotide binding domains, we cloned and expressed the isolated NBDs as maltose binding protein (MBP) fusion proteins. We show that ATPase activity is associated with the isolated MBP-NBDs. However, mutations of amino acids located in conserved motifs did not result in striking reduction in activity despite well characterized roles in ATP binding and hydrolysis. We urge caution in the interpretation of results obtained from the study of isolated NBD fusions and their extrapolation to the mechanism of ATP hydrolysis in ABC transporter proteins

Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment

© The Author(s) 2020. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.The influenza virus fusion process, whereby the virus fuses its envelope with the host endosome membrane to release the genetic material, takes place in the acidic late endosome environment. Acidification triggers a large conformational change in the fusion protein, hemagglutinin (HA), which enables the insertion of the N-terminal region of the HA2 subunit, known as the fusion peptide, into the membrane of the host endosome. However, the mechanism by which pH modulates the molecular properties of the fusion peptide remains unclear. To answer this question, we performed the first constant-pH molecular dynamics simulations of the influenza fusion peptide in a membrane, extending for 40 µs of aggregated time. The simulations were combined with spectroscopic data, which showed that the peptide is twofold more active in promoting lipid mixing of model membranes at pH 5 than at pH 7.4. The realistic treatment of protonation introduced by the constant-pH molecular dynamics simulations revealed that low pH stabilizes a vertical membrane-spanning conformation and leads to more frequent contacts between the fusion peptide and the lipid headgroups, which may explain the increase in activity. The study also revealed that the N-terminal region is determinant for the peptide's effect on the membrane.This work was financially supported by FCT—Fundação para a Ciência e a Tecnologia, Portugal, through projects PTDC/QUI-BIQ/114774/2009, PTDC/CCI-BIO/28200/2017 and Pest-OE/EQB/LA0004/2011. This work was also financially supported by Project LISBOA-01-0145-FEDER-007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020—Programa Operacional Competitividade e Internacionalização (POCI) and by national funds through FCT—Fundação para a Ciência e a Tecnologia. DL was supported by FCT post-doc fellowship SFRH/BPD/92537/2013.info:eu-repo/semantics/publishedVersio

The amino acids motif-32GSSYN36-in the catalytic domain of E. coli flavorubredoxin NO reductase is essential for its activity

Funding Information: Funding: This study was financially supported by the Portuguese Fundação para a Ciência e Tec-nologia (FCT), grants PTDC/BIA-BQM/27959/2017 and PTDC/BIA-BQM/0562/2020, and Project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement 810856. MCM is the recipient of FCT grant SFRH/BD/143651/2019. BAS is the recipient of FCT grant DFA/BD/8066/2020. Funding Information: This study was financially supported by the Portuguese Funda??o para a Ci?ncia e Tecnologia (FCT), grants PTDC/BIA-BQM/27959/2017 and PTDC/BIA-BQM/0562/2020, and Project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020. This project has also received funding from the European Union?s Horizon 2020 research and innovation program under grant agreement 810856. MCM is the recipient of FCT grant SFRH/BD/143651/2019. BAS is the recipient of FCT grant DFA/BD/8066/2020. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Flavodiiron proteins (FDPs) are a family of modular and soluble enzymes endowed with nitric oxide and/or oxygen reductase activities, producing N2O or H2O, respectively. The FDP from Escherichia coli, which, apart from the two core domains, possesses a rubredoxin-like domain at the C-terminus (therefore named flavorubredoxin (FlRd)), is a bona fide NO reductase, exhibiting O2 reducing activity that is approximately ten times lower than that for NO. Among the flavorubredoxins, there is a strictly conserved amino acids motif,-G[S,T]SYN-, close to the catalytic diiron center. To assess its role in FlRd’s activity, we designed several site-directed mutants, replacing the conserved residues with hydrophobic or anionic ones. The mutants, which maintained the general characteristics of the wild type enzyme, including cofactor content and integrity of the diiron center, revealed a decrease of their oxygen reductase activity, while the NO reductase activity—specifically, its physiological function—was almost completely abolished in some of the mutants. Molecular modeling of the mutant proteins pointed to subtle changes in the predicted structures that resulted in the reduction of the hydration of the regions around the conserved residues, as well as in the elimination of hydrogen bonds, which may affect proton transfer and/or product release.publishe

Identification of novel candidate predisposing genes in familial nonmedullary thyroid carcinoma implicating DNA damage repair pathways

Funding Information: The authors are thankful to the patients and their families for their cooperation. The authors are thankful to Liga Portuguesa Contra o Cancro\u2014N\u00FAcleo Regional do Sul (LPCC\u2010NRS) that granted the researcher Marta Pojo. This study was funded by LPCC\u2010NRS, Televis\u00E3o Independente, Instituto Portugu\u00EAs de Oncologia de Lisboa Francisco Gentil \u2010 E.P.E (IPOLFG), iNOVA4Health R&D Unit (UIDB/04462/2020 and UIDP/04462/2020), a program financially supported by Funda\u00E7\u00E3o para a Ci\u00EAncia e a Tecnologia (FCT), Minist\u00E9rio da Ci\u00EAncia, Tecnologia e Ensino Superior (MCTES), Associa\u00E7\u00E3o de Endocrinologia Oncol\u00F3gica, MOSTMICRO\u2010ITQB R&D Unit (UIDB/04612/2020 and UIDP/04612/2020), and the Associated Laboratory LS4FUTURE (LA/P/0087/2020). Carolina Pires was granted a PhD scholarship by FCT\u20142020.07120.BD ( https://doi.org/10.54499/2020.07120.BD ). In\u00EAs J. Marques was a recipient of a PhD scholarship from the PhD Programme ProRegeM (Mechanisms of Disease and Regenerative Medicine) approved by FCT\u2014PD/BD/108086/2015. Publisher Copyright: © 2024 The Author(s). International Journal of Cancer published by John Wiley & Sons Ltd on behalf of UICC.The genetic basis of nonsyndromic familial nonmedullary thyroid carcinoma (FNMTC) is still poorly understood, as the susceptibility genes identified so far only account for a small percentage of the genetic burden. Recently, germline mutations in DNA repair-related genes have been reported in cases with thyroid cancer. In order to clarify the genetic basis of FNMTC, 94 genes involved in hereditary cancer predisposition, including DNA repair genes, were analyzed in 48 probands from FNMTC families, through targeted next-generation sequencing (NGS). Genetic variants were selected upon bioinformatics analysis and in silico studies. Structural modeling and network analysis were also performed. In silico results of NGS data unveiled likely pathogenic germline variants in 15 families with FNMTC, in genes encoding proteins involved in DNA repair (ATM, CHEK2, ERCC2, BRCA2, ERCC4, FANCA, FANCD2, FANCF, and PALB2) and in the DICER1, FLCN, PTCH1, BUB1B, and RHBDF2 genes. Structural modeling predicted that most missense variants resulted in the disruption of networks of interactions between residues, with implications for local secondary and tertiary structure elements. Functional annotation and network analyses showed that the involved DNA repair proteins functionally interact with each other, within the same DNA repair pathway and across different pathways. MAPK activation was a common event in tumor progression. This study supports that rare germline variants in DNA repair genes may be accountable for FNMTC susceptibility, with potential future utility in patients' clinical management, and reinforces the relevance of DICER1 in disease etiology.publishersversionepub_ahead_of_prin

Parainfluenza fusion peptide promotes membrane fusion by assembling into oligomeric porelike structures

© 2022 The Authors. Published by American Chemical SocietyParamyxoviruses are enveloped viruses harboring a negative-sense RNA genome that must enter the host’s cells to replicate. In the case of the parainfluenza virus, the cell entry process starts with the recognition and attachment to target receptors, followed by proteolytic cleavage of the fusion glycoprotein (F) protein, exposing the fusion peptide (FP) region. The FP is responsible for binding to the target membrane, and it is believed to play a crucial role in the fusion process, but the mechanism by which the parainfluenza FP (PIFP) promotes membrane fusion is still unclear. To elucidate this matter, we performed biophysical experimentation of the PIFP in membranes, together with coarse grain (CG) and atomistic (AA) molecular dynamics (MD) simulations. The simulation results led to the pinpointing of the most important PIFP amino acid residues for membrane fusion and show that, at high concentrations, the peptide induces the formation of a water-permeable porelike structure. This structure promotes lipid head intrusion and lipid tail protrusion, which facilitates membrane fusion. Biophysical experimental results validate these findings, showing that, depending on the peptide/lipid ratio, the PIFP can promote fusion and/or membrane leakage. Our work furthers the understanding of the PIFP-induced membrane fusion process, which might help foster development in the field of viral entry inhibition.This work was financially supported by FCT-Fundação para a Ciência e a Tecnologia, Portugal, through project PTDC/CCI-BIO/28200/2017 and by the European Union (H2020-FETOPEN-2018-2019-2020-01, grant no. 828774). This work was also financially supported by Project LISBOA-01-0145-FEDER-007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020_Programa Operacional Competitividade e Internacionalização (POCI). M.V. and D.A.M. thank FCT for their PhD fellowships (SFRH/BD/148542/2019 and PD/BD/136752/2018, respectively). M.N.M. thanks FCT for the Post-Doc fellowship CEECIND/04124/2017. M.N.M. and D.L. thank the MACC for the computing hours in their HPC center (CPCA/A0/7329/2020 and CPCA/A0/7305/2020).info:eu-repo/semantics/publishedVersio

Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli

Funding Information: The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This project has received funding from the European Union\u2019s Horizon 2020 research and innovation programme under grant agreement 814408 SHIKIFACTORY100\u2013Modular cell factories for the production of 100 compounds from the Shikimate pathway. This work was supported by FCT\u2013Funda\u00E7\u00E3o para a Ci\u00EAncia e a Tecnologia, I.P., through MOSTMICRO-ITQB R&D Unit (UIDB/04612/2020, UIDP/04612/2020) and LS4FUTURE Associated Laboratory (LA/P/0087/2020). Publisher Copyright: Copyright © 2024 Ferreira, Balola, Sveshnikova, Hatzimanikatis, Vilaça, Maia, Carreira, Stoney, Carbonell, Souza, Correia, Lousa, Soares and Rocha.Developing efficient bioprocesses requires selecting the best biosynthetic pathways, which can be challenging and time-consuming due to the vast amount of data available in databases and literature. The extension of the shikimate pathway for the biosynthesis of commercially attractive molecules often involves promiscuous enzymes or lacks well-established routes. To address these challenges, we developed a computational workflow integrating enumeration/retrosynthesis algorithms, a toolbox for pathway analysis, enzyme selection tools, and a gene discovery pipeline, supported by manual curation and literature review. Our focus has been on implementing biosynthetic pathways for tyrosine-derived compounds, specifically L-3,4-dihydroxyphenylalanine (L-DOPA) and dopamine, with significant applications in health and nutrition. We selected one pathway to produce L-DOPA and two different pathways for dopamine–one already described in the literature and a novel pathway. Our goal was either to identify the most suitable gene candidates for expression in Escherichia coli for the known pathways or to discover innovative pathways. Although not all implemented pathways resulted in the accumulation of target compounds, in our shake-flask experiments we achieved a maximum L-DOPA titer of 0.71 g/L and dopamine titers of 0.29 and 0.21 g/L for known and novel pathways, respectively. In the case of L-DOPA, we utilized, for the first time, a mutant version of tyrosinase from Ralstonia solanacearum. Production of dopamine via the known biosynthesis route was accomplished by coupling the L-DOPA pathway with the expression of DOPA decarboxylase from Pseudomonas putida, resulting in a unique biosynthetic pathway never reported in literature before. In the context of the novel pathway, dopamine was produced using tyramine as the intermediate compound. To achieve this, tyrosine was initially converted into tyramine by expressing TDC from Levilactobacillus brevis, which, in turn, was converted into dopamine through the action of the enzyme encoded by ppoMP from Mucuna pruriens. This marks the first time that an alternative biosynthetic pathway for dopamine has been validated in microbes. These findings underscore the effectiveness of our computational workflow in facilitating pathway enumeration and selection, offering the potential to uncover novel biosynthetic routes, thus paving the way for other target compounds of biotechnological interest.publishersversionpublishe