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Submitted
Mendo, AS, Figueiredo S, Roma-Rodrigues C, Videira PA, Ma Z, Diniz M, Larguinho M, Costa PM, Lima JC, Pombeiro AJL, Baptista PV, Fernandes AR.  Submitted.  {Characterization of antiproliferative potential and biological targets of a copper compound containing 4'-phenyl terpyridine}, {SEP}. {JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY}. {20}:{935-948}., Number {6} Abstract
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Romero, MA, Basilio N, Moro AJ, Domingues M, Gonzalez-Delgado JA, Arteaga JF, Pischel U.  Submitted.  {Photocaged Competitor Guests: A General Approach Toward Light-Activated Cargo Release From Cucurbiturils}, {SEP 21}. {CHEMISTRY-A EUROPEAN JOURNAL}. {23}:{13105-13111}., Number {53} Abstract
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Costa, D, Galvao AM, Di Paolo RE, Freitas AA, Lima JC, Quina FH, Macanita AL.  Submitted.  {Photochemistry of the hemiketal form of anthocyanins and its potential role in plant protection from UV-B radiation}, {MAY 20}. {TETRAHEDRON}. {71}:{3157-3162}., Number {20} Abstract
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Huang, R, Avo J, Northey T, Chaning-Pearce E, dos Santos PL, Ward JS, Data P, Etherington MK, Fox MA, Penfold TJ, Berberan-Santos MN, Lima JC, Bryce MR, Dias FB.  Submitted.  {The contributions of molecular vibrations and higher triplet levels to the intersystem crossing mechanism in metal-free organic emitters}, {JUL 7}. {JOURNAL OF MATERIALS CHEMISTRY C}. {5}:{6269-6280}., Number {25} Abstract
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Delgado, JM, Raymundo A, Vilarigues M, Branco LC, Laia CAT.  Submitted.  {Characterization of a Novel Intrinsic Luminescent Room-Temperature Ionic Liquid Based on {[}P-6,P-6,P-6,P-14]{[}ANS]}, {JAN 7}. {CHEMISTRY-A EUROPEAN JOURNAL}. {21}:{726-732}., Number {2} Abstract
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Mendoza, J, Basilio N, Dangles O, Mora N, Al Bittar S, Pina F.  Submitted.  {Binding of the five multistate species of the anthocyanin analog 7-beta-D-glucopyranosyloxy-4'-hydroxyflavylium to the beta-cyclodextrin derivative captisol}, {AUG}. {DYES AND PIGMENTS}. {143}:{479-487}. Abstract
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Santoro, S, Vidorreta IM, Sebastian V, Moro A, Coelhoso IM, Portugal CAM, Lima JC, Desiderio G, Lombardo G, Drioli E, Mallada R, Crespo JG, Criscuoli A, Figoli A.  Submitted.  {A non-invasive optical method for mapping temperature polarization in direct contact membrane distillation}, {AUG 15}. {JOURNAL OF MEMBRANE SCIENCE}. {536}:{156-166}. Abstract
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Delgado, JM, Nunes D, Fortunato E, Laia CAT, Branco LC, Vilarigues M.  Submitted.  {The effect of three luminescent ionic liquids on corroded glass surfaces - A first step into stained-glass cleaning}, {APR}. {CORROSION SCIENCE}. {118}:{109-117}. Abstract
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Martins, ICB, Conceicao Oliveira M, Diogo HP, Branco LC, Duarte TM.  Submitted.  {MechanoAPI-ILs: Pharmaceutical Ionic Liquids Obtained through Mechanochemical Synthesis}, {APR 10}. {CHEMSUSCHEM}. {10}:{1360-1363}., Number {7} Abstract
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Thales, P, Vale TM, Dias RJ, Lourenço JM.  Submitted.  Empowering a Relational Database with Lazy State Determination.
Viciosa, MT, Santos G, Costa A, Danede F, Branco LC, Jordao N, Correia NT, Dionisio M.  Submitted.  {Dipolar motions and ionic conduction in an ibuprofen derived ionic liquid}. {PHYSICAL CHEMISTRY CHEMICAL PHYSICS}. {17}:{24108-24120}., Number {37} Abstract
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Pikramenou, Z, Weinstein J, Pan Q, Lewis F, Bassani DM, Wuerthner F, Moucheron C, Slota M, Diaz-Moscoso A, Karlsson J, Basilio N, Adams D, Scandola F, Bohne C, Lemon C, Campagna S, Rohacova J, Ohashi K, Ploetz P-A, Monti F, Kelly JM, Keane P, Gibson E, Lemercier G, Ruggi A, Cucinotta F, Gust D, Bradberry S, Vos J, Pistolis G, Mauro M, Tuite E, De Cola L, Ceroni P, Maneiro M, Galoppini E, Gunnlaugsson T.  Submitted.  {Self-organization of photo-active nanostructures: general discussion}. {FARADAY DISCUSSIONS}. {185}:{529-548}. Abstract
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Diniz, AM, Basilio N, Cruz H, Pina F, Parola JA.  Submitted.  {Spatiotemporal control over the co-conformational switching in pH-responsive flavylium-based multistate pseudorotaxanes}. {FARADAY DISCUSSIONS}. {185}:{361-379}. Abstract
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Basilio, N, Garnier T, Avo J, Danel M, Chassaing S, Pina F.  Submitted.  {Synthesis and multistate characterization of bis-flavylium dications - symmetric resorcinol- and phloroglucinol-type derivatives as stochastic systems}. {RSC ADVANCES}. {6}:{69698-69707}., Number {74} Abstract
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In Press
Simoes, SG, Dias L, Gouveia JP, Seixas J, de Miglio R, Gargiulo M, Long G, Giannakidis G.  In Press.  InSmart – A methodology for combining modelling with stakeholder input towards EU cities decarbonisation.. Journal of Cleaner Production.
2025
Duarte, M, Carvalho AL, Ferreira MC, Caires B, Romão MJ, Prates JAM, Najmudin S, Bayer EA, Fontes CMGA, Bule P.  2025.  Tripartite binding mode of cohesin-dockerin complexes from Ruminococcus flavefaciens involving naturally truncated dockerins, 2025. 301(7):110325. AbstractWebsite

Polysaccharides in plant cell walls serve as a rich carbon and energy source, yet their structural complexity presents a barrier to efficient degradation. To address this, anaerobic microorganisms like R. flavefaciens have developed sophisticated multi-enzyme complexes known as cellulosomes, which enable the efficient breakdown of these recalcitrant polysaccharides. These complexes are assembled through high-affinity interactions between cohesin (Coh) modules in scaffoldin proteins and dockerin (Doc) modules in cellulosomal enzymes. R. flavefaciens FD-1 harbors one of the most intricate cellulosomes described to date, comprising over 200 Doc-containing proteins encoded in its genome. Despite substantial research on this cellulosome, the role of a group of truncated but functional dockerins, known as group-2 Docs, remains unclear. In this study, we present a detailed structural and binding analysis of a Coh-Doc complex involving the cohesin from the cell-anchoring scaffoldin ScaE and a group-2 Doc that bears only one of the two Ca+2-coordinating loops that characterise the canonical Docs. Our findings reveal a novel tripartite binding mechanism, in which the cohesin can simultaneously bind two distinct dockerin units in three alternative conformations. This discovery provides new insights into the modular versatility of the R. flavefaciens cellulosome and sheds light on the mechanisms that enhance its efficiency in polysaccharide degradation.

2024
Sarrato, J, Raimundo B, Domingues L, Filipe SR, Lima CJ, Branco PS.  2024.  Synthesis of inverse push-pull coumarin dyes and their application as solvatochromic probes and labelling agents for bacterial cell membranes, SEP. DYES AND PIGMENTS. 228 Abstract
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Bravo, {AC}, Morão B, Luz A, Dourado R, Oliveira B, Guedes A, Moreira-Barbosa C, Fidalgo C, Mascarenhas-Lemos L, Costa-Santos {MP}, Maio R, Paulino J, {Viana Baptista} P, Fernandes {AR}, Cravo M.  2024.  Bringing Hope to Improve Treatment in Pancreatic Ductal Adenocarcinoma: A New Tool for Molecular Profiling of KRAS Mutations in Tumor and Plasma Samples, oct. Cancers. 16, Number 20: MDPI - Multidisciplinary Digital Publishing Institute Abstract

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) incidence is rising, and prognosis remains poor due to late diagnosis and limited effective therapies. Currently, patients are treated based on TNM staging, without molecular tumor characterization. This study aimed to validate a technique that combines the amplification refractory mutation system (ARMS) with high-resolution melting analysis (HRMA) for detecting mutations in codon 12 of KRAS in tumor and plasma, and to assess its prognostic value. Methods: Prospective study including patients with newly diagnosed PDAC with tumor and plasma samples collected before treatment. Mutations in codon 12 of KRAS (G12D, G12V, G12C, and G12R) were detected using ARMS–HRMA and compared to Sanger sequencing (SS). Univariate and multivariate analyses were used to evaluate the prognostic significance of these mutations. Results: A total of 88 patients, 93% with ECOG-PS 0–1, 57% with resectable disease. ARMS–HRMA technique showed a higher sensitivity than SS, both in tumor and plasma (77% vs. 51%; 25 vs. 0%, respectively). The most frequent mutation was G12D (n = 32, 36%), followed by G12V (n = 22, 25%). On multivariate analysis, patients with G12D and/or G12C mutations, either in tumor or plasma, had lower PFS (HR 1.792, 95% CI 1.061–3.02

{Franco Machado}, J, Cordeiro S, Duarte {JN }, Costa {PJ }, Mendes {PJ }, Garcia {MH}, Baptista {PV}, Fernandes {AR}, Morais {TS }.  2024.  Exploiting Co(III)-Cyclopentadienyl Complexes To Develop Anticancer Agents, apr. Inorganic Chemistry. 63:5783–5804., Number 13: ACS - American Chemical Society Abstract

In recent years, organometallic complexes have attracted much attention as anticancer therapeutics aiming at overcoming the limitations of platinum drugs that are currently marketed. Still, the development of half-sandwich organometallic cobalt complexes remains scarcely explored. Four new cobalt(III)-cyclopentadienyl complexes containing N,N-heteroaromatic bidentate, and phosphane ligands were synthesized and fully characterized by elemental analysis, spectroscopic techniques, and DFT methods. The cytotoxicity of all complexes was determined in vitro by the MTS assay in colorectal (HCT116), ovarian (A2780), and breast (MDA-MB-231 and MCF-7) human cancer cell lines and in a healthy human cell line (fibroblasts). The complexes showed high cytotoxicity in cancer cell lines, mostly due to ROS production, apoptosis, autophagy induction, and disruption of the mitochondrial membrane. Also, these complexes were shown to be nontoxic in vivo in an ex ovo chick embryo yolk sac membrane (YSM) assay.

Caseiro, C, McGregor NGS, Alves VD, Carvalho AL, Romão MJ, Davies GJ, Fontes CMGA, Bule P.  2024.  Family GH157 enzyme exhibits broad linkage tolerance and a dual endo/exo- β -glucanase activity on β-glucans, 2024. :137402. AbstractWebsite

The structural and chemical diversity of β-glucans is reflected on the variety of essential biological roles tackled by these polysaccharides. This natural heterogeneity requires an elaborate assortment of enzymatic mechanisms to assemble, degrade or modify, as well as to extract their full biotechnological potential. Recent metagenomic efforts have provided an unprecedented growth in potential new biocatalysts, most of which remain unconfirmed or uncharacterized. Here we report the first biochemical and structural characterization of two bacterial β-glucanases from the recently created glycoside hydrolase family 157 (LaGH157 and BcGH157) and investigate their molecular basis for substrate hydrolysis. Structural analysis by X-ray crystallography revealed that GH157 enzymes belong to clan GH-A, possessing a (β/α)8-barrel fold catalytic domain, two β-sandwich accessory domains and two conserved catalytic glutamates residues, with relative positions compatible with a retaining mechanism of hydrolysis. Specificity screening and enzyme kinetics suggest that the enzymes prefer mixed-linkage glucans over β-1,3-glucans. Activity screening showed that both enzymes exhibit pH optimum at 6.5 and temperature optimum for LaGH157 and BcGH157 at 25 °C and 48 °C, respectively. Product analysis with HPAEC-PAD and LC-MS revealed that both enzymes are endo-1,3(4)-β-glucanases, capable of cleaving β-1,3 and β-1,4-linked glucoses, when preceded by a β-1,3 linkage. Moreover, BcGH157 needs a minimum of 4 subsites occupied for hydrolysis to occur, while LaGH157 only requires 3 subsites. Additionally, LaGH157 possesses exohydrolytic activity on β-1,3 and branching β-1,6 linkages. This unusual bifunctional endo-1,3(4)/exo-1,3–1,6 activity constitutes an expansion on our understanding of β-glucan deconstruction, with the potential to inspire future applications.

Portela, PC, Silva MA, Almeida A, Damas GF, Salgueiro CA.  2024.  Tweaking the redox properties of PpcA from Geobacter metallireducens with protein engineering, 12. Biochemical Journal. 481(24):2017-2036. AbstractWebsite

Geobacter’s unique ability to perform extracellular electron transfer (EET) to electrodes in Microbial Fuel Cells (MFCs) has sparked the implementation of sustainable production of electrical energy. However, the electrochemical performance of Geobacter’s biofilms in MFCs remains challenging to implement industrially. Multiple approaches are being investigated to enhance MFC technologies. Protein engineering of multihaem cytochromes, key components of Geobacter’s EET pathways, can, conceivably, be pursued to improve the EET chain. The periplasmic cytochrome PpcA bridges ET from the inner to the outer membrane and its deletion impairs this crucial step. The functional characterisation of PpcA homologs from G. sulfurreducens (Gs) and G. metallireducens (Gm) revealed a significantly different redox behaviour even though they only differ by thirteen amino acids. In a previous study, we found that the single replacement of a tryptophan residue by methionine (W45M) in PpcAGm shifted the reduction potential value 33% towards that of PpcAGs. In this work, we expanded our investigation to include other non-conserved residues by conducting five mutation rounds. We identified the most relevant residues controlling the redox properties of PpcAGm. With just four mutations (K19, G25, N26, W45) the reduction potential value of PpcAGm was shifted 71% toward that of PpcAGs. Additionally, in the quadruple mutant, it was possible to replicate the haem oxidation order and the functional mechanisms of PpcAGs, which differ from those in PpcAGm. Overall, the mutants exhibit diverse redox and functional mechanisms that could be explored as a library for the future design of minimal, synthetic, ET chains in Geobacter.

2023
Duarte, M, Alves VD, Correia M, Caseiro C, Ferreira LMA, Romão MJ, Carvalho AL, Najmudin S, Bayer EA, Fontes CMGA, Bule P.  2023.  Structure-function studies can improve binding affinity of cohesin-dockerin interactions for multi-protein assemblies, 2023. 224:55-67. AbstractWebsite

The cellulosome is an elaborate multi-enzyme structure secreted by many anaerobic microorganisms for the efficient degradation of lignocellulosic substrates. It is composed of multiple catalytic and non-catalytic components that are assembled through high-affinity protein-protein interactions between the enzyme-borne dockerin (Doc) modules and the repeated cohesin (Coh) modules present in primary scaffoldins. In some cellulosomes, primary scaffoldins can interact with adaptor and cell-anchoring scaffoldins to create structures of increasing complexity. The cellulosomal system of the ruminal bacterium, Ruminococcus flavefaciens, is one of the most intricate described to date. An unprecedent number of different Doc specificities results in an elaborate architecture, assembled exclusively through single-binding-mode type-III Coh-Doc interactions. However, a set of type-III Docs exhibits certain features associated with the classic dual-binding mode Coh-Doc interaction. Here, the structure of the adaptor scaffoldin-borne ScaH Doc in complex with the Coh from anchoring scaffoldin ScaE is described. This complex, unlike previously described type-III interactions in R. flavefaciens, was found to interact in a dual-binding mode. The key residues determining Coh recognition were also identified. This information was used to perform structure-informed protein engineering to change the electrostatic profile of the binding surface and to improve the affinity between the two modules. The results show that the nature of the residues in the ligand-binding surface plays a major role in Coh recognition and that Coh-Doc affinity can be manipulated through rational design, a key feature for the creation of designer cellulosomes or other affinity-based technologies using tailored Coh-Doc interactions.

Pimenta, AI, Paquete CM, Morgado L, Edwards MJ, Clarke TA, Salgueiro CA, Pereira IAC, Duarte AG.  2023.  Characterization of the inner membrane cytochrome ImcH from Geobacter reveals its importance for extracellular electron transfer and energy conservation. Protein Science. 32:e4796., Number 11 AbstractWebsite

Abstract Electroactive bacteria combine the oxidation of carbon substrates with an extracellular electron transfer (EET) process that discharges electrons to an electron acceptor outside the cell. This process involves electron transfer through consecutive redox proteins that efficiently connect the inner membrane to the cell exterior. In this study, we isolated and characterized the quinone-interacting membrane cytochrome c ImcH from Geobacter sulfurreducens, which is involved in the EET process to high redox potential acceptors. Spectroscopic and electrochemical studies show that ImcH hemes have low midpoint redox potentials, ranging from −150 to −358 mV, and connect the oxidation of the quinol-pool to EET, transferring electrons to the highly abundant periplasmic cytochrome PpcA with higher affinity than to its homologues. Despite the larger number of hemes and transmembrane helices, the ImcH structural model has similarities with the NapC/NirT/NrfH superfamily, namely the presence of a quinone-binding site on the P-side of the membrane. In addition, the first heme, likely involved on the quinol oxidation, has apparently an unusual His/Gln coordination. Our work suggests that ImcH is electroneutral and transfers electrons and protons to the same side of the membrane, contributing to the maintenance of a proton motive force and playing a central role in recycling the menaquinone pool.

Portela, PC, Morgado L, Silva MA, Denkhaus L, Einsle O, Salgueiro CA.  2023.  Exploring oxidative stress pathways in Geobacter sulfurreducens: the redox network between MacA peroxidase and triheme periplasmic cytochromes. Frontiers in Microbiology. 14 AbstractWebsite

The recent reclassification of the strict anaerobe Geobacter sulfurreducens bacterium as aerotolerant brought attention for oxidative stress protection pathways. Although the electron transfer pathways for oxygen detoxification are not well established, evidence was obtained for the formation of a redox complex between the periplasmic triheme cytochrome PpcA and the diheme cytochrome peroxidase MacA. In the latter, the reduction of the high-potential heme triggers a conformational change that displaces the axial histidine of the low-potential heme with peroxidase activity. More recently, a possible involvement of the triheme periplasmic cytochrome family (PpcA-E) in the protection from oxidative stress in G. sulfurreducens was suggested. To evaluate this hypothesis, we investigated the electron transfer reaction and the biomolecular interaction between each PpcA-E cytochrome and MacA. Using a newly developed method that relies on the different NMR spectral signatures of the heme proteins, we directly monitored the electron transfer reaction from reduced PpcA-E cytochromes to oxidized MacA. The results obtained showed a complete electron transfer from the cytochromes to the high-potential heme of MacA. This highlights PpcA-E cytochromes’ efficient role in providing the necessary reducing power to mitigate oxidative stress situations, hence contributing to a better knowledge of oxidative stress protection pathways in G. sulfurreducens.

Dias, AMGC, Moreira IP, Lychko I, Lopes Soares C, Nurrito A, Moura Barbosa AJ, Lutz-Bueno V, Mezzenga R, Carvalho AL, Pina AS, Roque ACA.  2023.  Hierarchical self-assembly of a reflectin-derived peptide. Frontiers in Chemistry. 11 AbstractWebsite

Reflectins are a family of intrinsically disordered proteins involved in cephalopod camouflage, making them an interesting source for bioinspired optical materials. Understanding reflectin assembly into higher-order structures by standard biophysical methods enables the rational design of new materials, but it is difficult due to their low solubility. To address this challenge, we aim to understand the molecular self-assembly mechanism of reflectin’s basic unit—the protopeptide sequence YMDMSGYQ—as a means to understand reflectin’s assembly phenomena. Protopeptide self-assembly was triggered by different environmental cues, yielding supramolecular hydrogels, and characterized by experimental and theoretical methods. Protopeptide films were also prepared to assess optical properties. Our results support the hypothesis for the protopeptide aggregation model at an atomistic level, led by hydrophilic and hydrophobic interactions mediated by tyrosine residues. Protopeptide-derived films were optically active, presenting diffuse reflectance in the visible region of the light spectrum. Hence, these results contribute to a better understanding of the protopeptide structural assembly, crucial for the design of peptide- and reflectin-based functional materials.

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