Coelho, C, Muthukumaran J, Santos-Silva T, Romão MJ.
2019.
Systematic exploration of predicted destabilizing nonsynonymous single nucleotide polymorphisms (nsSNPs) of human aldehyde oxidase: A Bio-informatics study. Pharmacology Research & Perspectives. 7:e00538., Number 6
AbstractAbstract Aldehyde Oxidase (hAOX1) is a cytosolic enzyme involved in the metabolism of drugs and xenobiotic compounds. The enzyme belongs to the xanthine oxidase (XO) family of Mo containing enzyme and is a homo-dimer of two 150 kDa monomers. Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs) of hAOX1 have been reported as affecting the ability of the enzyme to metabolize different substrates. Some of these nsSNPs have been biochemically and structurally characterized but the lack of a systematic and comprehensive study regarding all described and validated nsSNPs is urgent, due to the increasing importance of the enzyme in drug development, personalized medicine and therapy, as well as in pharmacogenetic studies. The objective of the present work was to collect all described nsSNPs of hAOX1 and utilize a series of bioinformatics tools to predict their effect on protein structure stability with putative implications on phenotypic functional consequences. Of 526 nsSNPs reported in NCBI-dbSNP, 119 are identified as deleterious whereas 92 are identified as nondeleterious variants. The stability analysis was performed for 119 deleterious variants and the results suggest that 104 nsSNPs may be responsible for destabilizing the protein structure, whereas five variants may increase the protein stability. Four nsSNPs do not have any impact on protein structure (neutral nsSNPs) of hAOX1. The prediction results of the remaining six nsSNPs are nonconclusive. The in silico results were compared with available experimental data. This methodology can also be used to identify and prioritize the stabilizing and destabilizing variants in other enzymes involved in drug metabolism.
Branco, PS, Peixoto D, Figueiredo M, Malta G, Roma-Rodrigues C, Batista PV, Fernandes AR, Barroso S, Carvalho AL, Afonso CAM, Ferreira LM.
2018.
Synthesis, cytotoxicity evaluation in human cell lines and in vitro DNA interaction of a hetero arylidene-9(10H)-anthrone. European Journal of Organic Chemistry. :n/a–n/a.
AbstractA new and never yet reported hetero arylidene-9(10H)-anthrone structure (4) was unexpectedly isolated on reaction of 1,2-dimethyl-3-ethylimidazolium iodide (2) and 9-anthracenecarboxaldehyde (3) under basic conditions. Its structure was unequivocally attributed by X-ray crystallography. No cytotoxicity in human healthy fibroblasts and in two different cancer cell lines was observed indicating its applicability in biological systems. Compound 4 interacts with CT-DNA by intercalation between the adjacent base pairs of DNA with a high binding affinity (Kb = 2.0(± 0.20) x 105 M-1) which is 10x higher than that described for doxorubicin (Kb = 3.2 (±0.23) × 104 M-1). Furthermore, compound 4 quenches the fluorescence emission of GelRed-CT-DNA system with a quenching constant (KSV) of 3.3(±0.3) x 103 M-1 calculated by the Stern-Volmer equation.
Outis, M, Rosa V, Laia CAT, Lima JC, Barroso S, Carvalho AL, Calhorda MJ, Avilés T.
2020.
Synthesis, Crystal Structure, and DFT Study of Two New Dinuclear Copper(I) Complexes Bearing Ar-BIAN Ligands Functionalized with NO2 Groups. European Journal of Inorganic Chemistry. 2020:2900-2911., Number 30
Abstract{Two new bis(aryl-imino)-acenaphthene, Ar-BIAN (Ar = 2
Moreira, IP, Esteves C, Palma SICJ, Ramou E, Carvalho ALM, Roque ACA.
2022.
Synergy between silk fibroin and ionic liquids for active gas-sensing materials. Materials Today Bio. :100290.
AbstractSilk fibroin is a biobased material with excellent biocompatibility and mechanical properties, but its use in bioelectronics is hampered by the difficult dissolution and low intrinsic conductivity. Some ionic liquids are known to dissolve fibroin but removed after fibroin processing. However, ionic liquids and fibroin can cooperatively give rise to functional materials, and there are untapped opportunities in this combination. The dissolution of fibroin, followed by gelation, in designer ionic liquids from the imidazolium chloride family with varied alkyl chain lengths (2–10 carbons) is shown here. The alkyl chain length of the anion has a large impact on fibroin secondary structure which adopts unconventional arrangements, yielding robust gels with distinct hierarchical organization. Furthermore, and due to their remarkable air-stability and ionic conductivity, fibroin ionogels are exploited as active electrical gas sensors in an electronic nose revealing the unravelled possibilities of fibroin in soft and flexible electronics.
Romao, MJ, Barata BAS, Archer M, Lobeck K, Moura I, Carrondo MA, Legall J, Lottspeich F, Huber R, Moura JJG.
1993.
SUBUNIT COMPOSITION, CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC STUDIES OF THE DESULFOVIBRIO-GIGAS ALDEHYDE OXIDOREDUCTASE CONTAINING MOLYBDENUM AND 2FE-2S CENTERS. European Journal of Biochemistry. 215:729-732., Number 3
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Vilela-Alves, G, Manuel RR, Viegas A, Carpentier P, Biaso F, Guigliarelli B, Pereira IAC, Romão MJ, Mota C.
2024.
Substrate-dependent oxidative inactivation of a W-dependent formate dehydrogenase involving selenocysteine displacement. bioRxiv. : Cold Spring Harbor Laboratory
AbstractMetal-dependent formate dehydrogenases are very promising targets for enzyme optimization and design of bio-inspired catalysts for CO2 reduction, towards novel strategies for climate change mitigation. For effective application of these enzymes, the catalytic mechanism must be fully understood, and the molecular determinants clarified. Despite numerous studies, several doubts persist, namely regarding the role played by the possible dissociation of the SeCys ligand from the Mo/W active site. Additionally, the O2 sensitivity of these enzymes must also be understood as it poses an important obstacle for biotechnological applications. Here we present a combined biochemical, spectroscopic, and structural characterization of Desulfovibrio vulgaris FdhAB (DvFdhAB) when exposed to oxygen in the presence of a substrate (formate or CO2). This study reveals that O2 inactivation is promoted by the presence of either substrate and involves forming a new species in the active site, captured in the crystal structures, where the SeCys ligand is displaced from tungsten coordination and replaced by a dioxygen or peroxide molecule. This new form was reproducibly obtained and supports the conclusion that, although W-DvFdhAB can catalyze the oxidation of formate in the presence of oxygen for some minutes, it gets irreversibly inactivated after prolonged O2 exposure in the presence of either substrate. These results reveal that oxidative inactivation does not require reduction of the metal, as widely assumed, as it can also occur in the oxidized state in the presence of CO2.Competing Interest StatementThe authors have declared no competing interest.AORAldehyde Oxido-reductaseDTTDithiothreitolDvDesulfovibrio vulgarisEPRElectron Paramagnetic ResonanceFdhFormate dehydrogenaseHPHigh PressureMGDMolybdopterin Guanine DinucleotidesNDNew dropROSReactive Oxygen SpeciesSODSuperoxide dismutaseTSAThermal Shift Assay
Huber, R, Hof P, Duarte RO, Moura JJG, Moura I, Liu MY, Legall J, Hille R, Archer M, Romao MJ.
1996.
A structure-based catalytic mechanism for the xanthine oxidase family of molybdenum enzymes. Proceedings of the National Academy of Sciences of the United States of America. 93:8846-8851., Number 17
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Terao, M, Romão MJ, Leimkühler S, Bolis M, Fratelli M, Coelho C, Santos-Silva T, Garattini E.
2016.
Structure and function of mammalian aldehyde oxidases. Archives of Toxicology. 90:753–780., Number 4
AbstractMammalian aldehyde oxidases (AOXs; EC1.2.3.1) are a group of conserved proteins belonging to the family of molybdo-flavoenzymes along with the structurally related xanthine dehydrogenase enzyme. AOXs are characterized by broad substrate specificity, oxidizing not only aromatic and aliphatic aldehydes into the corresponding carboxylic acids, but also hydroxylating a series of heteroaromatic rings. The number of AOX isoenzymes expressed in different vertebrate species is variable. The two extremes are represented by humans, which express a single enzyme (AOX1) in many organs and mice or rats which are characterized by tissue-specific expression of four isoforms (AOX1, AOX2, AOX3, and AOX4). In vertebrates each AOX isoenzyme is the product of a distinct gene consisting of 35 highly conserved exons. The extant species-specific complement of AOX isoenzymes is the result of a complex evolutionary process consisting of a first phase characterized by a series of asynchronous gene duplications and a second phase where the pseudogenization and gene deletion events prevail. In the last few years remarkable advances in the elucidation of the structural characteristics and the catalytic mechanisms of mammalian AOXs have been made thanks to the successful crystallization of human AOX1 and mouse AOX3. Much less is known about the physiological function and physiological substrates of human AOX1 and other mammalian AOX isoenzymes, although the importance of these proteins in xenobiotic metabolism is fairly well established and their relevance in drug development is increasing. This review article provides an overview and a discussion of the current knowledge on mammalian AOX.
Goncalves, LML, Cunha C, Almeida G, Macieira S, Costa C, Lampreia J, Romao MJ, Moura JJG, Moura I.
2001.
Structural studies on Desulfovibrio desulfuricans ATCC 27774 multiheme nitrite reductase - characterization of the subunits. Journal of Inorganic Biochemistry. 86:316-316., Number 1
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Lima, CDL, Coelho H, Gimeno A, Trovão F, Diniz A, Dias JS, Jiménez-Barbero J, Corzana F, Carvalho AL, Cabrita EJ, Marcelo F.
2021.
Structural insights into the molecular recognition mechanism of the cancer and pathogenic epitope, LacdiNAc by immune-related lectins, 2021. Chemistry – A European JournalChemistry – A European Journal. n/a(n/a): John Wiley & Sons, Ltd
AbstractInteractions of glycan-specific epitopes to human lectin receptors represent novel immune checkpoints for investigating cancer and infection diseases. By employing a multidisciplinary approach that combines isothermal titration calorimetry, NMR spectroscopy, molecular dynamics simulations, and X-ray crystallography, we disclosed the molecular determinants that govern the recognition of the tumour and pathogenic glycobiomarker LacdiNAc (GalNAc?1-4GlcNAc, LDN), including their comparison with the ubiquitous LacNAc epitope (Gal?1-4GlcNAc, LN), by two human immune-related lectins, galectin-3 (hGal-3) and the macrophage galactose C-type lectin (hMGL). A different mechanism of binding and interactions is observed for the hGal-3/LDN and hMGL/LDN complexes, which explains the remarkable difference in the binding specificity of LDN and LN by these two lectins. The new structural clues reported herein are fundamental for the chemical design of mimetics targeting hGal-3/hMGL recognition process.
Bras, JLA, Cartmell A, Carvalho ALM, Verze G, Bayer EA, Vazana Y, Correia MAS, Prates JAM, Ratnaparkhe S, Boraston AB, Romao MJ, Fontes CMGA, Gilbert HJ.
2011.
Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis. Proceedings of the National Academy of Sciences of the United States of America. 108:5237-5242., Number 13
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Nóbrega, CS, Carvalho AL, Romão MJ, Pauleta SR.
2023.
Structural Characterization of Neisseria gonorrhoeae Bacterial Peroxidase—Insights into the Catalytic Cycle of Bacterial Peroxidases. International Journal of Molecular Sciences. 24, Number 7
AbstractNeisseria gonorrhoeae is an obligate human pathogenic bacterium responsible for gonorrhea, a sexually transmitted disease. The bacterial peroxidase, an enzyme present in the periplasm of this bacterium, detoxifies the cells against hydrogen peroxide and constitutes one of the primary defenses against exogenous and endogenous oxidative stress in this organism. The 38 kDa heterologously produced bacterial peroxidase was crystallized in the mixed-valence state, the active state, at pH 6.0, and the crystals were soaked with azide, producing the first azide-inhibited structure of this family of enzymes. The enzyme binds exogenous ligands such as cyanide and azide, which also inhibit the catalytic activity by coordinating the P heme iron, the active site, and competing with its substrate, hydrogen peroxide. The inhibition constants were estimated to be 0.4 ± 0.1 µM and 41 ± 5 mM for cyanide and azide, respectively. Imidazole also binds and inhibits the enzyme in a more complex mechanism by binding to P and E hemes, which changes the reduction potential of the latest heme. Based on the structures now reported, the catalytic cycle of bacterial peroxidases is revisited. The inhibition studies and the crystal structure of the inhibited enzyme comprise the first platform to search and develop inhibitors that target this enzyme as a possible new strategy against N. gonorrhoeae.
Palma, AS, Pinheiro B, Liu Y, Takeda Y, Chai W, Ito Y, Romao MJ, Carvalho AL, Feizi T.
2013.
The Structural Basis of the Recognition of Di-glucosylated N-glycans by the ER Lectin Malectin. Glycobiology. 23:1368-1369., Number 11
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