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Garattini, E, Mendel R, Romao MJ, Wright R, Terao M.  2003.  Mammalian molybdo-flavoenzymes, an expanding family of proteins: structure, genetics, regulation, function and pathophysiology. Biochemical Journal. 372:15-32. AbstractWebsite
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Garcia-Alvarez, B, Melero R, Dias FMV, Prates JAM, Fontes CMGA, Smith SP, Romao MJ, Carvalho AL, Llorca O.  2011.  Molecular Architecture and Structural Transitions of a Clostridium thermocellum Mini-Cellulosome. Journal of Molecular Biology. 407:571-580., Number 4 AbstractWebsite
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Gavel, OY, Kladova AV, Bursakov SA, Dias JM, Texeira S, Shnyrov VL, Moura JJG, Moura I, Romao MJ, Trincao J.  2008.  Purification, crystallization and preliminary X-ray diffraction analysis of adenosine triphosphate sulfurylase (ATPS) from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774. Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 64:593-595. AbstractWebsite
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Glatigny, A, Hof P, Romao MJ, Huber R, Scazzocchio C.  1998.  Altered specificity mutations define residues essential for substrate positioning in xanthine dehydrogenase. Journal of Molecular Biology. 278:431-438., Number 2 AbstractWebsite
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Gomes, D, Correia MAS, Romão MJ, Passarinha LA, Sousa A.  2023.  Integrated approaches for the separation and purification of recombinant HPV16 E6 protein from Escherichia coli crude extracts, 2023. 315:123647. AbstractWebsite

Human papillomavirus (HPV) is a sexually transmissible virus responsible for 5% of global human cancers and associated with 99% of cervical cancer cases. The oncogenic potential of high-risk HPVs is mainly related to the E6 and E7 oncoproteins, which are responsible, at least in part, for inactivating the p53 and pRb tumor suppressor proteins. Due to the critical role of the E6 protein in malignant tumorigenesis, it is widely recognized as a therapeutic target for anti-HPV drug development. Nevertheless, it is required to obtain large amounts of protein with high purity to perform biointeraction studies with the potential inhibitor drugs. In this work, recombinant dual-tagged E6 protein (His6-MBP-E6) was expressed from Escherichia coli (E. coli) cultures and successfully extracted by sonication/ice cycles. Affinity chromatography using MBPtrap columns allowed 85 ± 5% protein recovery with the elimination of major host heterologous proteins in a single fraction. Subsequently, a polishing step was studied by applying anionic exchange (QSepharose), size exclusion (Superdex), or immobilized-metal affinity chromatography (HisTrap). The combination of affinity chromatography with size exclusion or two affinity chromatography techniques allowed us to obtain 82 ± 2% and 94 ± 3%, of highly pure His6-MBP-E6, respectively. Also, the secondary structure of His6-MBP-E6 is preserved in both purification strategies, as appraised by circular dichroism and western-blot studies. Thermal shift assay confirmed the CD results and suggested potential additives for protein stabilization. Altogether, the reproducible strategies established for the purification of His6-MBP-E6 protein could be successfully applied to later perform biointeraction studies and structural characterization of protein–ligand complexes.

Gomes, AS, Trovão F, Andrade Pinheiro B, Freire F, Gomes S, Oliveira C, Domingues L, Romão MJ, Saraiva L, Carvalho AL.  2018.  The Crystal Structure of the R280K Mutant of Human p53 Explains the Loss of DNA Binding. International Journal of Molecular Sciences. 19, Number 4}, ARTICLE NUMBER = {1184 AbstractWebsite

The p53 tumor suppressor is widely found to be mutated in human cancer. This protein is regarded as a molecular hub regulating different cell responses, namely cell death. Compelling data have demonstrated that the impairment of p53 activity correlates with tumor development and maintenance. For these reasons, the reactivation of p53 function is regarded as a promising strategy to halt cancer. In the present work, the recombinant mutant p53R280K DNA binding domain (DBD) was produced for the first time, and its crystal structure was determined in the absence of DNA to a resolution of 2.0 Å. The solved structure contains four molecules in the asymmetric unit, four zinc(II) ions, and 336 water molecules. The structure was compared with the wild-type p53 DBD structure, isolated and in complex with DNA. These comparisons contributed to a deeper understanding of the mutant p53R280K structure, as well as the loss of DNA binding related to halted transcriptional activity. The structural information derived may also contribute to the rational design of mutant p53 reactivating molecules with potential application in cancer treatment.

Gomes, AS, Ramos H, Gomes S, Loureiro JB, Soares J, Barcherini V, Monti P, Fronza G, Oliveira C, Domingues L, Bastos M, Dourado DFAR, Carvalho AL, Romão MJ, Pinheiro B, Marcelo F, Carvalho A, Santos MMM, Saraiva L.  2020.  SLMP53-1 interacts with wild-type and mutant p53 DNA-binding domain and reactivates multiple hotspot mutations, 2020. 1864(1):129440. AbstractWebsite

BackgroundHalf of human cancers harbour TP53 mutations that render p53 inactive as a tumor suppressor. As such, reactivation of mutant (mut)p53 through restoration of wild-type (wt)-like function represents one of the most promising therapeutic strategies in cancer treatment. Recently, we have reported the (S)-tryptophanol-derived oxazoloisoindolinone SLMP53-1 as a new reactivator of wt and mutp53 R280K with in vitro and in vivo p53-dependent antitumor activity. The present work aimed a mechanistic elucidation of mutp53 reactivation by SLMP53-1.
Methods and results
By cellular thermal shift assay (CETSA), it is shown that SLMP53-1 induces wt and mutp53 R280K thermal stabilization, which is indicative of intermolecular interactions with these proteins. Accordingly, in silico studies of wt and mutp53 R280K DNA-binding domain with SLMP53-1 unveiled that the compound binds at the interface of the p53 homodimer with the DNA minor groove. Additionally, using yeast and p53-null tumor cells ectopically expressing distinct highly prevalent mutp53, the ability of SLMP53-1 to reactivate multiple mutp53 is evidenced.
Conclusions
SLMP53-1 is a p53-activating agent with the ability to directly target wt and a set of hotspot mutp53.
General Significance
This work reinforces the encouraging application of SLMP53-1 in the personalized treatment of cancer patients harboring distinct p53 status.

Gonçalves, AM, Sousa Â, Pedro AQ, Romão MJ, Queiroz JA, Gallardo E, Passarinha LA.  2022.  Advances in Membrane-Bound Catechol-O-Methyltransferase Stability Achieved Using a New Ionic Liquid-Based Storage Formulation. International Journal of Molecular Sciences. 23, Number 13 AbstractWebsite

Membrane-bound catechol-O-methyltransferase (MBCOMT), present in the brain and involved in the main pathway of the catechol neurotransmitter deactivation, is linked to several types of human dementia, which are relevant pharmacological targets for new potent and nontoxic inhibitors that have been developed, particularly for Parkinson’s disease treatment. However, the inexistence of an MBCOMT 3D-structure presents a blockage in new drugs’ design and clinical studies due to its instability. The enzyme has a clear tendency to lose its biological activity in a short period of time. To avoid the enzyme sequestering into a non-native state during the downstream processing, a multi-component buffer plays a major role, with the addition of additives such as cysteine, glycerol, and trehalose showing promising results towards minimizing hMBCOMT damage and enhancing its stability. In addition, ionic liquids, due to their virtually unlimited choices for cation/anion paring, are potential protein stabilizers for the process and storage buffers. Screening experiments were designed to evaluate the effect of distinct cation/anion ILs interaction in hMBCOMT enzymatic activity. The ionic liquids: choline glutamate [Ch][Glu], choline dihydrogen phosphate ([Ch][DHP]), choline chloride ([Ch]Cl), 1- dodecyl-3-methylimidazolium chloride ([C12mim]Cl), and 1-butyl-3-methylimidazolium chloride ([C4mim]Cl) were supplemented to hMBCOMT lysates in a concentration from 5 to 500 mM. A major potential stabilizing effect was obtained using [Ch][DHP] (10 and 50 mM). From the DoE 146% of hMBCOMT activity recovery was obtained with [Ch][DHP] optimal conditions (7.5 mM) at −80 °C during 32.4 h. These results are of crucial importance for further drug development once the enzyme can be stabilized for longer periods of time.

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 AbstractWebsite
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Goodfellow, BJ, Freire F, Carvalho AL, Aveiro SS, Charbonnier P, Moulis J-M, Delgado L, Ferreira GC, Rodrigues JE, Poussin-Courmontagne P, Birck C, McEwen A, Macedo AL.  2021.  The SOUL family of heme-binding proteins: Structure and function 15 years later, 2021. 448:214189. AbstractWebsite

The SOUL, or heme-binding protein HBP/SOUL, family represents a group of evolutionary conserved putative heme-binding proteins that contains a number of members in animal, plant andbacterial species. The structures of the murine form of HEBP1, or p22HBP, and the human form of HEBP2, or SOUL, have been determined in 2006 and 2011 respectively. In this work we discuss the structures of HEBP1 and HEBP2 in light of new X-ray data for heme bound murine HEBP1. The interaction between tetrapyrroles and HEBP1, initially proven to be hydrophobic in nature, was thought to also involve electrostatic interactions between heme propionate groups and positively charged amino acid side chains. However, the new X-ray structure, and results from murine HEBP1 variants and human HEBP1, confirm the hydrophobic nature of the heme-HEBP1 interaction, resulting in Kd values in the low nanomolar range, and rules out any electrostatic stabilization. Results from NMR relaxation time measurements for human HEBP1 describe a rigid globular protein with no change in motional regime upon heme binding. X-ray structures deposited in the PDB for human HEBP2 are very similar to each other and to the new heme-bound murine HEBP1 X-ray structure (backbone rmsd ca. 1 Å). Results from a HSQC spectrum centred on the histidine side chain Nδ-proton region for HEBP2 confirm that HEBP2 does not bind heme via H42 as no chemical shift differences were observed upon heme addition for backbone NH and Nδ protons. A survey of the functions attributed to HEBP1 and HEBP2 over the last 20 years span a wide range of cellular pathways. Interestingly, many of them are specific to higher eukaryotes, particularly mammals and a potential link between heme release under oxidative stress and human HEBP1 is also examined using recent data. However, at the present moment, trying to relate function to the involvement of heme or tetrapyrrole binding, specifically, makes little sense with our current biological knowledge and can only be applied to HEBP1, as HEBP2 does not interact with heme. We suggest that it may not be justified to call this very small family of proteins, heme-binding proteins. The family may be more correctly called “the SOUL family of proteins related to cellular fate” as, even though only HEBP1 binds heme tightly, both proteins may be involved in cell survival and/or proliferation.

Goodfellow, BJ, Tavares P, Romao MJ, Czaja C, Rusnak F, Legall J, Moura I, Moura JJG.  1996.  The solution structure of desulforedoxin, a simple iron-sulfur protein - An NMR study of the zinc derivative. Journal of Biological Inorganic Chemistry. 1:341-354., Number 4 AbstractWebsite
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