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2017
dos Santos, R, Carvalho AL, Roque CAA.  2017.  Renaissance of protein crystallization and precipitation in biopharmaceuticals purification, 2017/1//. Biotechnology Advances. 35(1):41-50. AbstractWebsite

AbstractThe current chromatographic approaches used in protein purification are not keeping pace with the increasing biopharmaceutical market demand. With the upstream improvements, the bottleneck shifted towards the downstream process. New approaches rely in Anything But Chromatography methodologies and revisiting former techniques with a bioprocess perspective. Protein crystallization and precipitation methods are already implemented in the downstream process of diverse therapeutic biological macromolecules, overcoming the current chromatographic bottlenecks. Promising work is being developed in order to implement crystallization and precipitation in the purification pipeline of high value therapeutic molecules. This review focuses in the role of these two methodologies in current industrial purification processes, and highlights their potential implementation in the purification pipeline of high value therapeutic molecules, overcoming chromatographic holdups.

Pires, VMR, Pereira PMM, Brás JLA, Correia M, Cardoso V, Bule P, Alves VD, Najmudin S, Venditto I, Ferreira LMA, Romão MJ, Carvalho AL, Fontes CMGA, Prazeres DM.  2017.  Stability and ligand promiscuity of type A carbohydrate-binding modules are illustrated by the structure of Spirochaeta thermophila StCBM64C, mar. Journal of Biological Chemistry. 292:4847–4860., Number 12 AbstractWebsite

Deconstruction of cellulose, the most abundant plant cell wall polysaccharide, requires the cooperative activity of a large repertoire of microbial enzymes. Modular cellulases contain non-catalytic type A Carbohydrate-Binding Modules (CBMs) that specifically bind to the crystalline regions of cellulose, thus promoting enzyme efficacy through proximity and targeting effects. Although type A CBMs play a critical role in cellulose recycling, their mechanism of action remains poorly understood. Here we produced a library of recombinant CBMs representative of the known diversity of type A modules. The binding properties of 40 CBMs, in fusion with an N-terminal green fluorescence protein (GFP) domain, revealed that type A CBMs possess the ability to recognize different crystalline forms of cellulose and chitin over a wide range of temperatures, pHs and ionic strengths. A Spirochaeta thermophila CBM64, in particular, displayed plasticity in its capacity to bind both crystalline and soluble carbohydrates under a wide range of extreme conditions. The structure of S. thermophila StCBM64C revealed an untwisted, flat, carbohydrate-binding interface comprising the side chains of four tryptophan residues in a coplanar linear arrangement. Significantly, two highly conserved asparagine side chains, each one located between two tryptophan residues, are critical to insoluble and soluble glucan recognition but not to bind xyloglucan. Thus, CBM64 compact structure and its extended and versatile ligand interacting platform illustrates how type A CBMs target their appended plant cell wall degrading enzymes to a diversity of recalcitrant carbohydrates under a wide range of environmental conditions.

Kryshtafovych, A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring G-W, Koning RI, {Lo Leggio} L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T.  2017.  Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016), oct. Proteins: Structure, Function, and Bioinformatics. AbstractWebsite

The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment. This article is protected by copyright. All rights reserved.

2018
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.

Kumar, K, Correia M, Pires VR, Dhillon A, Sharma K, Rajulapati V, Fontes CMGA, Carvalho AL, Goyal A.  2018.  Novel insights into the degradation of β-1,3-glucans by the cellulosome of Clostridium thermocellum revealed by structure and function studies of a family 81 glycoside hydrolase. International Journal of Biological Macromolecules. :-. AbstractWebsite

Abstract The family 81 glycoside hydrolase (GH81) from Clostridium thermocellum is a β-1,3-glucanase belonging to cellulosomal complex. The gene encoding \{GH81\} from Clostridium thermocellum (CtLam81A) was cloned and expressed displaying a molecular mass of  82 kDa. CtLam81A showed maximum activity against laminarin (100 U/mg), followed by curdlan (65 U/mg), at pH 7.0 and 75 °C. CtLam81A displayed Km, 2.1 ± 0.12 mg/ml and Vmax, 109 ± 1.8 U/mg, against laminarin under optimized conditions. CtLam81A activity was significantly enhanced by Ca2+ or Mg2+ ions. Melting curve analysis of CtLam81A showed an increase in melting temperature from 91 °C to 96 °C by Ca2+ or Mg2+ ions and decreased to 82 °C by EDTA, indicating that Ca2+ and Mg2+ ions may be involved in catalysis and in maintaining structural integrity. \{TLC\} and MALDI-TOF analysis of β-1,3-glucan hydrolysed products released initially, showed β-1,3-glucan-oligosaccharides degree of polymerization (DP) from \{DP2\} to DP7, confirming an endo-mode of action. The catalytically inactive mutant CtLam81A-E515A generated by site-directed mutagenesis was co-crystallized and tetragonal crystals diffracting up to 1.4 Å resolution were obtained. CtLam81A-E515A contained 15 α-helices and 38 β-strands forming a four-domain structure viz. a β-sandwich domain I at N-terminal, an α/β-domain II, an (α/α)6 barrel domain III, and a small 5-stranded β-sandwich domain IV.

Ribeiro, DO, Pinheiro BA, Carvalho AL, Palma AS.  2018.  Targeting protein-carbohydrate interactions in plant cell-wall biodegradation: the power of carbohydrate microarrays. Carbohydrate Chemistry: Chemical and Biological Approaches Volume 43. 43:159-176.: The Royal Society of Chemistry Abstract

The plant cell-wall is constituted by structurally diverse polysaccharides. The biodegradation of these is a crucial process for life sustainability. Cellulolytic microorganisms are highly efficient in this process by assembling modular architectures of carbohydrate-active enzymes with appended non-catalytic carbohydrate-binding modules (CBMs). Carbohydrate microarrays offer high-throughput and sensitive tools for uncovering carbohydrate-binding specificities of CBMs{,} which is pivotal to understand the function of these modules in polysaccharide biodegradation mechanisms. Features of this technology will be here briefly reviewed with highlights of microarray approaches to study plant-carbohydrates and CBM-carbohydrate interactions{,} along with an overview of plant polysaccharides and microorganisms strategies for their recognition.

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. AbstractWebsite

A 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.

Mota, C, Coelho C, Leimkühler S, Garattini E, Terao M, Santos-Silva T, Romão MJ.  2018.  Critical overview on the structure and metabolism of human aldehyde oxidase and its role in pharmacokinetics, 2018. 368:35-59. AbstractWebsite

Aldehyde oxidases are molybdenum and flavin dependent enzymes characterized by a very wide substrate specificity and performing diverse reactions that include oxidations (e.g., aldehydes and aza-heterocycles), hydrolysis of amide bonds, and reductions (e.g., nitro, S-oxides and N-oxides). Oxidation reactions and amide hydrolysis occur at the molybdenum site while the reductions are proposed to occur at the flavin site. AOX activity affects the metabolism of different drugs and xenobiotics, some of which designed to resist other liver metabolizing enzymes (e.g., cytochrome P450 monooxygenase isoenzymes), raising its importance in drug development. This work consists of a comprehensive overview on aldehyde oxidases, concerning the genetic evolution of AOX, its diversity among the human population, the crystal structures available, the known catalytic reactions and the consequences in pre-clinical pharmacokinetic and pharmacodynamic studies. Analysis of the different animal models generally used for pre-clinical trials and comparison between the human (hAOX1), mouse homologs as well as the related xanthine oxidase (XOR) are extensively considered. The data reviewed also include a systematic analysis of representative classes of molecules that are hAOX1 substrates as well as of typical and well characterized hAOX1 inhibitors. The considerations made on the basis of a structural and functional analysis are correlated with reported kinetic and metabolic data for typical classes of drugs, searching for potential structural determinants that may dictate substrate and/or inhibitor specificities.

Leisico, F, V. Vieira D, Figueiredo TA, Silva M, Cabrita EJ, Sobral RG, Ludovice AM, Trincão J, Romão MJ, de Lencastre H, Santos-Silva T.  2018.  First insights of peptidoglycan amidation in Gram-positive bacteria - the high-resolution crystal structure of Staphylococcus aureus glutamine amidotransferase GatD, 2018. Scientific Reports. 8(1):5313. AbstractWebsite

Gram-positive bacteria homeostasis and antibiotic resistance mechanisms are dependent on the intricate architecture of the cell wall, where amidated peptidoglycan plays an important role. The amidation reaction is carried out by the bi-enzymatic complex MurT-GatD, for which biochemical and structural information is very scarce. In this work, we report the first crystal structure of the glutamine amidotransferase member of this complex, GatD from Staphylococcus aureus, at 1.85 Å resolution. A glutamine molecule is found close to the active site funnel, hydrogen-bonded to the conserved R128. In vitro functional studies using 1H-NMR spectroscopy showed that S. aureus MurT-GatD complex has glutaminase activity even in the absence of lipid II, the MurT substrate. In addition, we produced R128A, C94A and H189A mutants, which were totally inactive for glutamine deamidation, revealing their essential role in substrate sequestration and catalytic reaction. GatD from S. aureus and other pathogenic bacteria share high identity to enzymes involved in cobalamin biosynthesis, which can be grouped in a new sub-family of glutamine amidotransferases. Given the ubiquitous presence of GatD, these results provide significant insights into the molecular basis of the so far undisclosed amidation mechanism, contributing to the development of alternative therapeutics to fight infections.

Bule, P, Pires VMR, Alves VD, Carvalho AL, Prates JAM, Ferreira LMA, Smith SP, Gilbert HJ, Noach I, Bayer EA, Najmudin S, Fontes CMGA.  2018.  Higher order scaffoldin assembly in Ruminococcus flavefaciens cellulosome is coordinated by a discrete cohesin-dockerin interaction, 2018. Scientific Reports. 8(1):6987. AbstractWebsite

Cellulosomes are highly sophisticated molecular nanomachines that participate in the deconstruction of complex polysaccharides, notably cellulose and hemicellulose. Cellulosomal assembly is orchestrated by the interaction of enzyme-borne dockerin (Doc) modules to tandem cohesin (Coh) modules of a non-catalytic primary scaffoldin. In some cases, as exemplified by the cellulosome of the major cellulolytic ruminal bacterium Ruminococcus flavefaciens, primary scaffoldins bind to adaptor scaffoldins that further interact with the cell surface via anchoring scaffoldins, thereby increasing cellulosome complexity. Here we elucidate the structure of the unique Doc of R. flavefaciens FD-1 primary scaffoldin ScaA, bound to Coh 5 of the adaptor scaffoldin ScaB. The RfCohScaB5-DocScaA complex has an elliptical architecture similar to previously described complexes from a variety of ecological niches. ScaA Doc presents a single-binding mode, analogous to that described for the other two Coh-Doc specificities required for cellulosome assembly in R. flavefaciens. The exclusive reliance on a single-mode of Coh recognition contrasts with the majority of cellulosomes from other bacterial species described to date, where Docs contain two similar Coh-binding interfaces promoting a dual-binding mode. The discrete Coh-Doc interactions observed in ruminal cellulosomes suggest an adaptation to the exquisite properties of the rumen environment.

Santarsia, S, Grosso AS, Trovão F, Jiménez-Barbero J, Carvalho AL, Nativi C, Marcelo F.  2018.  Molecular recognition of a Thomsen-Friedenreich antigen mimetic targeting human galectin-3, 2018. ChemMedChem. Aug 9. doi: 10.1002/cmdc.201800525. [Epub ahead of print](ja): Wiley-Blackwell AbstractWebsite

Overexpression of the Thomsen-Friedenreich (TF) antigen in cell membrane proteins occurs in 90% of adenocarcinomas. Additionally, the binding of the TF-antigen to human galectin-3 (Gal-3), also frequently overexpressed in malignancy, promotes cancer progression and metastasis. In this context, structures that interfere with this specific interaction display the potential to prevent cancer metastasis. Herein, a multidisciplinary approach, combining the optimized synthesis of a TF-antigen mimetic with NMR, X-ray crystallography methods and isothermal titration calorimetry assays has been employed to unravel the molecular structural details that govern the Gal-3/TF-mimetic interaction. The TF-mimetic presents a binding affinity for Gal-3 similar to the TF-natural antigen and retains the binding epitope and the bioactive conformation observed for the native antigen. Furthermore, from a thermodynamic perspective a decrease in the enthalpic contribution was observed for the Gal-3/TF-mimetic complex, however this behaviour is compensated by a favourable entropy gain. From a structural perspective, these results establish our TF-mimetic as a scaffold to design multivalent solutions to potentially interfere with Gal-3 aberrant interactions and likely be used to hamper Gal-3-mediated cancer cells adhesion and metastasis.

Carvalho, AL, Santos-Silva T, Romão MJ, Eurico J, Marcelo F.  2018.  {CHAPTER 2 Structural Elucidation of Macromolecules}, sep. Essential Techniques for Medical and Life Scientists: A Guide to Contemporary Methods and Current Applications with the Protocols. :30–91.: BENTHAM SCIENCE PUBLISHERS AbstractWebsite
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2019
Mota, C, Esmaeeli M, Coelho C, Santos-Silva T, Wolff M, Foti A, Leimkühler S, Romão MJ.  2019.  Human aldehyde oxidase (hAOX1): structure determination of the Moco-free form of the natural variant G1269R and biophysical studies of single nucleotide polymorphisms. FEBS Open Bio. 9:925-934., Number 5 AbstractWebsite

Human aldehyde oxidase (hAOX1) is a molybdenum enzyme with high toxicological importance, but its physiological role is still unknown. hAOX1 metabolizes different classes of xenobiotics and is one of the main drug-metabolizing enzymes in the liver, along with cytochrome P450. hAOX1 oxidizes and inactivates a large number of drug molecules and has been responsible for the failure of several phase I clinical trials. The interindividual variability of drug-metabolizing enzymes caused by single nucleotide polymorphisms (SNPs) is highly relevant in pharmaceutical treatments. In this study, we present the crystal structure of the inactive variant G1269R, revealing the first structure of a molybdenum cofactor (Moco)-free form of hAOX1. These data allowed to model, for the first time, the flexible Gate 1 that controls access to the active site. Furthermore, we inspected the thermostability of wild-type hAOX1 and hAOX1 with various SNPs (L438V, R1231H, G1269R or S1271L) by CD spectroscopy and ThermoFAD, revealing that amino acid exchanges close to the Moco site can impact protein stability up to 10 °C. These results correlated with biochemical and structural data and enhance our understanding of hAOX1 and the effect of SNPs in the gene encoding this enzyme in the human population. Enzymes Aldehyde oxidase (EC1.2.3.1); xanthine dehydrogenase (EC1.17.1.4); xanthine oxidase (EC1.1.3.2). Databases Structural data are available in the Protein Data Bank under the accession number 6Q6Q.

Correia, VG, Pinheiro BA, Carvalho AL, Palma AS.  2019.  Resistance to Aminoglycosides. Antibiotic Drug Resistance. :1-38.: John Wiley & Sons, Ltd Abstract

Summary The emergence of bacterial resistance to different antibiotics in clinical use, together with the knowledge on the mechanisms by which bacteria resist the action of aminoglycosides, have contributed to the renewed interest in these molecules as potential antimicrobials. Here, we give an overview on natural and semisynthetic aminoglycosides and their structural features and modes of action, focusing on the structural insight underlying resistance mechanisms. Developments on carbohydrate chemistry and microarray technology are highlighted as powerful approaches toward generation of new aminoglycosides and for screening their interactions with RNAs and proteins. The link between antibiotic uptake and the human gut microbiome is also addressed, focusing on gut microbiome function and composition, antibiotic-induced alterations in host health, and antibiotic resistance. In addition, strategies to modulate human microbiome responses to antibiotics are discussed as novel approaches for aminoglycoside usage and for the effectiveness of antibiotic therapy.

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 AbstractWebsite

Abstract 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.

Mota, C, Santos Silva T, Terao M, Garattini E, Romão MJ, Leimkuehler S.  2019.  Aldehyde Oxidases as Enzymes in Phase I Drug Metabolism. Pharmaceutical Biocatalysis. (Peter Grunwald, Ed.)., New York: Jenny Stanford Publishing
Peixoto, D, Malta G, Cruz H, Barroso S, Carvalho AL, Ferreira LM, Branco PS.  2019.  N-Heterocyclic olefin catalysis for the ring opening of cyclic amidine compounds: a pathway to the synthesis of ε-caprolactam and γ-lactam-derived amines, 2019. The Journal of Organic Chemistry. : American Chemical Society AbstractWebsite

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Ferreira, P, Cerqueira NMFSA, Coelho C, Fernandes PA, Romão MJ, Ramos MJ.  2019.  New insights about the monomer and homodimer structures of the human AOX1, 2019. Physical Chemistry Chemical Physics. 21(25):13545-13554.: The Royal Society of Chemistry AbstractWebsite

Human aldehyde oxidase (hAOX1) is a molybdenum dependent enzyme that plays an important role in the metabolism of various compounds either endogenous or xenobiotics. Due to its promiscuity, hAOX1 plays a major role in the pharmacokinetics of many drugs and therefore has gathered a lot of attention from the scientific community and, particularly, from the pharmaceutical industry. In this work, homology modelling, molecular docking and molecular dynamics simulations were used to study the structure of the monomer and dimer of human AOX. The results with the monomer of hAOX1 allowed to shed some light on the role played by thioridazine and two malonate ions that are co-crystalized in the recent X-ray structure of hAOX1. The results show that these molecules endorse several conformational rearrangements in the binding pocket of the enzyme and these changes have an impact in the active site topology as well as in the stability of the substrate (phthalazine). The results show that the presence of both molecules open two gates located at the entrance of the binding pocket, from which results the flooding of the active site. They also endorse several modifications in the shape of the binding pocket (namely the position of Lys893) that, together with the presence of the solvent molecules, favour the release of the substrate to the solvent. Further insights were also obtained with the assembled homodimer of hAOX1. The allosteric inhibitor (THI) binds closely to the region where the dimerization of both monomers occur. These findings suggest that THI can interfere with protein dimerization.

2020
Ribeiro, DO, Viegas A, Pires VMR, Medeiros-Silva J, Bule P, Chai W, Marcelo F, Fontes CMGA, Cabrita EJ, Palma AS, Carvalho AL.  2020.  Molecular basis for the preferential recognition of β1,3-1,4-glucans by the family 11 carbohydrate-binding module from Clostridium thermocellum. The FEBS Journal. 287:2723-2743., Number 13 AbstractWebsite

Understanding the specific molecular interactions between proteins and β1,3-1,4-mixed-linked d-glucans is fundamental to harvest the full biological and biotechnological potential of these carbohydrates and of proteins that specifically recognize them. The family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11) is known for its binding preference for β1,3-1,4-mixed-linked over β1,4-linked glucans. Despite the growing industrial interest of this protein for the biotransformation of lignocellulosic biomass, the molecular determinants of its ligand specificity are not well defined. In this report, a combined approach of methodologies was used to unravel, at a molecular level, the ligand recognition of CtCBM11. The analysis of the interaction by carbohydrate microarrays and NMR and the crystal structures of CtCBM11 bound to β1,3-1,4-linked glucose oligosaccharides showed that both the chain length and the position of the β1,3-linkage are important for recognition, and identified the tetrasaccharide Glcβ1,4Glcβ1,4Glcβ1,3Glc sequence as a minimum epitope required for binding. The structural data, along with site-directed mutagenesis and ITC studies, demonstrated the specificity of CtCBM11 for the twisted conformation of β1,3-1,4-mixed-linked glucans. This is mediated by a conformation–selection mechanism of the ligand in the binding cleft through CH-π stacking and a hydrogen bonding network, which is dependent not only on ligand chain length, but also on the presence of a β1,3-linkage at the reducing end and at specific positions along the β1,4-linked glucan chain. The understanding of the detailed mechanism by which CtCBM11 can distinguish between linear and mixed-linked β-glucans strengthens its exploitation for the design of new biomolecules with improved capabilities and applications in health and agriculture. Database Structural data are available in the Protein Data Bank under the accession codes 6R3M and 6R31.

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 AbstractWebsite

{Two new bis(aryl-imino)-acenaphthene, Ar-BIAN (Ar = 2

Ferreira, P, Cerqueira NSMFA, Fernandes PA, Romão MJ, Ramos MJ.  2020.  Catalytic Mechanism of Human Aldehyde Oxidase, 2020. ACS CatalysisACS Catalysis. 10(16):9276-9286.: American Chemical Society AbstractWebsite

The mechanism of oxidation of N-heterocycle phthalazine to phthalazin-1(2H)-one and its associated free energy profile, catalyzed by human aldehyde oxidase (hAOX1), was studied in atomistic detail using QM/MM methodologies. The studied reaction was found to involve three sequential steps: (i) protonation of the substrate’s N2 atom by Lys893, (ii) nucleophilic attack of the hydroxyl group of the molybdenum cofactor (Moco) to the substrate, and (iii) hydride transfer from the substrate to the sulfur atom of the Moco. The free energy profile that was calculated revealed that the rate-limiting step corresponds to hydride transfer. It was also found that Lys893 plays a relevant role in the reaction, being important not only for the anchorage of the substrate close to the Moco, but also in the catalytic reaction. The variations of the oxidation state of the molybdenum ion throughout the catalytic cycle were examined too. We found out that during the displacement of the products away from the Moco, the transfer of electrons from the catalytic site to the FAD site was proton-coupled. As a consequence, the most favorable and fastest pathway for the enzyme to complete its catalytic cycle was that with MoV and a deprotonated SH ligand of the Moco with the FAD molecule converted to its semiquinone form, FADH•.The mechanism of oxidation of N-heterocycle phthalazine to phthalazin-1(2H)-one and its associated free energy profile, catalyzed by human aldehyde oxidase (hAOX1), was studied in atomistic detail using QM/MM methodologies. The studied reaction was found to involve three sequential steps: (i) protonation of the substrate’s N2 atom by Lys893, (ii) nucleophilic attack of the hydroxyl group of the molybdenum cofactor (Moco) to the substrate, and (iii) hydride transfer from the substrate to the sulfur atom of the Moco. The free energy profile that was calculated revealed that the rate-limiting step corresponds to hydride transfer. It was also found that Lys893 plays a relevant role in the reaction, being important not only for the anchorage of the substrate close to the Moco, but also in the catalytic reaction. The variations of the oxidation state of the molybdenum ion throughout the catalytic cycle were examined too. We found out that during the displacement of the products away from the Moco, the transfer of electrons from the catalytic site to the FAD site was proton-coupled. As a consequence, the most favorable and fastest pathway for the enzyme to complete its catalytic cycle was that with MoV and a deprotonated SH ligand of the Moco with the FAD molecule converted to its semiquinone form, FADH•.

Terao, M, Garattini E, Romão MJ, Leimkühler S.  2020.  Evolution, expression, and substrate specificities of aldehyde oxidase enzymes in eukaryotes, 2020. Journal of Biological ChemistryJournal of Biological Chemistry. 295(16):5377-5389.: Elsevier AbstractWebsite

Aldehyde oxidases (AOXs) are a small group of enzymes belonging to the larger family of molybdo-flavoenzymes, along with the well-characterized xanthine oxidoreductase. The two major types of reactions that are catalyzed by AOXs are the hydroxylation of heterocycles and the oxidation of aldehydes to their corresponding carboxylic acids. Different animal species have different complements of AOX genes. The two extremes are represented in humans and rodents; whereas the human genome contains a single active gene (AOX1), those of rodents, such as mice, are endowed with four genes (Aox1-4), clustering on the same chromosome, each encoding a functionally distinct AOX enzyme. It still remains enigmatic why some species have numerous AOX enzymes, whereas others harbor only one functional enzyme. At present, little is known about the physiological relevance of AOX enzymes in humans and their additional forms in other mammals. These enzymes are expressed in the liver and play an important role in the metabolisms of drugs and other xenobiotics. In this review, we discuss the expression, tissue-specific roles, and substrate specificities of the different mammalian AOX enzymes and highlight insights into their physiological roles.Aldehyde oxidases (AOXs) are a small group of enzymes belonging to the larger family of molybdo-flavoenzymes, along with the well-characterized xanthine oxidoreductase. The two major types of reactions that are catalyzed by AOXs are the hydroxylation of heterocycles and the oxidation of aldehydes to their corresponding carboxylic acids. Different animal species have different complements of AOX genes. The two extremes are represented in humans and rodents; whereas the human genome contains a single active gene (AOX1), those of rodents, such as mice, are endowed with four genes (Aox1-4), clustering on the same chromosome, each encoding a functionally distinct AOX enzyme. It still remains enigmatic why some species have numerous AOX enzymes, whereas others harbor only one functional enzyme. At present, little is known about the physiological relevance of AOX enzymes in humans and their additional forms in other mammals. These enzymes are expressed in the liver and play an important role in the metabolisms of drugs and other xenobiotics. In this review, we discuss the expression, tissue-specific roles, and substrate specificities of the different mammalian AOX enzymes and highlight insights into their physiological roles.

Vidossich, P, Castañeda Moreno LE, Mota C, de Sanctis D, Miscione GP, De Vivo M.  2020.  Functional Implications of Second-Shell Basic Residues for dUTPase DR2231 Enzymatic Specificity, 2020. ACS CatalysisACS Catalysis. 10(23):13825-13833.: American Chemical Society AbstractWebsite

Nucleotide-processing enzymes are key players in biological processes. They often operate through high substrate specificity for catalysis. How such specificity is achieved is unclear. Here, we dealt with this question by investigating all-α dimeric deoxyuridine triphosphate nucleotidohydrolases (dUTPases). Typically, these dUTPases hydrolyze either dUTP or deoxyuridine diphosphate (dUDP) substrates. However, the dUTPase enzyme DR2231 from Deinococcus radiodurans selectively hydrolyzes dUTP only, and not dUDP. By means of extended classical molecular dynamics simulations and quantum chemical calculations, we show that DR2231 achieves this specificity for dUTP via second-shell basic residues that, together with the two catalytic magnesium ions, contribute to properly orienting the γ-phosphate of dUTP in a prereactive state. This allows a nucleophilic water to be correctly placed and activated in order to perform substrate hydrolysis. We show that this enzymatic mechanism is not viable when dUDP is bound to DR2231. Importantly, in several other dUTPases capable of hydrolyzing either dUTP or dUDP, we detected that active site second-shell basic residues are more in number, anchoring the β-phosphate of the nucleotide substrate too, in contrast to what is observed in DR2231. Thus, strategically located basic second-shell residues mediate precise reactant positioning at the catalytic site, determining substrate specificity in dUTPases and possibly in other structurally similar nucleotide-processing metalloenzymes.Nucleotide-processing enzymes are key players in biological processes. They often operate through high substrate specificity for catalysis. How such specificity is achieved is unclear. Here, we dealt with this question by investigating all-α dimeric deoxyuridine triphosphate nucleotidohydrolases (dUTPases). Typically, these dUTPases hydrolyze either dUTP or deoxyuridine diphosphate (dUDP) substrates. However, the dUTPase enzyme DR2231 from Deinococcus radiodurans selectively hydrolyzes dUTP only, and not dUDP. By means of extended classical molecular dynamics simulations and quantum chemical calculations, we show that DR2231 achieves this specificity for dUTP via second-shell basic residues that, together with the two catalytic magnesium ions, contribute to properly orienting the γ-phosphate of dUTP in a prereactive state. This allows a nucleophilic water to be correctly placed and activated in order to perform substrate hydrolysis. We show that this enzymatic mechanism is not viable when dUDP is bound to DR2231. Importantly, in several other dUTPases capable of hydrolyzing either dUTP or dUDP, we detected that active site second-shell basic residues are more in number, anchoring the β-phosphate of the nucleotide substrate too, in contrast to what is observed in DR2231. Thus, strategically located basic second-shell residues mediate precise reactant positioning at the catalytic site, determining substrate specificity in dUTPases and possibly in other structurally similar nucleotide-processing metalloenzymes.

Fernandes, AR, Mendonça-Martins I, Santos MFA, Raposo LR, Mendes R, Marques J, Romão CC, Romão MJ, Santos-Silva T, Baptista PV.  2020.  Improving the Anti-inflammatory Response via Gold Nanoparticle Vectorization of CO-Releasing Molecules, 2020. ACS Biomaterials Science & EngineeringACS Biomaterials Science & Engineering. 6(2):1090-1101.: American Chemical Society AbstractWebsite

CO-releasing molecules (CORMs) have been widely studied for their anti-inflammatory, antiapoptotic, and antiproliferative effects. CORM-3 is a water-soluble Ru-based metal carbonyl complex, which metallates serum proteins and readily releases CO in biological media. In this work, we evaluated the anti-inflammatory and wound-healing effects of gold nanoparticles–CORM-3 conjugates, AuNPs@PEG@BSA·Ru(CO)x, exploring its use as an efficient CO carrier. Our results suggest that the nanoformulation was capable of inducing a more pronounced cell effect, at the anti-inflammatory level and a faster tissue repair, probably derived from a rapid cell uptake of the nanoformulation that results in the increase of CO inside the cell.CO-releasing molecules (CORMs) have been widely studied for their anti-inflammatory, antiapoptotic, and antiproliferative effects. CORM-3 is a water-soluble Ru-based metal carbonyl complex, which metallates serum proteins and readily releases CO in biological media. In this work, we evaluated the anti-inflammatory and wound-healing effects of gold nanoparticles–CORM-3 conjugates, AuNPs@PEG@BSA·Ru(CO)x, exploring its use as an efficient CO carrier. Our results suggest that the nanoformulation was capable of inducing a more pronounced cell effect, at the anti-inflammatory level and a faster tissue repair, probably derived from a rapid cell uptake of the nanoformulation that results in the increase of CO inside the cell.

dos Santos, R, Iria I, Manuel AM, Leandro AP, Madeira CAC, Goncalves J, Carvalho AL, Roque AC.  2020.  Magnetic Precipitation: A New Platform for Protein Purification, 2020. Biotechnology JournalBiotechnology Journal. n/a(n/a):2000151.: John Wiley & Sons, Ltd AbstractWebsite

One of the trends in downstream processing comprises the use of ?anything-but-chromatography? methods to overcome the current downfalls of standard packed-bed chromatography. Precipitation and magnetic separation are two techniques already proven to accomplish protein purification from complex media, yet never used in synergy. With the aim to capture antibodies directly from crude extracts, a new approach combining precipitation and magnetic separation was developed and named as affinity magnetic precipitation. A precipitation screening, based on the Hofmeister series, and a commercial precipitation kit were tested with affinity magnetic particles to assess the best condition for antibody capture from human serum plasma and clarified cell supernatant. The best conditions were obtained when using PEG3350 as precipitant at 4°C for 1h, reaching 80% purity and 50% recovery of polyclonal antibodies from plasma, and 99% purity with 97% recovery yield of anti-TNFα mAb from cell supernatants. These results show that the synergetic use of precipitation and magnetic separation can represent an alternative for the efficient capture of antibodies. This article is protected by copyright. All rights reserved