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- Evaluation of dry protonated calcium alginate beads for biosorption applications and studies of lead uptakePublication . Lagoa, Ricardo; Rodrigues, Joaquim RuiAlginate polysaccharide is a promising biosorbent for metal uptake. Dry protonated calcium alginate beads for biosorption applications were prepared, briefly characterized and tested for lead uptake. Several advantages of this biosorbent are reported and discussed in comparison with other alginate-based sorbents. The alginate beads contained 4.7 mmol/g of COOH groups, which suffered hydrolysis near pH 4. The Weber and Morris model, applied to kinetic results of lead uptake, showed that intraparticle diffusion was the rate-controlling step in lead sorption by dry alginate beads. Equilibrium experiments were performed and the data were fitted with different isotherm models. The Langmuir equation was the most adequate to model lead sorption. The maximum uptake capacity (qmax) was estimated as 339 mg/g and the Langmuir constant (b) as 0.84 l/mg. These values were compared with that of other sorbents found in the literature, indicating that dry protonated calcium alginate beads are among the best biosorbents for the treatment and recovery of heavy metals from aqueous streams.
- Molecular Bases of Catalysis and ADP-Ribose Preference of Human Mn2+-Dependent ADP-Ribose/CDP-Alcohol Diphosphatase and Conversion by Mutagenesis to a Preferential Cyclic ADP-Ribose PhosphohydrolasePublication . Cabezas, Alicia; Ribeiro, João Meireles; Rodrigues, Joaquim Rui; López-Villamizar, Iralis; Fernández, Ascensión; Canales, José; Pinto, Rosa María; Costas, María Jesús; Cameselle, José CarlosAmong metallo-dependent phosphatases, ADP-ribose/CDP-alcohol diphosphatases form a protein family (ADPRibase-Mn-like) mainly restricted, in eukaryotes, to vertebrates and plants, with preferential expression, at least in rodents, in immune cells. Rat and zebrafish ADPRibase-Mn, the only biochemically studied, are phosphohydrolases of ADP-ribose and, somewhat less efficiently, of CDP-alcohols and 2´,3´-cAMP. Furthermore, the rat but not the zebrafish enzyme displays a unique phosphohydrolytic activity on cyclic ADP-ribose. The molecular basis of such specificity is unknown. Human ADPRibase-Mn showed similar activities, including cyclic ADP-ribose phosphohydrolase, which seems thus common to mammalian ADPRibase-Mn. Substrate docking on a homology model of human ADPRibase-Mn suggested possible interactions of ADP-ribose with seven residues located, with one exception (Cys253), either within the metallo-dependent phosphatases signature (Gln27, Asn110, His111), or in unique structural regions of the ADPRibase-Mn family: s2s3 (Phe37 and Arg43) and h7h8 (Phe210), around the active site entrance. Mutants were constructed, and kinetic parameters for ADP-ribose, CDP-choline, 2´,3´-cAMP and cyclic ADP-ribose were determined. Phe37 was needed for ADP-ribose preference without catalytic effect, as indicated by the increased ADP-ribose Km and unchanged kcat of F37A-ADPRibase-Mn, while the Km values for the other substrates were little affected. Arg43 was essential for catalysis as indicated by the drastic efficiency loss shown by R43A-ADPRibase-Mn. Unexpectedly, Cys253 was hindering for cADPR phosphohydrolase, as indicated by the specific tenfold gain of efficiency of C253A-ADPRibase-Mn with cyclic ADP-ribose. This allowed the design of a triple mutant (F37A+L196F+C253A) for which cyclic ADP-ribose was the best substrate, with a catalytic efficiency of 3.5´104 M-1s-1 versus 4´103 M-1s-1 of the wild type.
- Kinetic studies of alginate gelationPublication . Rodrigues, Joaquim Rui; Lagoa, Ricardo
- Copper ions binding in cu‐alginate gelationPublication . Rodrigues, Joaquim Rui; Lagoa, RicardoAlginate polysaccharide forms viscous aqueous dispersions and has the ability to form gels in the presence of divalent cations such as calcium and copper. In this work, we have studied cooper ions binding during Cu‐alginate gelation, obtaining quantitative information about the amount and kinetics of cation binding. Our results indicate that copper binding during gelation occurs until a Langmuir‐type equilibrium is reached between bound and free ions in the gel‐contacting solution. The kinetics of metal ions binding can be modeled using Ritchie equation–derived models, allowing the prediction of ionic binding and gel formation temporal evolution. The ratio between cationic and polysaccharide quantities in the gelation system determines the kinetics of gelation and the characteristics of the gel formed. The experimental results and models applied in the work give more insights on alginate gelation and contribute to a reliable design and control of production methods for alginate gel structures.
- Specific cyclic ADP-ribose phosphohydrolase obtained by mutagenic engineering of Mn2+-dependent ADP-ribose/CDP-alcohol diphosphatasePublication . Ribeiro, João Meireles; Canales, José; Cabezas, Alicia; Rodrigues, Joaquim Rui; Pinto, Rosa María; López-Villamizar, Iralis; Costas, María Jesús; Cameselle, José CarlosCyclic ADP-ribose (cADPR) is a messenger for Ca2+ mobilization. Its turnover is believed to occur by glycohydrolysis to ADP-ribose. However, ADP-ribose/CDP-alcohol diphosphatase (ADPRibase-Mn) acts as cADPR phosphohydrolase with much lower efficiency than on its major substrates. Recently, we showed that mutagenesis of human ADPRibase-Mn at Phe37, Leu196 and Cys253 alters its specificity: the best substrate of the mutant F37A + L196F + C253A is cADPR by a short difference, Cys253 mutation being essential for cADPR preference. Its proximity to the ‘northern’ ribose of cADPR in docking models indicates Cys253 is a steric constraint for cADPR positioning. Aiming to obtain a specific cADPR phosphohydrolase, new mutations were tested at Asp250, Val252, Cys253 and Thr279, all near the ‘northern’ ribose. First, the mutant F37A + L196F + C253G, with a smaller residue 253 (Ala > Gly), showed increased cADPR specificity. Then, the mutant F37A + L196F + V252A + C253G, with another residue made smaller (Val > Ala), displayed the desired specificity, with cADPR kcat/KM ≈20–200-fold larger than for any other substrate. When tested in nucleotide mixtures, cADPR was exhausted while others remained unaltered. We suggest that the specific cADPR phosphohydrolase, by cell or organism transgenesis, or the designed mutations, by genome editing, provide opportunities to study the effect of cADPR depletion on the many systems where it intervenes.
- Closure of the human TKFC active site: comparison of the apoenzyme and the complexes formed with either triokinase or FMN cyclase substratesPublication . Rodrigues, Joaquim Rui; Cameselle, José Carlos; Cabezas, Alicia; Ribeiro, JoãoHuman triokinase/flavin mononucleotide (FMN) cyclase (hTKFC) catalyzes the adenosine triphosphate (ATP)-dependent phosphorylation of D-glyceraldehyde and dihydroxyacetone (DHA), and the cyclizing splitting of flavin adenine dinucleotide (FAD). hTKFC structural models are dimers of identical subunits, each with two domains, K and L, with an L2-K1-K2-L1 arrangement. Two active sites lie between L2-K1 and K2-L1, where triose binds K and ATP binds L, although the resulting ATP-to-triose distance is too large (≈14 Å) for phosphoryl transfer. A 75-ns trajectory of molecular dynamics shows considerable, but transient, ATP-to-DHA approximations in the L2-K1 site (4.83 Å or 4.16 Å). To confirm the trend towards site closure, and its relationship to kinase activity, apo-hTKFC, hTKFC:2DHA:2ATP and hTKFC:2FAD models were submitted to normal mode analysis. The trajectory of hTKFC:2DHA:2ATP was extended up to 160 ns, and 120-ns trajectories of apo-hTKFC and hTKFC:2FAD were simulated. The three systems were comparatively analyzed for equal lengths (120 ns) following the principles of essential dynamics, and by estimating site closure by distance measurements. The full trajectory of hTKFC:2DHA:2ATP was searched for in-line orientations and short distances of DHA hydroxymethyl oxygens to ATP γ-phosphorus. Full site closure was reached only in hTKFC:2DHA:2ATP, where conformations compatible with an associative phosphoryl transfer occurred in L2-K1 for significant trajectory time fractions.
- Lessons on protein structure from interleukin‐4: All disulfides are not created equalPublication . Vaz, Daniela C.; Rodrigues, J. Rui; Loureiro‐Ferreira, Nuno; Müller, Thomas D.; Sebald, Walter; Redfield, Christina; Brito, Rui M. M.Interleukin-4 (IL-4) is a hematopoietic cytokine composed by a four-helix bundle stabilized by an antiparallel beta-sheet and three disulfide bonds: Cys3-Cys127, Cys24-Cys65, and Cys46-Cys99. IL-4 is involved in several immune responses associated to infection, allergy, autoimmunity, and cancer. Besides its physiological relevance, IL-4 is often used as a “model” for protein design and engineering. Hence, to understand the role of each disulfide in the structure and dynamics of IL-4, we carried out several spectroscopic analyses (circular dichroism [CD], fluorescence, nuclear magnetic resonance [NMR]), and molecular dynamics (MD) simulations on wild-type IL-4 and four IL-4 disulfide mutants. All disulfide mutants showed loss of structure, altered interhelical angles, and looser core packings, showing that all disulfides are relevant for maintaining the overall fold and stability of the four-helix bundle motif, even at very low pH. In the absence of the disulfide connecting both protein termini Cys3-Cys127, C3T-IL4 showed a less packed protein core, loss of secondary structure ( 9%) and fast motions on the sub-nanosecond time scale (lower S2 order parameters and larger τc correlation time), especially at the two protein termini, loops, beginning of helix A and end of helix D. In the absence of Cys24-Cys65, C24T-IL4 presented shorter alpha-helices (14% loss in helical content), altered interhelical angles, less propensity to form the small anti-parallel beta-sheet and increased dynamics. Simultaneously deprived of two disulfides (Cys3-Cys127 and Cys24-Cys65), IL-4 formed a partially folded “molten globule” with high 8-anilino1-naphtalenesulphonic acid-binding affinity and considerable loss of secondary structure ( 50%decrease), as shown by the far UV-CD, NMR, and MD data.
- Anthocyanins, effects in mitochondria and metabolismPublication . Marques-da-Silva, Dorinda; Rodrigues, Joaquim Rui; Lagoa, RicardoAlterations in mitochondrial function, cellular redox signaling, and metabolism participate in the etiology and progression of different pathological conditions, such as diabetes, cancer, cardiovascular, and neurodegenerative diseases. Epidemiological, preclinical, and clinical studies indicate that anthocyanins afford therapeutic benefits for these pathologies. It is thus important to revise the effects of anthocyanins on mitochondria and metabolism that hold potential for the development of novel health protective methods. The studies available support the ability of certain anthocyanins to prevent damage to mitochondria and to sustain its function. Evidence is more compelling for cyanidin and delphinidin compounds, but promising data could also be found for malvidin, pelargonidin, and protocatechuic acid. Additionally, berry extracts also demonstrated positive outcomes in different models of neurodegeneration, endothelial dysfunction, myocardial damage, metabolic disorders, longevity, and cancer. At the molecular level, major anthocyanins can modulate the expression and activity of mitochondrial proteins, apoptotic and biogenesis factors, antioxidant defenses, inflammation, and the AMPK pathway. Noteworthy, anthocyanins could balance abnormalities in ROS production, respiration, and mitochondrial fragmentation in cells exposed to toxicants or oxidizing agents.
- A comparative study of alginate beads and an ion-exchange resin for the removal of heavy metals from a metal plating effluentPublication . Silva, Rui M. P.; Manso, João P. H.; Rodrigues, Joaquim Rui; Lagoa, RicardoThe capacity of dry protonated calcium alginate beads to sorb metals from an industrial effluent was studied and compared with a commercial ion-exchange resin (Lewatit TP 207). Both sorbents decreased zinc, nickel, iron and calcium concentrations in the effluent, and released sodium during treatment. Alginate beads removed lower amounts of heavy metals than the resin, but exhibited faster uptake kinetics. Zinc desorption from the sorbents was achieved in 30 minutes using 0.1 M HCl or 0.1 M H(2)SO(4). Desorption ratios with these acids varied between 90 and 100% for alginate, and 98 to 100% for the ion-exchange resin. Reusability tests with HCl showed that alginate beads can stand acid desorption and recover binding capacity. Overall, the comparison of dry protonated alginate beads with the resin supports the potential of the biosorbent for the treatment of industrial effluents.
- Alginate films encapsulating polyphenols for nutraceutical and biomedical applicationsPublication . Lagoa, Ricardo; Vanat, Pavlo; Ferreira, Stefanie; Silva, João; Marques-da-Silva, Dorinda; Ribeiro, Vânia; Vaz, Daniela C.; Barreiros, Fátima; Rodrigues, Joaquim Rui