Marlene Barros

Multiplicity of aspartic proteinases from Cynara cardunculus L.

Aspartic proteinases (AP) play major roles in physiologic and pathologic scenarios in a wide range of organisms from vertebrates to plants or viruses. The present work deals with the purification and characterisation of four new APs from the cardoon Cynara cardunculus L., bringing the number of APs that have been isolated, purified and biochemically characterised from this organism to nine. This is, to our knowledge, one of the highest number of APs purified from a single organism, consistent with a specific and important biological function of these protein within C. cardunculus. These enzymes, cardosins E, F, G and H, are dimeric, glycosylated, pepstatin-sensitive APs, active at acidic pH, with a maximum activity around pH 4.3. Their primary structures were partially determined by N- and C-terminal sequence analysis, peptide mass fingerprint analysis on a MALDI-TOF/TOF instrument and by LC–MS/MS analysis on a Q-TRAP instrument. All four enzymes are present on C. cardunculus L. pistils, along with cyprosins and cardosins A and B. Their micro-heterogeneity was detected by 2D-electrophoresis and mass spectrometry. The enzymes resemble cardosin A more than they resemble cardosin B or cyprosin, with cardosin E and cardosin G being more active than cardosin A, towards the synthetic peptide KPAEFF(NO2)AL. The specificity of these enzymes was investigated and it is shown that cardosin E, although closely related to cardosin A, exhibits different specificity.

Computational prediction of the human-microbial oral interactome

BackgroundThe oral cavity is a complex ecosystem where human chemical compounds coexist with a particular microbiota. However, shifts in the normal composition of this microbiota may result in the onset of oral ailments, such as periodontitis and dental caries. In addition, it is known that the microbial colonization of the oral cavity is mediated by protein-protein interactions (PPIs) between the host and microorganisms. Nevertheless, this kind of PPIs is still largely undisclosed. To elucidate these interactions, we have created a computational prediction method that allows us to obtain a first model of the Human-Microbial oral interactome.ResultsWe collected high-quality experimental PPIs from five major human databases. The obtained PPIs were used to create our positive dataset and, indirectly, our negative dataset. The positive and negative datasets were merged and used for training and validation of a naïve Bayes classifier. For the final prediction model, we used an ensemble methodology combining five distinct PPI prediction techniques, namely: literature mining, primary protein sequences, orthologous profiles, biological process similarity, and domain interactions. Performance evaluation of our method revealed an area under the ROC-curve (AUC) value greater than 0.926, supporting our primary hypothesis, as no single set of features reached an AUC greater than 0.877. After subjecting our dataset to the prediction model, the classified result was filtered for very high confidence PPIs (probability ≥ 1-10−7), leading to a set of 46,579 PPIs to be further explored.ConclusionsWe believe this dataset holds not only important pathways involved in the onset of infectious oral diseases, but also potential drug-targets and biomarkers. The dataset used for training and validation, the predictions obtained and the network final network are available at http://bioinformatics.ua.pt/software/oralint.

OralCard: A bioinformatic tool for the study of oral proteome

OBJECTIVES The molecular complexity of the human oral cavity can only be clarified through identification of components that participate within it. However current proteomic techniques produce high volumes of information that are dispersed over several online databases. Collecting all of this data and using an integrative approach capable of identifying unknown associations is still an unsolved problem. This is the main motivation for this work. RESULTS We present the online bioinformatic tool OralCard, which comprises results from 55 manually curated articles reflecting the oral molecular ecosystem (OralPhysiOme). It comprises experimental information available from the oral proteome both of human (OralOme) and microbial origin (MicroOralOme) structured in protein, disease and organism. CONCLUSIONS This tool is a key resource for researchers to understand the molecular foundations implicated in biology and disease mechanisms of the oral cavity. The usefulness of this tool is illustrated with the analysis of the oral proteome associated with diabetes melitus type 2. OralCard is available at http://bioinformatics.ua.pt/oralcard.

Expression of Genes Encoding Extracellular Matrix Macromolecules and Metalloproteinases in Avian Tibial Dyschondroplasia

Avian tibial dyschondroplasia (TD) is a skeletal disease characterized by disruption of endochondral bone formation. The aim of this study was to determine the expression of extracellular matrix (ECM) macromolecules and ECM-degrading enzymes [matrix metalloproteinases (MMPs)] in the growth plates of normal and TD-affected 3-week-old broiler chicks (Cobb strain). Protein levels were analyzed by immunoblotting and gelatin zymography and gene expression by polymerase chain reaction. Expression of genes encoding the ECM macromolecules (collagen types II, IX, X and XI; and aggrecan) was not altered in dyschondroplasia; however, there was down-regulation of genes encoding MMP-9, MMP-13, MMP-10 and MMP-11 in addition to reduced amounts of MMP-2 and MMP-13 proteins. In contrast, there was up-regulation of genes encoding MMP-7 and the vascular endothelial growth factor. These findings suggest that the accumulation of cartilage associated with the disease may be the result of decreased proteolysis due to the down-regulation of MMPs and not to an increased production of ECM macromolecules.

Thermostability of cardosin A from Cynara cardunculus L.

The structural stability of cardosin A, a plant aspartic proteinase (AP) from Cynara cardunculusL., has been investigated by high-sensitivity differential scanning calorimetry, intrinsic fluorescence and circular dichroism spectroscopy, and enzymatic activity assays. Even though the thermal denaturation of cardosin A is partially irreversible, valid thermodynamic data can be obtained within a wide pH region. Also, although cardosin A is a heterodimeric enzyme its thermal denaturation occurs without simultaneous dissociation to unfolded monomers. Moreover, in the 3–7 pH region the excess heat capacity can be deconvoluted into two components corresponding to two elementary two-state transitions, suggesting that the two polypeptide chains of cardosin A unfold independently. Detailed thermodynamic and structural investigations of cardosin A at pH = 5.0, at which value the enzyme demonstrates maximum stability and enzymatic activity, revealed that after thermal denaturation the polypeptide chains of this protein retain most of their secondary structure motifs and are not completely hydrated.

Stability performance ofCynara cardunculus L. acid protease in aqueous-organic biphasic systems

Stability performance of the acid protease ofCynara cardunculus L. in biphasic systems containing ethyl acetate,n-hexane or isooctane was investigated and compared with that of pepsin. Activity retention was higher in the system containingn-hexane. In this system 100% retention was observed up to 144 hours. Pre-saturation of phases was found to increase enzyme stability in the cases ofn-hexane and isooctane and to be an absolute requirement in the case of ethyl acetate. The results obtained suggest also that, when dealing with pre-saturated phases, log P cannot be used straightforwardly to predict enzyme stability in biphasic systems.

Acetonitrile-induced unfolding of porcine pepsin A: A proposal for a critical role of hydration structures in conformational stability

In order to increase understanding of the basis of the stability of the native conformational state of porcine pepsin A, a strategy based on induction and monitoring of protein denaturation was developed. Structural perturbation was achieved by adding acetonitrile (MeCN) to the protein-solvent system. MeCN was found to induce non-coincident disruption of the secondary and tertiary structural features of pepsin A. It is proposed that gross unfolding is prompted by disruption of the protein hydration pattern induced by the organic co-solvent. It should be noted that the functional properties and thermal stability of the protein were already impaired before the onset of global unfolding. Low and intermediate contents of MeCN in the protein-solvent system affected the sharpness of the thermal transition and the degree of residual structure of the heat-denatured state. The importance of hydration to the conformational stability of pepsin A in its biologically active state is discussed.

The Characterisation of the Collagenolytic Activity of Cardosin A Demonstrates its Potential Application for Extracellular Matrix Degradative Processes

Type I collagen is the major fibrous protein of mammals being needed to strengthen and organise the extracellular matrix (ECM). Connective tissue components are modulated by matrix metalloproteinases, which are critical for disintegration and remodelling of ECM under physiological and pathological conditions. Cardosin A is an abundant aspartic proteinase (AP) from Cynara cardunculus L. that has been shown to be able to hydrolyse fibrillar collagen within the alpha-chains. The aim of this work is the characterisation of collagen degradation by cardosin A, since in the native state fibrillar collagen is resistant to most proteolytic enzymes. The pattern of type I collagen hydrolysis by cardosin A is defined and maintained for at least 24 hours of digestion, suggesting that cardosin A can hydrolyse collagen at a small number of specific peptide bonds. N-terminal sequencing of hydrolysis products identified one cleavage site as being Phe464-Gln465 in the alpha2 chain of collagen I. Two peptides were synthesised correspondent to collagen I specific sequences, in order to produce two polyclonal antibodies, that allowed the identification of three collagen fragments following cardosin A cleavage. Defining the mechanism of collagen cleavage by collagenases and other enzymes, like cardosin A, is important for the comprehension of physiological and pathological processes affecting the ECM. To our knowledge, this is the first study of in vitro collagenolytic activity of a plant AP. Therefore, in view of the cardosin A restricted specificity towards collagen this enzyme may be proposed for an eventual medical or technical procedures assisting ECM remodelling.

Immobilisation of Cardosin A in Chitosan Sponges as a Novel Implant for Drug Delivery

Cardosin A is extracted from the pistils of the plant Cynara cardunculus L. and chitosan is a polysaccharide derived from chitin with valuable properties as a biomaterial. In this work we report our experiments on the synthesis of chitosan sponges and immobilisation of cardosin A, by entrapment. We observed that 10-15% of the incorporated cardosin A were released over 6 days of incubation. In addition, we could also note that this immobilisation procedure did not induce any specificity alterations on cardosin A. The specificity study of the enzyme, using beta-chain of oxidised insulin, showed that the immobilised and released enzymes have the same hydrolysis pattern as the free enzyme. The ability of this enzyme to hydrolyse type I collagen was maintained, after the immobilisation procedure. The biocompatibility in vivo of these sponges was evaluated by histological staining after implantation in rats submitted to abdominal surgery. Results of this study demonstrated that these chitosan sponges are very promising vehicles for the application of cardosin A, in abdominal cavity for prevention and reduction of the adhesions formation.

Cardosin A as a model aspartic proteinase for the study of organic solvent effects. An overview on catalytic and structural aspects

Water has proven to be one of the several limitations for broadening the scope of applications of enzymes in biocatalysis, especially when the reactants involved are poorly water-soluble. The introduction of an organic solvent into the reaction system has numerous advantages. These include a direct action of the solvents on the reactants (improving their solubility) and on the reaction products (improving or diminishing their solubility), thereby increasing the productivity of the reaction system. Nevertheless, it has been documented that the introduction of an organic solvent into the reaction mixture may induce alterations on enzyme activity, enzyme stability and thermostability, and enzyme specificity thereby imprinting new properties to old enzymes.