Rui M. Ramos

Analysis of biogenic amines in wines by salting-out assisted liquid–liquid extraction and high-performance liquid chromatography with fluorimetric detection

Biogenic amines are nitrogenous organic compounds of low molecular weight that are either formed or metabolized in cells of living organisms and can be found in several food products, being produced mainly by amino acid decarboxylation. When ingested in high concentrations they can induce several health problems in humans. In alcoholic beverages, and especially in wine, they are formed during the vinification process as a result of the action of microorganisms. In this work it is proposed a new methodology for the determination of biogenic amines in wines, which includes a sample preparation approach based on salting-out assisted liquid-liquid extraction, the use of dansyl chloride for the derivatization and chromatographic separation by high-performance liquid chromatography with fluorimetric detection. The salting-out effect is used to promote phase separation between water and a water-miscible organic solvent, while improving the extraction of organic or inorganic species. Several extraction parameters were optimized, such as the dansyl chloride concentration, pH and the effects caused by the order in which the extraction and derivatization were performed. Extraction of amines, and consequent detection, depends on the presence of dansyl chloride in solution prior to extraction. The results showed the possibility to simultaneously perform the extraction and the derivatization, making sample preparation easier and less time-consuming. The methodology was successfully applied to the determination of biogenic amines in five wines (white, red and rosé). This method has the potential to be a good alternative to existing methods since it is cheaper, easier and simplifies the sample preparation step.

Understanding the importance of the aromatic amino-acid residues as hot-spots

Protein-protein interactions (PPI) are crucial for the establishment of life. However, its basic principles are still elusive and the recognition process is yet to be understood. It is important to look at the biomolecular structural space as a whole, in order to understand the principles behind conformation-function relationships. Since the application of an alanine scanning mutagenesis (ASM) study to the growth hormone it was demonstrated that only a small subset of residues at a protein-protein interface is essential for binding - the hot-spots (HS). Aromatic residues are some of the most typical HS at a protein-protein interface. To investigate the structural role of the interfacial aromatic residues in protein-protein interactions, we performed Molecular Dynamic (MD) simulations of protein-protein complexes in a water environment and calculated a variety of physical-chemical characteristics. ASM studies of single residues and of dimers or high-order clusters were performed to check for cooperativity within aromatic residues. Major differences were found between the behavior of non-HS aromatic residues and HS aromatic residues that can be used to design drugs to block the critical interactions or to predict major interactions at protein-protein complexes.

Computational Alanine Scanning Mutagenesis-An Improved Methodological Approach for Protein-DNA Complexes.

Proteins and protein-based complexes are the basis of many key systems in nature and have been the subject of intense research in the last decades, in an attempt to acquire comprehensive knowledge of reactions that take place in nature. Computational Alanine Scanning Mutagenesis approaches have been extensively used in the study of protein interfaces and in the determination of the most important residues for complex formation, the Hot-spots. However, as it is usually applied to the study of protein-protein interfaces, we tried to modify and apply it to the study of protein-DNA interfaces, which are also crucial in nature but have not been the subject of as much research. In this work, we carry out MD simulations of seven protein-DNA complexes and tested the influence of the variation of different parameters on the determination of the binding free energy terms (ΔΔGbinding) of 78 mutations: solvent representation, internal dielectric constant, Linear and Nonlinear Poisson-Boltzmann equation, Generalized Born model, simulation time, number of structures analyzed, number of MD trajectories, force field used, and energetic terms involved. Overall, this new approach gave an average error of 1.55 kcal/mol, and P, R, F1, accuracy, and specificity values of 0.78, 0.50, 0.61, 0.77, and 0.92, respectively. This improved computational alanine scanning mutagenesis approach may serve as a tool to explore the behavior of this important class of complexes.

Solvent-accessible surface area: How well can be applied to hot-spot detection?

A detailed comprehension of protein‐based interfaces is essential for the rational drug development. One of the key features of these interfaces is their solvent accessible surface area profile. With that in mind, we tested a group of 12 SASA‐based features for their ability to correlate and differentiate hot‐ and null‐spots. These were tested in three different data sets, explicit water MD, implicit water MD, and static PDB structure. We found no discernible improvement with the use of more comprehensive data sets obtained from molecular dynamics. The features tested were shown to be capable of discerning between hot‐ and null‐spots, while presenting low correlations. Residue standardization such as relSASAi or rel/resSASAi, improved the features as a tool to predict ΔΔGbinding values. A new method using support machine learning algorithms was developed: SBHD (Sasa‐Based Hot‐spot Detection). This method presents a precision, recall, and F1 score of 0.72, 0.81, and 0.76 for the training set and 0.91, 0.73, and 0.81 for an independent test set. Proteins 2014; 82:479–490.

Are hot-spots occluded from water?

Protein–protein interactions are the basis of many biological processes and are governed by focused regions with high binding affinities, the warm- and hot-spots. It was proposed that these regions are surrounded by areas with higher packing density leading to solvent exclusion around them – “the O-ring theory.” This important inference still lacks sufficient demonstration. We have used Molecular Dynamics (MD) simulations to investigate the validity of the O-ring theory in the context of the conformational flexibility of the proteins, which is critical for function, in general, and for interaction with water, in particular. The MD results were analyzed for a variety of solvent-accessible surface area (SASA) features, radial distribution functions (RDFs), protein–water distances, and water residence times. The measurement of the average solvent-accessible surface area features for the warm- and hot-spots and the null-spots, as well as data for corresponding RDFs, identify distinct properties for these two sets of residues. Warm- and hot-spots are found to be occluded from the solvent. However, it has to be borne in mind that water-mediated interactions have significant power to construct an extensive and strongly bonded interface. We observed that warm- and hot-spots tend to form hydrogen bond (H-bond) networks with water molecules that have an occupancy around 90%. This study provides strong evidence in support of the O-ring theory and the results show that hot-spots are indeed protected from the bulk solvent. Nevertheless, the warm- and hot-spots still make water-mediated contacts, which are also important for protein–protein binding.

Determination of ethyl carbamate in spirits using salting-out assisted liquid–liquid extraction and high performance liquid chromatography with fluorimetric detection

In this work, a simple methodology was developed for the determination of ethyl carbamate (EC) in spirits by high performance liquid chromatography with fluorimetric detection. The sample is subjected to salting-out assisted liquid–liquid extraction (SALLE) using a 9-xanthydrol/acetonitrile solution for the simultaneous extraction and derivatisation of EC. Extraction/derivatization occurs under acidic conditions (0.5 mol L−1 HCl) and NaCl was used for phase separation. The methodology showed low limits of detection and quantification (9 μg L−1 and 23 μg L−1, respectively) and good precision (4.4% intraday and 8.7% interday). The determined EC concentrations in the analysed samples varied between 51 and 266 μg L−1. The proposed sample preparation methodology is simple and low cost, it uses limited toxicity solvents and the obtained extract is readily compatible with reversed phase liquid chromatography. Moreover, the stability of the xanthyl-EC product was verified. More importantly it is a more robust alternative to the liquid chromatography based methodologies that do not apply any extraction procedure, which do not consider the problems associated with the long term deterioration of the analytical systems.

Determination of Carbonyl Compounds in Cork Agglomerates by GDME-HPLC-UV: Identification of the Extracted Compounds by HPLC-MS/MS

A new approach is proposed for the extraction and determination of carbonyl compounds in solid samples, such as wood or cork materials. Cork products are used as building materials due to their singular characteristics; however, little is known about its aldehyde emission potential and content. Sample preparation was done by using a gas-diffusion microextraction (GDME) device for the direct extraction of volatile aldehydes and derivatization with 2,4-dinitrophenylhydrazine. Analytical determination of the extracts was done by HPLC-UV, with detection at 360 nm. The developed methodology proved to be a reliable tool for aldehyde determination in cork agglomerate samples with suitable method features. Mass spectrometry studies were performed for each sample, which enabled the identification, in the extracts, of the derivatization products of a total of 13 aldehydes (formaldehyde, acetaldehyde, furfural, propanal, 5-methylfurfural, butanal, benzaldehyde, pentanal, hexanal, trans-2-heptenal, heptanal, octanal, and trans-2-nonenal) and 4 ketones (3-hydroxy-2-butanone, acetone, cyclohexanone, and acetophenone). This new analytical methodology simultaneously proved to be consistent for the identification and determination of aldehydes in cork agglomerates and a very simple and straightforward procedure.

Determination of ammonia nitrogen in solid and liquid high-complex matrices using one-step gas-diffusion microextraction and fluorimetric detection

This paper introduces a new method for a one-step determination of ammonia nitrogen (NH3) in high complex solid and liquid samples from the agricultural and livestock sectors. To this end, we developed a simultaneous extraction and fluorimetric labeling of NH3, using gas diffusion microextraction (GDME), followed by the fluorescence measurement under 96-well microplate format. The GDME ensured a selective diffusion of NH3 through a commercial hydrophobic membrane, and confined the acceptor solution, which included the fluorimetric labeling reagent o-phthalaldehyde (OPA). The OPA-NH3 labeling reaction was optimized resorting to a full factorial experimental design, which showed that the reducing agent (Na2SO3) concentration was critical to achieve the highest sensitivity. A similar optimization approach for GDME showed that time and temperature significantly influenced the sensitivity of the assay, and also that the modifications in these two factors could be used to adjust the sensitivity according to the concentrations present in the samples. In our final conditions, it was possible to quantify NH3 in the range between 0.38 and 6.27mgL-1 using a 10min extraction at 25°C in different samples (e.g., corn and grass silages, feces, urine). The developed method showed a high repeatability and reproducibility (intraday and interday relative standard deviations values of 4.5% and 9.5%, respectively) and an adequate limit of detection (0.22mgL-1). This new methodology also highlighted the simplicity and versatility of GDME for the determination of volatile components of high-complex matrices, which will certainly drive future developments in the analysis of environmental and biological samples.

Voltammetric determination of trace amounts of diacetyl at a mercury meniscus modified silver solid amalgam electrode following gas-diffusion microextraction

A new approach was developed for the determination of trace amounts of diacetyl in food products using gas-diffusion microextraction (GDME) and subsequent detection by differential pulse voltammetry (DPV) at a mercury meniscus modified silver solid amalgam electrode (m-AgSAE). Diacetyl is a vicinal diketone responsible for the buttery aroma in many fermented foods and beverages. Its determination is important not only for evaluation of the final product quality (note of mention: health related concerns were associated with continuous diacetyl exposure) but also to monitor fermentation. GDME, a technique combining gas-diffusion and microextraction, particularly aimed to volatile and semi-volatile analytes, seemed the best way to selective extract diacetyl. A solution of 0.05% o-phenylenediamine (OPDA) prepared in a Britton-Robinson buffer (pH 5.0) was chosen as the extracting solution. This solution simultaneously extracts, pre-concentrates and derivatizes diacetyl to 2,3-dimethylquinoxaline (DMQ), enhancing the extraction selectivity and making the analyte electroactive. After finding the optimum conditions for the extraction process (10min at 60°C with 1.0mL of OPDA at pH 5.0), the DPV measurements at the m-AgSAE were conducted with a scan rate of 7mVs-1, a modulation amplitude of 50mV and a modulation time of 100ms. Under these conditions, the resulting DMQ could be easily measured at a potential of -0.6V vs. Ag|AgCl (3molL-1 KCl). The amalgam electrode keeps the advantages of classic mercury electrodes, like high sensitivity, while being environmentally friendly. The GDME/m-AgSAE produced suitable method features for the determination of low amounts of diacetyl (as DMQ) in alcoholic beverages, and in fact, to the best of our knowledge, the limit of quantification of 0.18µgL-1 is one of the lowest reported in literature.

4-hydrazinobenzoic acid as a derivatizing agent for aldehyde analysis by HPLC-UV and CE-DAD

Aldehydes are relevant analytes in a wide range of samples, in particular, food and beverages but also body fluids. Hydrazines can undergo nucleophilic addition with aldehydes or ketones giving origin to hydrazones (a group of stable imines) that can be suitably used in the identification of aldehydes. Herein, 4-hydrazinobenzoic acid (HBA) was, for the first time, used as the derivatizing agent in analytical methodologies using liquid chromatography aiming the determination of low-molecular aldehydes. The derivatization reaction was simultaneously performed along with the extraction process, using gas-diffusion microextraction (GDME), which resulted in a clean extract containing the HBA-aldehyde derivates. The corresponding formed imines were determined by both high-performance liquid chromatography (LC) with UV spectrophotometric detection (HPLC-UV) and capillary electrophoresis with diode array detection (CE-DAD). HBA showed to be a rather advantageous derivatization reagent due to its stability, relatively high solubility in water and other solvents, high selectivity and sensibility, reduced impurities, simple preparation steps and applicability to different separation and/or different detection techniques. Limits of detections (LODs) of the optimized methodologies (in terms of time and pH among other experimental variables) were all below 0.5 mg L-1, using both instrumental techniques. Furthermore, for the first time, the HBA-aldehyde derivatives were analyzed by LC with mass spectrometry (LC-MS), demonstrating the possibility of identification by MS of each compound. The developed methodologies were also successfully applied in the analysis of formaldehyde and acetaldehyde in several alcoholic beverages. This was also the first time GDME was combined with CE, showing that it can be a valuable sample preparation tool for electrophoresis, in particular by eliminating the interference of ions and inorganic constituents present in the samples.