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Daniel Cabrol-Bass

Publications and source records attributed to Daniel Cabrol-Bass.

11 recordsLinked to original sources
PubMed2006

Molecular simulations reveal a new entry site in quercetin 2,3-dioxygenase. A pathway for dioxygen?

Molecular dynamics simulations performed on quercetin 2,3-dioxygenase have shown the existence of a channel linking the bulk solvent and the cavity of the enzyme. Although much is known about the the oxygenolysis reaction catalyzed by this enzyme, the way dioxygen enters the active site has not been firmly established. The size, orientation and hydrophobic character of this channel suggests that it could provide an entrance for molecular dioxygen into the cavity. Free energy calculations show that such a process is likely to occur.

Binding Sites↗
PubMed2004

Oxygenolysis of flavonoid compounds: DFT description of the mechanism for quercetin.

Flavonoids are naturally occurring phenol derivatives present in substantial amounts in a large variety of plants, fruits and vegetables daily eaten by humans. Most of these compounds exhibit several interesting biological activities, such as antiradical and antioxidant actions. Indeed, by complexation with specific enzymes, flavonoids are notably liable to metabolize molecular dioxygen. On the basis of experimental results describing oxygenolysis of the flavonoid quercetin, activated by the enzyme quercetin 2,3-dioxygenase (2,3-QD),ur attention has focused on the role of metal center in the activation of the substrate quercetin. Thus, in the present study, by means of DFT calculations at the B3LYP/ 6-31(+)G* level on model molecular systems, we describe different mechanisms for dioxygen metabolization by quercetin. Stationary points are described, and energetic and structural analyses along the reaction paths are reported. Our calculations show that the copper cation must act as an oxidant towards the substrate and that the reaction proceeds through a 1,3-cycloaddition.

Copper↗
PubMed2004

Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the loop of an RNA in complementary interaction with HIV-1 TAR. The simulations reveal that the mismatch GA base, mediated by a water molecule, leads to a complex that presents the best compromise between flexibility and energetic contributions. The mismatch CU base pair, in spite of the presence of an inserted water molecule, is too short to achieve a tight interaction at the closing-loop junction and seems to force TAR to reorganize upon binding. An energetic analysis has allowed us to quantify the strength of the interactions of the closing and the loop-loop pairs throughout the simulations. Although the water-mediated GA closing base pair presents an interaction energy similar to that found on fully geometry-optimized structure, the water-mediated CU closing base pair energy interaction reaches less than half the optimal value.

Aptamers, Nucleotide↗
PubMed2003

Molecular dynamics simulation of hepatitis C virus IRES IIId domain: structural behavior, electrostatic and energetic analysis.

The dynamic behavior of the HCV IRES IIId domain is analyzed by means of a 2.6-ns molecular dynamics simulation, starting from an NMR structure. The simulation is carried out in explicit water with Na+ counterions, and particle-mesh Ewald summation is used for the electrostatic interactions. In this work, we analyze selected patterns of the helix that are crucial for IRES activity and that could be considered as targets for the intervention of inhibitors, such as the hexanucleotide terminal loop (more particularly its three consecutive guanines) and the loop-E motif. The simulation has allowed us to analyze the dynamics of the loop substructure and has revealed a behavior among the guanine bases that might explain the different role of the third guanine of the GGG triplet upon molecular recognition. The accessibility of the loop-E motif and the loop major and minor groove is also examined, as well as the effect of Na+ or Mg2+ counterion within the simulation. The electrostatic analysis reveals several ion pockets, not discussed in the experimental structure. The positions of these ions are useful for locating specific electrostatic recognition sites for potential inhibitor binding.

Amino Acid Motifs↗
PubMed2003

Cyclic PNA-based compound directed against HIV-1 TAR RNA: modelling, liquid-phase synthesis and TAR binding.

A cyclic molecule including a hexameric PNA sequence has been designed and synthesized in order to target the TAR RNA loop of HIV-1 through the formation of a "kissing complex". For comparison, its linear analogue has also been investigated. The synthesis of the cyclic and linear PNA has been accomplished following a liquid-phase strategy using mixed PNA and fully N-protected (aminoethylglycinamide) fragments. The interactions of this cyclic PNA and its linear analogue with TAR RNA have been studied and the results indicate clearly that no interaction occurs between the cyclic antisense PNA and TAR RNA, whereas a tenuous interaction has been detected with its linear PNA analogue.

Cyclization↗
PubMed2003

A simple method for automated pretreatment of usable chromatographic profiles in pattern-recognition procedures: application to HPAEC-PAD chromatograms of honeys.

In this article a simple method for automated pretreatment of chromatograms is presented. The resulting data matrix can be used as input for multivariate statistical analysis. Application of this method to high-performance anion-exchange chromatography-pulsed amperometric detection (HPAEC-PAD) chromatograms of honeys before canonical discriminant analysis results in very good performance in the data reduction with regard to the preservation of the original information content of the data. This pretreatment of the chromatogram allows for the use of all the peaks corresponding to the sugars present in the sample. This results in a high-quality discrimination between honeys of various types. A versatile program has been developed to apply this method. This serves as a starting point for software suited for food characterization and adulteration detection by semi-automatic pattern recognition applied to chromatographic analysis.

Journal Article↗
PubMed2003

Honey characterization and adulteration detection by pattern recognition applied on HPAEC-PAD profiles. 1. Honey floral species characterization.

An improved COFRAC (COmité FRançais d'ACréditation) method for the analysis and evaluation of the quality of honey by high-performance anion-exchange chromatography of sugar profiles is proposed. With this method, both minor and major sugars are simultaneously analyzed and the technique is integrated in a new chemometric approach, which uses the entire chromatographic sugars profile of each analyzed sample to characterize honey floral species. Sixty-eight authentic honey samples (6 varieties) were analyzed by high-performance anion-exchange chromatography-pulsed amperometric detection. A new algorithm was developed to create automatically the corresponding normalized data matrix, ready-to-use in various chemometric procedures. This algorithm transforms the analytical profiles to produce the corresponding calibrated table of the surfaces or intensities according to retention times of peaks. The possibility of taking into account unknown peaks (those for which no standards are available) allows the maximum chemical information provided by the chromatograms to be retained. The parallel application of principal component analysis (PCA)/linear discriminant analysis (LDA) and artificial neural networks (ANN) shows a high capability in the classification of the analyzed samples (LDA, 93%; ANN, 100%) and a very good discrimination of honey groups. This work is the starting point of the elaboration of a new system designed for the automatic pattern recognition of food samples (first application on honey samples) from chromatographic analyses for food characterization and adulteration detection.

Algorithms↗
PubMed2002

Intramolecular allyl transfer reaction from allyl ether to aldehyde groups: experimental and theoretical studies.

The intramolecular transfer of the allyl group of functionalized allyl aryl ethers to an aldehyde group in the presence of Ni0 complexes was studied from chemical, electrochemical and theoretical points of view. The chemical reaction involves the addition of Ni0 to the allyl ether followed by stoichiometric allylation. The electrochemical process is catalytic in nickel and involves the reduction of intermediate eta3-allylnickel(II) complexes.

Journal Article↗
PubMed2002

Use of differential scanning calorimetry (DSC) as a new technique for detection of adulteration in honeys. 1. Study of adulteration effect on honey thermal behavior.

Differential scanning calorimetry (DSC) was used to study the thermal behavior of authentic honeys (Lavandula, Robinia, and Fir honeys) and industrial sugar syrups. Thermal or thermochemical parameters such as the glass transition temperature (Tg), enthalpies of fusion (DeltaH(fus)), and heat capacity variation (DeltaC(p)) were measured. The syrups and honeys showed significant differences in thermal phenomena, as well as in their amplitude and position on the temperature scale. Results showed good reproducibility of the method for all samples studied. The effect of adulteration of honey with different amounts of syrup (5, 10, 20, 40, and 60%) was investigated. A linear relationship was found between the percentage of added syrup and the glass transition temperature. A similar relationship was obtained from the enthalpy of fusion results in the temperature range of 40-90 degrees C. Under applied conditions, the effects of adulteration of honeys by industrial syrups appeared to be detectable from a level as low as 5%.

Calorimetry, Differential Scanning↗
PubMed2002

Modelling, synthesis and biological evaluation of an ethidium-arginine conjugate linked to a ribonuclease mimic directed against TAR RNA of HIV-1.

Using molecular modelling studies, an active anti-HIV ethidium-arginine conjugate targeted against the viral TAR RNA sequence has been linked to an artificial ribonuclease, with the aim to obtain an irreversible inhibitor. The ribonuclease moiety consists of an N-[N-(3-aminopropyl)-3-aminopropyl] glycine and has been constructed via two successive N-alkylations following the Fukuyama procedure.

Alkylation↗