Improving the sensitivity of the determination of ceftiofur by capillary electrophoresis in environmental water samples: in-line solid phase extraction and sample stacking techniques

This paper describes two different approaches for increasing the sensitivity for the analysis of ceftiofur by capillary electrophoresis (CE). Two different techniques based on the introduction of an enlarged volume of sample, namely large volume sample stacking (LVSS) and in-line solid phase extraction (SPE) were studied and compared. LVSS allowed the on-column electrophoretic preconcentration of ceftiofur without modification of the separation capillary. In-line SPE-CE was developed by using a home-made microcartridge that was filled with a reversed-phase sorbent (C₁₈). The microcartridge was coupled in-line near the inlet of the separation capillary. LVSS and in-line SPE-CE allowed automated operation and improved sensitivity for the analysis of ceftiofur with respect to conventional CE. When environmental water samples were analyzed, an additional pretreatment step based on off-line SPE was necessary in both cases to further decrease the detection limits. In terms of sensitivity for the determination of ceftiofur in river water samples, the combination of off-line SPE with in-line SPE-CE was found the most sensitive with a detection limit of 10 ng L⁻¹, whereas the method based on the use of off-line SPE with LVSS presented a detection limit of 100 ng L⁻¹.     

Catalytic itinerary in 1,3-1,4-β-glucanase unraveled by QM/MM metadynamics. Charge is not yet fully developed at the oxocarbenium ion-like transition state

Retaining glycoside hydrolases (GHs), key enzymes in the metabolism of polysaccharides and glycoconjugates and common biocatalysts used in chemoenzymatic oligosaccharide synthesis, operate via a double-displacement mechanism with the formation of a glycosyl-enzyme intermediate. However, the degree of oxocarbenium ion character of the reaction transition state and the precise conformational itinerary of the substrate during the reaction, pivotal in the design of efficient inhibitors, remain elusive for many GHs. By means of QM/MM metadynamics, we unravel the catalytic itinerary of 1,3-1,4-β-glucanase, one of the most active GHs, belonging to family 16. We show that, in the Michaelis complex, the enzyme environment restricts the conformational motion of the substrate to stabilize a (1,4)B/(1)S(3) conformation of the saccharide ring at the -1 subsite, confirming that this distortion preactivates the substrate for catalysis. The metadynamics simulation of the enzymatic reaction captures the complete conformational itinerary of the substrate during the glycosylation reaction ((1,4)B/(1)S(3) -(4)E/(4)H(3) - (4)C(1)) and shows that the transition state is not the point of maximum charge development at the anomeric carbon. The overall catalytic mechanism is of dissociative type, and proton transfer to the glycosidic oxygen is a late event, clarifying previous kinetic studies of this enzyme.     

Molecular Mechanism of a Hotdog‐Fold Acyl‐CoA Thioesterase

Thioesterases are enzymes that hydrolyze thioester bonds between a carbonyl group and a sulfur atom. They catalyze key steps in fatty acid biosynthesis and metabolism, as well as polyketide biosynthesis. The reaction molecular mechanism of most hotdog‐fold acyl‐CoA thioesterases remains unknown, but several hypotheses have been put forward in structural and biochemical investigations. The reaction of a human thioesterase (hTHEM2), representing a thioesterase family with a hotdog fold where a coenzyme A moiety is cleaved, was simulated by quantum mechanics/molecular mechanics metadynamics techniques to elucidate atomic and electronic details of its mechanism, its transition‐state conformation, and the free energy landscape of the process. A single‐displacement acid‐base‐like mechanism, in which a nucleophilic water molecule is activated by an aspartate residue acting as a base, was found, confirming previous experimental proposals. The results provide unambiguous evidence of the formation of a tetrahedral‐like transition state. They also explain the roles of other conserved active‐site residues during the reaction, especially that of a nearby histidine/serine pair that protonates the thioester sulfur atom, the participation of which could not be elucidated from mutation analyses alone.     

Substrate‐Guided Front‐Face Reaction Revealed by Combined Structural Snapshots and Metadynamics for the Polypeptide N‐Acetylgalactosaminyltransferase 2

The retaining glycosyltransferase GalNAc‐T2 is a member of a large family of human polypeptide GalNAc‐transferases that is responsible for the post‐translational modification of many cell‐surface proteins. By the use of combined structural and computational approaches, we provide the first set of structural snapshots of the enzyme during the catalytic cycle and combine these with quantum‐mechanics/molecular‐mechanics (QM/MM) metadynamics to unravel the catalytic mechanism of this retaining enzyme at the atomic‐electronic level of detail. Our study provides a detailed structural rationale for an ordered bi–bi kinetic mechanism and reveals critical aspects of substrate recognition, which dictate the specificity for acceptor Thr versus Ser residues and enforce a front‐face S_Ni‐type reaction in which the substrate N‐acetyl sugar substituent coordinates efficient glycosyl transfer.     

Two polydimethylsiloxane rod extraction methods for the sensitive determination of phenolic compounds in water samples

Simple, precise, and low‐cost methods for the simultaneous determination of phenolic endocrine disrupting compounds such as bisphenol A, trichlorophenol, pentachlorophenol, 4‐nonylphenol, and 4‐octylphenol in water samples were developed. The Direct, in situ derivatization methods are based on polydimethylsiloxane rod extraction followed by liquid desorption and chromatographic analysis by liquid chromatography and diode array detection. Several parameters affecting the extraction and desorption of the phenolic compounds and their acetylated derivates were studied, as well as the chromatographic and detection conditions. For the direct method, determination coefficients (r²) > 0.990 and LODs in the 0.6–2 μg/L range were obtained for all compounds except bisphenol A (9.5 μg/L). With the derivatization‐based method, based on in situ acetylation, lower limits of detection (0.3–0.9 μg/L) were obtained for all the compounds with r² > 0.988 and RSDs in the 2–9% range. The developed methods were applied to the analysis of spiked water samples obtaining recoveries of between 60.2 and 131.7% for the direct method, and of between 76.6 and 108.2% for the derivatization‐based method. The results demonstrate the feasibility of using these two methods for determining bisphenol A, trichlorophenol, pentachlorophenol, 4‐nonylphenol, and 4‐octylphenol in water.     

Integration of enzyme kinetic models and isotopomer distribution analysis for studies of <Emphasis Type="Italic">in situ</Emphasis>cell operation

A current trend in neuroscience research is the use of stable isotope tracers in order to address metabolic processes in vivo. The tracers produce a huge number of metabolite forms that differ according to the number and position of labeled isotopes in the carbon skeleton (isotopomers) and such a large variety makes the analysis of isotopomer data highly complex. On the other hand, this multiplicity of forms does provide sufficient information to address cell operation in vivo. By the end of last millennium, a number of tools have been developed for estimation of metabolic flux profile from any possible isotopomer distribution data. However, although well elaborated, these tools were limited to steady state analysis, and the obtained set of fluxes remained disconnected from their biochemical context. In this review we focus on a new numerical analytical approach that integrates kinetic and metabolic flux analysis. The related computational algorithm estimates the dynamic flux based on the time-dependent distribution of all possible isotopomers of metabolic pathway intermediates that are generated from a labeled substrate. The new algorithm connects specific tracer data with enzyme kinetic characteristics, thereby extending the amount of data available for analysis: it uses enzyme kinetic data to estimate the flux profile, and vice versa, for the kinetic analysis it uses in vivo tracer data to reveal the biochemical basis of the estimated metabolic fluxes.     

Electronic structure and charge transfer in the ternary intercalated graphite beta-KS0.25C3

The electronic structure of the ternary intercalated graphite beta-KS(0.25)C3 is studied by means of a first-principles density functional theory approach. The nature of the partially filled bands is analyzed, and the K sublayers of the intercalate are shown to have an important contribution to the Fermi surface. This K-based contribution confers a sizable three-dimensional character to the conductivity even if considerably less than that for the related binary KC8. The electronic structure of beta-KS(0.25)C3 differs noticeably from that of the related ternary compound, KH(x)C4. The charge transfer is analyzed, and a way to evaluate it, which can be used in general for intercalated graphites, is proposed. The charge transfer per C atom in this ternary material is shown to be smaller than that in the KC8 binary compound despite a more favorable stoichiometry ratio between K and C.