Mass spectrometric and peptide chip characterization of an assembled epitope: analysis of a polyclonal antibody model serum directed against the Sjøgren/systemic lupus erythematosus autoantigen TRIM21

We demonstrate the development of a mass spectrometry‐based epitope‐mapping procedure in combination with Western blot analysis that works also with antigens that are insoluble in nondenaturing buffers consuming minute amounts of antigen (approximately 200 pmol) and antibody (approximately 15 pmol), respectively. A polyclonal anti‐TRIM21 rabbit antibody serum is applied as a model serum for future patient analyses to set up the system. The major epitope that is recognized by the anti‐TRIM21 serum spans the central TRIM21 region LQ‐EE REL GE‐KE, showing that immunization with a 139‐amino acid residue long peptide resulted in a ‘monospecific’ polyclonal antibody repertoire. Protein structure investigations, secondary structure predictions, and surface area calculations revealed that the best matching partial sequence to fulfill all primary and secondary structure requirements was the four amino acid spanning motif ‘L–E–Q–L’, which is present in both the sequential and the α‐helical peptide conformation. Peptide chip analyses confirmed the mass spectrometric results and showed that the peptide chip platform is an appropriate method for displaying secondary structure‐relying epitope conformations. As the same secondary structures are present in vivo, patient antibody screening, e.g., to identify subgroups of patients according to distinct epitope antibody reactivities, is feasible. Copyright © 2013 John Wiley & Sons, Ltd.     

Attenuated total reflection infrared microspectroscopy combined with multivariate analysis: a novel tool to study the presence of cocoa polyphenol metabolites in urine samples

The detection and quantification of polyphenols in biological samples is mainly performed by liquid chromatography in tandem with mass spectrometry (HPLC-MS/MS). This technique requires the use of organic solvents and needs control and maintenance of several MS/MS parameters, which makes the method expensive and time consuming. The main objective of this study was to evaluate, for the first time, the potential of using attenuated total reflection infrared microspectroscopy (ATR-IRMS) coupled with multivariate analysis to detect and quantify phenolic compounds excreted in human urine. Samples were collected from 5 healthy volunteers before and 6, 12 and 24 h after ingestion of 40 g cocoa powder with 250 mL of water or whole milk, and stored at -80 °C. Each sample was centrifuged at 5000 rpm for 10 min and at 4 °C and applied onto grids of a hydrophobic membrane. Spectra were collected in the attenuated total reflection (ATR) mode in the mid-infrared region (4000-800 cm(-1)) and were analyzed by a multivariate analysis technique, soft independent modeling of class analogy (SIMCA). Spectral models showed that IR bands responsible for chemical differences among samples were related to aromatic rings. Therefore, ATR-IRMS could be an interesting and straightforward technique for the detection of phenolic compounds excreted in urine. Moreover, it could be a valuable tool in studies aimed to identify biomarkers of consumption of polyphenol-rich diets.     

Microwave plasma in argon produced by a surface wave: study of the effect of pressure on the optical emission and the potentials for analysis of gaseous samples

The possibility of chemical analysis of gaseous samples by optical emission spectroscopy has been evaluated using a microwave induced plasma created by a surface wave at 210 MHz. Methane has been introduced at low concentration (1–20 ppm) in argon gas. The emission of excited CH, CN, C₂ at atmospheric pressure, was observed along the discharge and studied as a function of the methane concentration. The influence of the pressure on CH emission is presented from 10 Torr to atmospheric pressure. Contrary to usual predictions, the emission of CH bands is maximum at about 100 Torr and not at atmospheric pressure.     

Comprehensive two-dimensional gas chromatography in the analysis of volatile samples of natural origin: a multidisciplinary approach to evaluate the influence of second dimension column coated with mixed stationary phases on system orthogonality

The study evaluates the influence of selectivity tuning of the stationary phase of the second dimension on the orthogonality of a comprehensive two-dimensional gas chromatography (GC x GC) system. Two different sets of columns, providing independent and semi-independent separation mechanisms were used. The first consisted of a first dimension separating analytes on a volatility basis (i.e. a non-polar polydimethylsiloxane (OV1) column) combined with a second dimension separating by polarity, using columns coated with 100% polyethylene glycol (CW20M), CW20M/OV1 mixtures in ratios of 25-75%, and polydimethylsiloxane, 7% phenyl, 7% cyanopropyl (OV1701). The second set consisted of a first dimension separating analytes on a polarity basis (100% CW20M column) combined with a second dimension separating by volatility, consisting of columns coated with 100% OV1, OV1/CW20M mixtures in ratios of 25-75%, and 100% OV1701. Medium-complexity mixtures of natural origin (i.e. peppermint essential oil and a standard mixture of suspected allergens) consisting of components in a relatively limited range of molecular weights (MW) and volatilities, but belonging to different classes of compounds in a wide range of polarity (mono- and sesquiterpenoids, hydrocarbons and oxygenated compounds) were analysed with the above sets of columns. Different approaches were used to evaluate peak spreading on the GC x GC separation plane and degree of orthogonality of the column sets, namely: (1) a Factor Analysis (FA) approach, estimating the correlation coefficients and spreading angles of the sample components in the two-dimensional chromatographic plane; (2) an Informational Theory (IT) approach, based on determining a group of parameters including: informational entropy, % synentropy and similarity (H); and (3) an approach based on estimating the amount of separation space used, i.e. a practical parameter that directly refers to the experimental separation plane of the GC x GC chromatogram. Results showed that peak spreading in the chromatographic plane, when CW20M and OV1 are combined in different ratios, can be predicted from retention mechanisms, and that the degree of orthogonality measured with different approaches, is consistent with the divergent nature, in terms of polarity of the stationary phases combined in the GC x GC system.     

Universal method for synthesis of artificial gel antibodies by the imprinting approach combined with a unique electrophoresis technique for detection of minute structural differences of proteins, viruses, and cells (bacteria). III: gel antibodies against cells (bacteria)

Artificial antibodies in the form of gel granules were synthesized from the monomers acrylamide and N,N'-methylenebisacrylamide by the imprinting method in the presence of Echerichia coli bacteria as template. The electrophoretic migration velocities of the gel antibodies (i) saturated with the antigen (Escherichia coli MRE-600), (ii) freed of the antigen, and (iii) resaturated with bacteria, were determinated by electrophoresis in a rotating narrow-bore tube of 245 mm length and the 2.5 and 9.6 mm inner and outer diameters, respectively. Removal of bacteria from the gel antibodies was made by treatment with enzymes, followed by washing with SDS and buffer. Gel granules becoming charged by adsorption of bacteria move in an electrical field. We obtained a significant selectivity of gel antibodies for E. coli MRE-600, since the granules did not interact with Lactococcus lactis; and when E. coli BL21 bacteria were added to the gels selective for E. coli MRE-600, a significant difference in the migration rate of the complexes formed with the two strains was observed indicating the ability of differentiation between the two strains. The gel antibodies can be used repeatedly. The new imprinting method for the synthesis of artificial gel antibodies against bioparticles described herein, and the classical electrophoretic analysis technique employed, thus represent - when combined - a new approach to distinguish between different types and strains of bacteria. The application area can certainly be extended to cover other classes of cells.     

Universal method for synthesis of artificial gel antibodies by the imprinting approach combined with a unique electrophoresis technique for detection of minute structural differences of proteins, viruses, and cells (bacteria): Ia. gel antibodies against proteins (transferrins)

Artificial antibodies in the form of gel granules were prepared by the molecular imprinting technique from the monomers acrylamide and N,N'-methylene-bis-acrylamide. Gel granules, freed from the selectively adsorbed protein (the antigen), are neutral and, accordingly, do not migrate in an electrical field. However, upon selective interaction with the antigen at a pH different from its pI, the granules become charged. The selectivity of the gel antibodies was studied by free zone electrophoresis in a tube with inside diameter larger than the size of the granules. Such electrophoretic analyses showed that gel antibodies against iron-free transferrin had a high selectivity for this protein, although some crossreaction took place with iron-saturated transferrin, indicating that these artificial antibodies can easily distinguish the minute differences in the 3-D structure of the transferrins. Analogously, gel antibodies against iron-saturated transferrin were highly selective for this protein with some crossreaction with iron-free transferrin. The mobilities of iron-free and iron-saturated transferrin are very similar, and, therefore, capillary free zone electrophoresis cannot distinguish between these structurally related proteins. However, significant differences in the mobilities of the selective gel granules can be observed depending on their interaction with iron-free or iron-saturated transferrin, i.e., the artificial gel antibodies may become powerful analytical tools.     

Universal method for synthesis of artificial gel antibodies by the imprinting approach combined with a unique electrophoresis technique for detection of minute structural differences of proteins, viruses, and cells (bacteria): II. Gel antibodies against virus (Semliki Forest Virus)

Artificial and highly selective antibodies (in the form of gel granules) against proteins can easily be synthesized by a simple, cost-effective imprinting technique [Liao, J.-L. et al., Chromatographia 1996, 42, 259-262]. Using the same method for synthesis of gel antibodies against viruses in combination with analysis by free zone electrophoresis in a rotating narrow bore tube we have shown that artificial gel antibodies against Semliki Forest Virus (wild type) can sense the difference between this virus and a mutant, although they differ in their chemical composition only by three amino acids in one of the three proteins on the surface of the virus particle. The reason for this extremely high resolution is explained by the fact that we use three types of selectivity: (i) shape selectivity (created by the close fit between the antigen and its imprint in the gel), (ii) bond selectivity in the contact area between the antigen and its imprint in the gel antibody, and (iii) charge selectivity, originating from slightly different structures or/and conformations of the antigens.     

Insights into the selective catalytic reduction of NO by NH_3 over Mn_3O_4(110):a DFT study coupled with microkinetic analysis

Nitric oxide(NO_x), as one of the main pollutants, can contribute to a series of environmental problems, and to date the selective catalytic reduction(SCR) of NO_x with NH_3 in the presence of excess of O_2 over the catalysts has served as one of the most effective methods, in which Mn-based catalysts have been widely studied owing to their excellent low-temperature activity toward NH3-SCR. However, the related structure-activity relation was not satisfactorily explored at the atomic level. By virtue of DFT+U calculations together with microkinetic analysis, we systemically investigate the selective catalytic reduction process of NO with NH_3 over Mn_3 O_4(110), and identify the crucial thermodynamic and kinetic factors that limit the catalytic activity and selectivity.It is found that NH3 prefers to adsorb on the Lewis acid site and then dehydrogenates into NH_2~* assisted by either the two-or three-fold lattice oxygen; NH_2~* would then react with the gaseous NO to form an important intermediate NH_2 NO that prefers to convert into N_2 O rather than N_2 after the sequential dehydrogenation, while the residual H atoms interact with O_2 and left the surface in the form of H_2 O. The rate-determining step is proposed to be the coupling reaction between NH_2~* and gaseous NO.Regarding the complex surface structure of Mn_3 O_4(110),the main active sites are quantitatively revealed to be O_(3 c) and Mn_(4 c).     

Stereoselective formation of dicondensed spiropyran product obtained from the reaction of excess Fischer base with salicylaldehydes: first full characterization by X-ray crystal structure analysis of a DC·acetone crystal

The structure and stereochemistry of the dicondensed spiropyran product (DC-1, X=COOH) obtained from reaction of excess Fischer base with substituted salicylaldehydes has been fully assigned as C with (8R, 10R) configuration on the basis of single crystal X-ray diffraction analysis. The stereoselective formation of DC molecules indicates that the most plausible mechanism for DC formation involves dehydration of the cyclic carbinol intermediate with the aid of intramolecular H-bonding via transition structure TS₁^‡.     

Titania as a chemo-affinity support for the column-switching HPLC analysis of phosphopeptides: application to the characterization of phosphorylation sites in proteins by combination with protease digestion and electrospray ionization mass spectrometry.

A method for the determination of phosphorylation sites in phosphoproteins based on column-switching high-performance liquid chromatography (HPLC) has been developed. The HPLC system consisted of a titania precolumn for the selective adsorption of phosphopeptides, an anion-exchange analytical column and a UV detector (215 nm). Rabbit muscle phosphorylase a (RPa) and porcine stomach pepsin (PSP) were tested as model phosphoproteins. After protease digestion, the resulting phosphopeptides were successfully isolated by column-switching HPLC. The phosphopeptide fractions were analyzed by electrospray ionization mass spectrometry with a positive or negative ion mode after purification by reversed-phase HPLC. Pseudo-molecular ion peaks corresponding to Gln-Ile-Ser(p)-Val-Arg (MW 681.7) and Glu-Ala-Thr-Ser(p)-Gln-Glu-Leu (MW 856.8) were detected from the tryptic digest of RPa and chymotryptic digest of PSP, respectively, which agreed with the theoretically expected phosphopeptide fragments.     

Insights into the selective catalytic reduction of NO by NH<Subscript>3</Subscript> over Mn<Subscript>3</Subscript>O<Subscript>4</Subscript>(110): a DFT study coupled with microkinetic analysis

Nitric oxide (NO_x), as one of the main pollutants, can contribute to a series of environmental problems, and to date the selective catalytic reduction (SCR) of NO_x with NH₃ in the presence of excess of O₂ over the catalysts has served as one of the most effective methods, in which Mn-based catalysts have been widely studied owing to their excellent low-temperature activity toward NH₃-SCR. However, the related structure-activity relation was not satisfactorily explored at the atomic level. By virtue of DFT+U calculations together with microkinetic analysis, we systemically investigate the selective catalytic reduction process of NO with NH₃ over Mn₃O₄(110), and identify the crucial thermodynamic and kinetic factors that limit the catalytic activity and selectivity. It is found that NH₃ prefers to adsorb on the Lewis acid site and then dehydrogenates into NH₂* assisted by either the two- or three-fold lattice oxygen; NH₂* would then react with the gaseous NO to form an important intermediate NH₂NO that prefers to convert into N₂O rather than N₂ after the sequential dehydrogenation, while the residual H atoms interact with O₂ and left the surface in the form of H₂O. The rate-determining step is proposed to be the coupling reaction between NH₂* and gaseous NO. Regarding the complex surface structure of Mn₃O₄(110), the main active sites are quantitatively revealed to be O_3c and Mn_4c.