Parahydrogen induced polarization of barbituric acid derivatives: 1H hyperpolarization studies

Homogeneous hydrogenation of barbituric acid derivatives with parahydrogen yields a substantial increase of the (1)H NMR signals of the reaction products. These physiologically relevant compounds were hydrogenated at both ambient and elevated temperatures and pressures using a standard cationic rhodium catalyst. The resulting nonthermal nuclear spin polarization (hyperpolarization) is limited by the spin-lattice relaxation time T(1) of the corresponding nuclei in the products, being shorter than the time constant of the hydrogenation. The signal-to-noise ratio of the NMR spectra could be further increased upon signal averaging the antiphase PHIP signals of 25 successive scans following 30 degrees pulse experiments and a delay of 10 s.     

Simple synthesis of new chiral oxindole derivative

A synthesis of chiral optically active 3-hydroxyoxindoles with 1,3-disubstituted 2,2-dimethyl-cyclobutane structural fragment by the Et₂NH-catalyzed aldol reaction of indoline-2,3-diones with (−)-(1S,3S)-pinonic acid derivatives is described. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 7, pp. 1540–1543, July, 2008.     

Using support vector machine to predict beta- and gamma-turns in proteins

By using the composite vector with increment of diversity, position conservation scoring function, and predictive secondary structures to express the information of sequence, a support vector machine (SVM) algorithm for predicting beta- and gamma-turns in the proteins is proposed. The 426 and 320 nonhomologous protein chains described by Guruprasad and Rajkumar (Guruprasad and Rajkumar J. Biosci 2000, 25,143) are used for training and testing the predictive model of the beta- and gamma-turns, respectively. The overall prediction accuracy and the Matthews correlation coefficient in 7-fold cross-validation are 79.8% and 0.47, respectively, for the beta-turns. The overall prediction accuracy in 5-fold cross-validation is 61.0% for the gamma-turns. These results are significantly higher than the other algorithms in the prediction of beta- and gamma-turns using the same datasets. In addition, the 547 and 823 nonhomologous protein chains described by Fuchs and Alix (Fuchs and Alix Proteins: Struct Funct Bioinform 2005, 59, 828) are used for training and testing the predictive model of the beta- and gamma-turns, and better results are obtained. This algorithm may be helpful to improve the performance of protein turns' prediction. To ensure the ability of the SVM method to correctly classify beta-turn and non-beta-turn (gamma-turn and non-gamma-turn), the receiver operating characteristic threshold independent measure curves are provided.     

Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling

Ongoing efforts to model P2Y receptors for extracellular nucleotides, i.e., endogenous ADP, ATP, UDP, UTP, and UDP-glucose, were summarized and correlated for the eight known subtypes. The rhodopsin-based homology modeling of the P2Y receptors is supported by a growing body of site-directed mutagenesis data, mainly for P2Y₁ receptors. By comparing molecular models of the P2Y receptors, it was concluded that nucleotide binding could occur in the upper part of the helical bundle, with the ribose moiety accommodated between transmembrane domain (TM) 3 and TM7. The nucleobase was oriented towards TM1, TM2, and TM7, in the direction of the extracellular side of the receptor. The phosphate chain was oriented towards TM6, in the direction of the extracellular loops (ELs), and was coordinated by three critical cationic residues. In particular, in the P2Y₁, P2Y₂, P2Y₄, and P2Y₆ receptors the nucleotide ligands had very similar positions. ADP in the P2Y₁₂ receptor was located deeper inside the receptor in comparison to other subtypes, and the uridine moiety of UDP-glucose in the P2Y₁₄ receptor was located even deeper and shifted toward TM7. In general, these findings are in agreement with the proposed binding site of small molecules to other class A GPCRs.     

(Liquid + liquid) equilibria of (water + propionic acid + methyl isoamyl ketone or diisobutyl ketone or ethyl isoamyl keton) at T = 298.2 K

(Liquid + liquid) equilibrium (LLE) data for (water + propionic acid + solvent) were measured at T = 298.2 K and atmospheric pressure. The solvents were methyl isoamyl ketone (5-methyl-2-hexanone), ethyl isoamyl ketone (5-methyl-3-heptanone) and diisobutyl ketone. The tie-line data were correlated by means of the NRTL and UNIQUAC equation, and compared with results predicted by the UNIFAC method. A comparison of the extracting capabilities of the solvents was made with respect to distribution coefficients, separation factors, and solvent free selectivity bases.     

Electrochemical and Spectroscopic Properties of Fly Ash–Polyaniline Matrix Nanorod Composites

Polyaniline (PANI) nanocomposites were prepared with fly ash (FA) either by aging the starting materials (aniline and FA) before oxidative polymerisation or by including poly(styrene sulphonic acid) (PSSA) eliminating the aging step. The aging procedure formed polymer nanotubes that have cross-sectional diameters of 50–110 nm. The procedure involving PSSA produced nanorods and nanofibres composites that have diameters of 100–500 nm and length of up to 10 μm attributed to the presence of metal oxides and silica in FA. The electrochemical analysis of the PANI–PSSA–FA nanorod composites shows three redox couples with formal potentials, , values of 105 mV, 455 mV and 670 mV, and conductance, C, value of 1.21 × 10⁻² S. The UV-Vis spectroscopy of the polymeric nanorod shows absorption maxima at 340 and 370 nm (due to π–π^* transition of the benzoid rings), and 600–650 nm (due to charge transfer excitons of the quinoid structure), which are characteristic of emeraldine base.     

Activation of PPAR�� induces profound multilocularization of adipocytes in adult mouse white adipose tissues

We sought to determine the effects of activation of peroxisome proliferator-activated receptor-γ (PPAR-γ) on multilocularization of adipocytes in adult white adipose tissue (WAT). Male C57BL/6 normal, db/db, and ob/ob mice were treated with agonists of PPAR-γ, PPAR-α, or β₃-adrenoceptor for 3 weeks. To distinguish multilocular adipocytes from unilocular adipocytes, whole-mounted adipose tissues were co-immunostained for perilipin and collagen IV. PPAR-γ activation with rosiglitazone or pioglitazone induced a profound change of unilocular adipocytes into smaller, multilocular adipocytes in adult WAT in a time-dependent, dose-dependent, and reversible manner. PPAR-α activation with fenofibrate did not affect the number of locules or remodeling. db/db and ob/ob obese mice exhibited less multilocularization in response to PPAR-γ activation compared to normal mice. Nevertheless, all adipocytes activated by PPAR-γ contained a single nucleus regardless of locule number. Multilocular adipocytes induced by PPAR-γ activation contained substantially increased mitochondrial content and enhanced expression of uncoupling protein-1, PPAR-γ coactivator-1-α , and perilipin. Taken together, PPAR-γ activation induces profound multilocularization and enhanced mitochondrial biogenesis in the adipocytes of adult WAT. These changes may affect the overall function of WAT.     

Identification of amyloidogenic peptide sequences using a coarse-grained physicochemical model

Cross-beta amyloid is implicated in over 20 human diseases. Experiments suggest that specific sequence elements within amyloidogenic proteins play a major role in seeding amyloid formation. Identifying these seeding sequences is important for rationalizing the molecular mechanisms of amyloid formation and for elaborating therapeutic strategies that target amyloid. Theoretical techniques play an important role in facilitating the identification and structural characterization of putative seeding sequences; most amyloid species are not amenable to high resolution experimental structure techniques. In this study we have combined a coarse-grained physicochemical protein model with a highly efficient Monte Carlo sampling technique to identify amyloidogenic sequences in four proteins for which respective experimental peptide fragmentation data exist. Peptide sequences were defined as amyloidogenic if the ensemble structure predicted for three interacting peptides described a stable and regular three-stranded beta-sheet. For such peptides, free energies were calculated to provide a measure of amyloid propensity. The overall agreement between the experimental and predicted data is good, and we correctly identify several self-recognition motifs proposed to define the cross-beta amyloid fibril architectures of two of the proteins. Our results compare very favorably with those obtained using atomistic molecular dynamics methods, though our simulations are 30-40 times faster.     

Preparative isolation of pseudolaric acids A and B,and their glucosides from the root bark of Pseudolarix kaempferi using high‐speed counter‐current chromatography

In order to provide the chemical markers for the quality control of herbal medicines, four diterpenoids, pseudolaric acids A and B (PAA and PAB), and their glucosides were isolated from the methanol extract of the Chinese herb Pseudolarix kaempferi using high‐speed counter‐current chromatography (HSCCC). The diphase solvent system was n‐hexane/EtOAc/MeOH/H₂O which was used at two ratios (5:5:5:5 and 1:9:4:6 by volume) in the separation of pseudolaric acids and their glycosides, respectively. As a result, PAA (14 mg), PAB (129 mg), PAA‐O‐β‐D ‐glucopyranoside (8 mg, PAAG), and PAB‐O‐β‐D ‐glucopyranoside (42 mg, PABG) were obtained from 0.5 g of the crude extract. Their purities were determined to be above 97% by HPLC analysis. Their chemical structures were confirmed by ¹H and ¹³C NMR analysis or HPLC comparison with the reference compounds.     

Confocal microscopy study of uptake kinetics of α‐lactalbumin and β‐lactoglobulin onto the cation‐exchanger SP Sepharose FF

Confocal laser scanning microscopy (CLSM) was used to study single‐ and two‐component protein uptake for α‐lactalbumin (ALA) and β‐lactoglobulin (BLG), as models for whey proteins, to SP Sepharose FF at pH 3.7 during batch experiments in a finite bath. By coupling a fluorescent dye with the protein molecule, the penetration into individual adsorbent particles at different times during batch uptake was visualised. In a single‐component system, BLG penetrated fast into the adsorbent beads and gradually filled them in a shell‐wise fashion, while adsorption of ALA was mostly confined to the outer shells of the adsorbent. For the two‐component studies, the results showed that ALA was able to displace BLG despite its lower affinity to the adsorbent under the employed conditions. CLSM results were then compared both qualitatively and quantitatively to their counterparts obtained in traditional experiments by indirect measurements of the protein concentration in the fluid phase. A novel quantitative approach was undertaken by modifying the simple kinetic rate model traditionally used to determine the kinetic rate constant, k₁, for batch uptake experiments, in order to describe batch uptake kinetics based on CLSM data. Although BLG results were in good agreement, there was a discrepancy in ALA results.