Molecular modeling study of the differential ligand–receptor interaction at the μ, δ and κ opioid receptors

3D models of the opioid receptors , and were constructed using BUNDLE, an in-house program to build de novo models of G-protein coupled receptors at the atomic level. Once the three opioid receptors were constructed and before any energy refinement, models were assessed for their compatibility with the results available from point-site mutations carried out on these receptors. In a subsequent step, three selective antagonists to each of three receptors (naltrindole, naltrexone and nor-binaltorphamine) were docked onto each of the three receptors and subsequently energy minimized. The nine resulting complexes were checked for their ability to explain known results of structure-activity studies. Once the models were validated, analysis of the distances between different residues of the receptors and the ligands were computed. This analysis permitted us to identify key residues tentatively involved in direct interaction with the ligand.     

Z/E-photoisomerizations of olefins with 4npi- or (4n + 2)pi-electron substituents: zigzag variations in olefin properties along the T(1) state energy surfaces

[Figure: see text]. A quantum chemical study has been performed to assess changes in aromaticity along the T1 state Z/E-isomerization pathways of annulenyl-substituted olefins. It is argued that the point on the T1 energy surface with highest substituent aromaticity corresponds to the minimum. According to Baird (J. Am. Chem. Soc. 1972, 94, 4941), aromaticity and antiaromaticity are interchanged when going from S0 to T1. Thus, olefins with S0 aromatic substituents (set A olefins) will be partially antiaromatic in T1 and vice versa for olefins with S0 antiaromatic substituents (set B olefins). Twist of the C=C bond to a structure with a perpendicular orientation of the 2p(C) orbitals (3p*) in T1 should lead to regaining substituent aromaticity in set A and loss of aromaticity in set B olefins. This hypothesis is verified through quantum chemical calculations of T1 energies, geometries (bond lengths and harmonic oscillator measure of aromaticity), spin densities, and nucleus independent chemical shifts whose differences along the T1 PES display zigzag dependencies on the number of -electrons in the annulenyl substituent of the olefin. Aromaticity changes are reflected in the profiles of the T1 potential energy surfaces (T1 PESs) for Z/E-isomerizations because olefins in set A have minima at 3p* whereas those in set B have maxima at such structures. The proper combination (fusion) of the substituents of set A and B olefins could allow for design of novel optical switch compounds that isomerize adiabatically with high isomerization quantum yields.     

Application of strategically designed sample composition to the rapid analytical screening of milk samples for polychlorinated biphenyls

Strategically designed sample composition (SSC) is a new technique that decreases the number of analytical determinations needed in routine screening to as few as the number of original sample specimens while providing information that is specific to them. Although this new technique has been applied to environmental studies, this paper describes its first application to food safety studies. Contamination of milk samples with polychlorinated biphenyls (PCBs) was chosen as a case study to show the usefulness and potential of the SSC technique with a fast analytical procedure that involves saponification of the samples and solid-phase microextraction of the PCBs. A total of 20 sample specimens can be analyzed in 11 determinations with excellent predictions of the positive samples and the concentration levels of the contaminants. The robustness of the strategy was investigated and demonstrated.     

Solid-phase microextraction–capillary gas chromatography combined with microwave-induced plasma atomic-emission spectrometry for selenite determination

The use of solid-phase microextraction (SPME) with gas chromatography coupled to microwave-induced plasma atomic-emission detection (GC–MIP-AED) is described for selenite [Se(IV)] speciation. Aqueous standards were derivatised with sodium tetraethyl- or tetrapropylborate and extracted by SPME. Headspace extraction of the ethyl and propyl derivatives was studied. Relevant experimental conditions were optimised, including conditions for derivatisation and extraction and those of gas chromatographic analysis. The limits of detection achieved for headspace sampling of derivatised Se(IV) were in the low ng mL^–1 range for both ethylation and propylation. When the method was applied to analysis of selenite in selenised yeast reference material results were in good agreement with the indicated values.     

The Effect of Cyclodextrins on the Photochemical Stability of 7-Amino-4-methylcoumarin in Aqueous Solution

The effect of -, - and -cyclodextrin onthe photochemical stability of 7-amino-4-methylcoumarin (C120)was studied. Using spectroscopic techniques (UV/Vis absorption spectroscopy, fluorescence, fluorescence anisotropy and circular dichroism) combined with HPLC/MS and MS analysis it was demonstrated that addition of -cyclodextrin to the aqueoussolution of C120 markedly inhibits the photodegradation of that dye. This results from theformation of an inclusion complex between C120 and -cyclodextrin.     

Pretreatment of sugarcane bagasse hemicellulose hydrolysate for xylitol production byCandida guilliermondii

Applied Biochemistry and Biotechnology - In order to remove or reduce the concentrations of toxic substances present in the sugarcane bagasse hemicellulose hydrolysate for xyloseto-xylitol...     

On finite {1,2,3}-semiaffine planes

In this paper, we investigate {1,2,3}-semiaffine planes. All such planes of order n >51 shall be classified. It turns out that they are embeddable into projective planes of the same order n in the most natural way.Work supported by National Research Project on Strutture Geometriche Combinatoria, loro applicazioni of Italian M.P.I. and G.N.S.A.G.A. of C.N.R.     

Parameterization of peptide 13C carbonyl chemical shielding anisotropy in molecular dynamics simulations.

NMR chemical shielding anisotropy (CSA) relaxation is an important tool in the study of dynamical processes in proteins and nucleic acids in solution. Herein, we investigate how dynamical variations in local geometry affect the chemical shielding anisotropy relaxation of the carbonyl carbon nucleus, using the following protocol: 1) Using density functional theory, the carbonyl (13)C' CSA is computed for 103 conformations of the model peptide group N-methylacetamide (NMA). 2) The variations in computed (13)C' CSA parameters are fitted against quadratic hypersurfaces containing cross terms between the variables. 3) The predictive quality of the CSA hypersurfaces is validated by comparing the predicted and de novo calculated (13)C' CSAs for 20 molecular dynamics snapshots. 4) The CSA fluctuations and their autocorrelation and cross correlation functions due to bond-length and bond-angle distortions are predicted for a chemistry Harvard molecular mechanics (CHARMM) molecular dynamics trajectory of Ca(2+)-saturated calmodulin and GB3 from the hypersurfaces, as well as for a molecular dynamics (MD) simulation of an NMA trimer using a quantum mechanically correct forcefield. We find that the fluctuations can be represented by a 0.93 scaling factor of the CSA tensor for both R(1) and R(2) relaxations for residues in helix, coil, and sheet alike. This result is important, as it establishes that (13)C' relaxation is a valid tool for measurement of interesting dynamical events in proteins.     

Ascorbate-induced oxidation of formate by peroxodisulfate: product yields,kinetics and mechanism

The slow reaction between peroxodisulfate and formate is significantly accelerated by ascorbate at room temperature. The products of this induced oxidation, CO₂ and oxalate (C₂O^2– ₄), were analyzed by several methods and the kinetics of this reaction were measured. The overall mechanism involves free radical species. Ascorbate reacts with peroxodisulfate to initiate production of the sulfate radical ion (SO^– ₄), which reacts with formate to produce carbon dioxide radical ion (CO^– ₂) and sulfate. The carbon dioxide radical reacts with peroxodisulfate to form CO₂ or self-combines to form oxalate. Competition occurring between these two processes determines the overall fate of the carbon dioxide radical species. As pH decreases, protonation of the carbon dioxide radical ion tends to favor production of CO₂.     

Efficient RNase H-directed cleavage of RNA promoted by antisense DNA or 2'F-ANA constructs containing acyclic nucleotide inserts

The ability of modified antisense oligonucleotides (AONs) containing acyclic interresidue units to support RNase H-promoted cleavage of complementary RNA is described. Manipulation of the backbone and sugar geometries in these conformationally labile monomers shows great benefits in the enzymatic recognition of the nucleic acid hybrids, while highlighting the importance of local strand conformation on the hydrolytic efficiency of the enzyme more conclusively. Our results demonstrate that the duplexes support remarkably high levels of enzymatic degradation when treated with human RNase HII, making them efficient mimics of the native substrates. Furthermore, interesting linker-dependent modulation of enzymatic activity is observed during in vitro assays, suggesting a potential role for this AON class in an RNase H-dependent pathway of controlling RNA expression. Additionally, the butyl-modified 2'F-ANA AONs described in this work constitute the first examples of a nucleic acid species capable of eliciting high RNase H activity while possessing a highly flexible molecular architecture at predetermined sites along the AON.