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Query: UNIPROT:P06889 (Mol)
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The extraction efficiency for organic molecules using synthetic receptors is highly dependent on solvent properties. Solvent influences the partitioning of both the desired compound and the interfering species. Solvent also influences the solubility of the receptor and its affinity for the substrate. Therefore the free energy involved in extraction can be optimized by using a carefully selected solvent. In this paper we demonstrate the use of a solvatochromic model to predict the influence of solvent dipolarity, H-bond acidity and H-bond basicity on selectivity and yield of phenobarbital extraction. We also used this method to estimate the purity and yield of phenobarbital extraction in 12 poly(vinyl chloride) plasticizers and solvents. This approach can be generalized for assisting the selection of optimal solvent and provide insight into the rational design of solvent and receptor for industrial extractions.
J Mol Recognit 1998
PMID:Prediction of molecular recognition-enhanced phenobarbital extraction based on solvatochromic analysis. 1007 2

We examine the ligand requirements for the divinylsulphone (DVS) based T-gel to bind immunoglobulins. The original gel consisted of 2-mercaptoethanol coupled to a DVS activated support, with both the thioether and sulphone sulphurs thought necessary for protein binding. No differences in the capacity for human IgG were observed for a highly activated gel coupled with mercaptoethanol, or when the same activated gel was incubated at high pH to hydrolyse the majority of its reactive groups before the remainder were coupled with the thiol, indicating that the thioether S may be replaced with a hydroxyl O. Increasing the time of the DVS-activation results in gels with higher concentrations of immobilised sulphone but lower concentrations of active groups. The IgG capacities of the mercaptoethanol coupled gels were found to increase with the time of the activation reaction, which may be exploited to produce high capacity gels while minimising the concentration of DVS. Reducing the vinyl of the DVS-activated gel with borohydride was found to decrease the amount of protein binding, with residual binding being attributed to the presence of hydrolysed or cross-linked sulphones in the gel. Reacting the activated gels with amines decreased the capacity for IgG still further, suggesting that not only are these ligands unable to bind IgG, they also prevent its interacting with neighbouring sulphones, perhaps due to the small amount of positive charge they carry.
J Mol Recognit 1998
PMID:Structure of the IgG-binding ligand of the T-gel. 1007 22

A new silver halide-containing holographic recording material has been designed and developed specifically for holographic chemical sensors. The hologram enables very small volume changes to be measured in a polymer layer throughout which the hologram is located. The holographic film is based on a fine-grain silver bromide emulsion suspended in a poly(vinyl alcohol) matrix crosslinked with Cr(III) ions. Cross-linking gives the material sufficient spatial integrity to allow a holographic image to be recorded, while maintaining adequate porosity and elasticity of the polymer matrix for sensing applications. The new material has been characterized with respect to its response to pH and compared with a traditional gelatin holographic film. The response to some ions and small molecules typically found in analytical samples has also been measured. Functional groups introduced covalently into the poly(vinyl alcohol) matrix transform the base matrix into a pH-responsive polymer with predictable swelling properties and which can be further derivatized to incorporate specific ligands. A rationally designed holographic sensor for trypsin has been developed from chemically synthesized artificial polymers. A trypsin substrate, the poly(amino acid) poly(L-lysine), was incorporated into poly(vinyl alcohol) holograms to create a 'designed' holographic material which was degraded in a concentration-dependent manner by trypsin. Extensions of this approach to other hydrolytic enzymes are briefly discussed.
J Mol Recognit 1998
PMID:A holographic sensor based on a rationally designed synthetic polymer. 1007 32

Displacement chromatography was demonstrated to perform separations efficiently under mass-overloaded conditions, offering advantages such as increased product recovery and purity, superior resolving power, and concentration and purification in a single processing step. The use of water-soluble polymers for protein displacement in dye-ligand chromatography was initiated in our laboratory. The polymers for displacement were selected using differences spectroscopy to monitor their interactions with a dye-ligand in solution. Non-charged polymers such as poly(N-vinyl pyrrolidone) and poly(N-vinyl caprolactam) efficiently displaced lactate dehydrogenase from porcine muscle from a Blue Sepahrose column. The latter polymer, being thermosensitive, could be easily removed from the eluate and recovered by precipitation at 45 degrees C and low-speed centrifugation. The positively charged polymer poly(ethylene imine) proved to be an even more efficient displacer. The dye-ligand column could be regenerated after application of displacer either by washing with a solution of the soluble ligand Cibacron Blue (in the case of non-charged polymers) or by washing with highly alkaline solutions containing polyanions (in the case of poly(ethylene imine)) The latter formed a soluble complex with poly(ethylene imine) and stripped the column from the polymer.
J Mol Recognit 1998
PMID:Protein displacement in dye-ligand chromatography using neutral and charged polymers. 1007 52

The first high-resolution infrared spectra of the unstable molecule vinyl alcohol are reported. The spectra have been obtained using a new precursor, 2-chloroethanol, which when pyrolyzed at 1050 degrees C gives strong infrared spectra of vinyl alcohol free of interfering hydrocarbon absorption bands. In this work, we have analyzed the strong nu(13) fundamental at 817 cm(-1) and substantially improved the ground state rotational constants by a simultaneous fitting of previous microwave data and a large number of infrared combination differences. The 13(1) upper state was found to be perturbed by the 15(2) "dark" state at 775.7 cm(-1), and a complete analysis of the perturbed rotational structure has been achieved using an interacting two-state model. Further small perturbations at high K(a) and J have been identified as interactions with the nu(10) and nu(12) fundamentals at 948 and 960 cm(-1), respectively. Copyright 1999 Academic Press.
J Mol Spectrosc 1999 Sep
PMID:High-Resolution Fourier Transform Infrared Spectroscopy of Vinyl Alcohol: Rotational Analysis of the nu(13) CH(2) Wagging Fundamental at 817 cm(-1). 1043 43

Lipid peroxidation products, as well as the metabolic products of vinyl chloride, react with cellular DNA producing the mutagenic adduct 3,N(4)-etheno-2'-deoxycytidine (epsilondC), along with several other exocyclic derivatives. High-resolution NMR spectroscopy and restrained molecular dynamics simulations were used to establish the solution structure of an 11-mer duplex containing an epsilondC.dC base-pair at its center. The NMR data suggested a regular right-handed helical structure having all residues in the anti orientation around the glycosydic torsion angle and Watson-Crick alignments for all canonical base-pairs of the duplex. Restrained molecular dynamics generated a three-dimensional model in excellent agreement with the spectroscopic data. The (epsilondC. dC)-duplex structure is a regular right-handed helix with a slight bend at the lesion site and no severe distortions of the sugar-phosphate backbone. The epsilondC adduct and its partner dC were displaced towards opposite grooves of the helix, resulting in a lesion-containing base-pair that was highly sheared but stabilized to some degree by the formation of a single hydrogen bond. Such a sheared base-pair alignment at the lesion site was previously observed for epsilondC.dG and epsilondC.T duplexes, and was also present in the crystal structures of duplexes containing dG.T and dG. U mismatches. These observations suggest the existence of a substrate structural motif that may be recognized by specific DNA glycosylases during the process of base excision repair.
J Mol Biol 2000 Feb 25
PMID:Solution structure of an 11-mer duplex containing the 3, N(4)-ethenocytosine adduct opposite 2'-deoxycytidine: implications for the recognition of exocyclic lesions by DNA glycosylases. 1067 86

Boc-resin-bound alpha-hydroxy-beta-amino-aldehydes are accessible starting from N-terminally bound amino acid esters by using Dondoni's C1-homologation reaction sequence. The conversion of these synthons to two different peptide mimetics--2-hydroxy-1,3-ethyl-diamines and gamma-hydroxy-delta-amino-vinyl sulfones--has been investigated. The successful transfer of the complex alpha-amino acid homologation reaction sequence into solid-phase chemistry demonstrates the potentials of the Boc-resin for synthesis of peptidomimetics.
Mol Divers 1998
PMID:Synthesis of peptidomimetics using a polymer-bound Boc-linker. 1072 5

The infrared (3200-30 cm(-1) spectra of gaseous and solid, the Raman spectra (3200-30 cm(-1)) of the liquid and solid vinyl silyl bromide, CH2CHSiH2Br, have been recorded. Additionally, quantitative depolarization values have been obtained. Both the gauche and cis conformers have been identified in the fluid phases but only the gauche conformer remains in the solid. Variable temperature studies from 0 to -87 degrees C of the Raman spectrum of the liquid was carried out. From these data, the enthalpy difference has been determined to be 22 +/- 6 cm(-1) (0.26 +/- 0.08 kJ/mol), with the gauche conformer being the more stable form. The predictions from the ab initio calculations up to MP2/6-311 + + G(2d,2p) basis set favor the gauche as the more stable form. A complete vibrational assignment is proposed for both the gauche and cis conformers based on infrared band contours, relative intensities, depolarization values and group frequencies. The vibrational assignments are supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G(d) calculations and the potential energy terms for the conformer interconversion have been obtained from the same calculations. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing a variety of basis sets up to 6-311 + + G(2d,2p) at levels of restricted Hartree-Fock (RHF) and/or Moller-Plesset (MP) to second order. The results are discussed and compared to those obtained for some similar molecules.
Spectrochim Acta A Mol Biomol Spectrosc 2000 May
PMID:Infrared and Raman spectra, conformational stability, barriers to internal rotation, normal-coordinate calculations and vibrational assignments for vinyl silyl bromide. 1084 36

The role of nitric oxide (NO) in the vagal modulation of heart rate (HR) is controversial. We tested the hypothesis that NO acts via a pre-synaptic, guanylyl cyclase (GC) dependent pathway. The effects of inhibiting NO synthase (NOS) and GC were evaluated in isolated atrial/right vagal nerve preparations from adult (550-750 g) and young (150-250 g) female guinea pigs. Levels of NOS protein were quantified in right atria using Western blotting and densitometry. The non-specific NOS inhibitor N- omega -nitro- L -arginine (L -NA, 100 microM, n=5) significantly reduced the negative chronotropic response to vagal nerve stimulation (VNS) at 3 and 5 Hz in the adult guinea pig. This effect was reversed with 1 m ML -arginine. Similar results were observed with the specific neuronal NOS inhibitor vinyl-N5-(1-imino-3-butenyl)- L -ornithine (L -VNIO, 100 microM, n=7). Inhibition of GC with 1H-(1,2,4)-oxadiazolo-(4, 3-a)-quinoxalin-1-one (ODQ, 10 microM, n=7) also significantly reduced the negative chronotropic response to VNS at 3 and 5 Hz in adult guinea pigs. Neither L -NA (n=6), L -VNIO (n=5) nor ODQ (n=6) changed the HR response to cumulative doses of carbamylcholine in adult guinea pig atria suggesting that the action of NO is pre-synaptic. The HR response to VNS was unaffected by L -NA (n=7) or ODQ (n=7) in young guinea pigs and Western blot analysis showed significantly lower levels of nNOS protein in right atria from young animals. These results suggest a pre-synaptic NO-cGMP pathway modulates cardiac cholinergic transmission, although this may depend on the developmental stage of the guinea pig.
J Mol Cell Cardiol 2000 Oct
PMID:Pre-synaptic NO-cGMP pathway modulates vagal control of heart rate in isolated adult guinea pig atria. 1101 24

Unlike other cytochromes, c-type cytochromes have two covalent bonds formed between the two vinyl groups of haem and two cysteines of the protein. This haem ligation requires specific assembly proteins in prokaryotes or eukaryotic mitochondria and chloroplasts. Here, it is shown that Bordetella pertussis is an excellent bacterial model for the widespread system II cytochrome c synthesis pathway. Mutations in four different genes (ccsA, ccsB, ccsX and dipZ) result in B. pertussis strains unable to synthesize any of at least seven c-type cytochromes. Using a cytochrome c4:alkaline phosphatase fusion protein as a bifunctional reporter, it was demonstrated that the B. pertussis wild-type and mutant strains secrete an active alkaline phosphatase fusion protein. However, unlike the wild type, all four mutants are unable to attach haem covalently, resulting in a degraded N-terminal apocytochrome c4 component. Thus, apocytochrome c secretion is normal in each of the four mutants, but all are defective in a periplasmic assembly step (or export of haem). CcsX is related to thioredoxins, which possess a conserved CysXxxXxxCys motif. Using phoA gene fusions as reporters, CcsX was proven to be a periplasmic thioredoxin-like protein. Both the B. pertussis dipZ (i. e. dsbD) and ccsX mutants are corrected for their assembly defects by the thiol-reducing compounds, dithiothreitol and 2-mercaptoethanesulphonic acid. These results indicate that DipZ and CcsX are required for the periplasmic reduction of the cysteines of apocytochromes c before ligation. In contrast, the ccsA and ccsB mutants are not corrected by exogenous reducing agents, suggesting that CcsA and CcsB are required for the haem ligation step itself in the periplasm (or export of haem to the periplasm). Related to this suggestion, the topology of CcsB was determined experimentally, demonstrating that CcsB has four transmembrane domains and a large 435-amino-acid periplasmic region.
Mol Microbiol 2000 Nov
PMID:Four genes are required for the system II cytochrome c biogenesis pathway in Bordetella pertussis, a unique bacterial model. 1106 71


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