Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: UNIPROT:P06889 (Mol)
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Infrared spectroscopy studies of six beta-alkoxyvinyl methyl ketones, with common structure R(1)O-CR(2)CH-COR(3), where R(1)=R(3)=CH(3), R(2)=H (1); R(1)=C(2)H(5), R(2)=H (2); R(3)=CF(3); R(1)=R(2)=CH(3), R(3)=CF(3) (3); R(1)=C(2)H(5), R(2)=C(6)H(5), R(3)=CF(3) (4); R(1)=C(2)H(5), R(2)=4-O(2)NC(6)H(4), R(3)=CF(3) (5); R(1)=C(2)H(5), R(2)=C(CH(3))(3), R(3)=CF(3) (6) in 11 pure organic solvents of different polarity were undertaken to investigate the solute-solvent interactions and to correlate solvent properties by means of linear solvation energy relationships (LSER) with the carbonyl and vinyl stretching vibrations of existing stereoisomeric forms. It was shown that contrary to simple carbonyl-containing compounds where solvent HBD acidity (alpha) has the largest influence on the nu (CO) band shift to lower wavenumbers, the dipolarity/polarizability (pi) term plays the main role in the interactions of conjugated enones with solvent molecules leading to the nu (CO) and nu (CC) bathochromic band shifts. The trifluoroacetyl group possesses a reduced ability to form hydrogen bonds with solvents. For the nu (CC) band of non-fluorinated enone 1 solvent HBD acidity (alpha) and solvent HBA basicity term (beta) play a perceptible role, whereas for 2 these terms are not significant. beta-Substituents in fluorinated enones such as R(2)=H, C(6)H(5), and C(CH(3))(3) assist in the intermolecular hydrogen bond formation of the carbonyl moiety with HBD solvents, while beta-substituents such as CH(3) and 4-NO(2)C(6)H(4) prevent the CO group to form the H-bonds with HBD solvents (the solvent HBD acidity term (alpha) is not significant). The comparison of four conformers of the enone 1 reveals that (EEE) form is the most polarizable conformer; the influences of the solvent dipolarity/polarizability (pi) and solvent HBD acidity (alpha) term on the bathochromic nu (CO) band shift are opposite to one another.
Spectrochim Acta A Mol Biomol Spectrosc 2008 Dec 01
PMID:Solvent effects on the infrared spectra of beta-alkoxyvinyl methyl ketones I. Carbonyl and vinyl stretching vibrations. 1834 89

Isotope-coded two-dimensional maps, with either D(0)/D(3)-acrylamide or D(0)/D(4) 2-vinyl pyridine, are described in detail. They have the advantage of running the two samples under investigation within a single slab gel, thus minimizing errors because of spot matching with software packages when samples are run in parallel maps. Labeling with deuterated acrylamide is very simple and inexpensive, because this chemical is commercially available. The experiment has to be carried out at alkaline pH values (pH 8.5-9.0) and with high molarities of alkylating agent (50-100 mM) to ensure good conversion efficiency. On the contrary, labeling with 2-vinyl pyridine (2-VP) can be performed in much lower alkylant molarities (20 mM) and at neutral pH values, thus ensuring essentially 100% conversion efficiency coupled with 100% specificity, because the reaction is sustained by the partial positive and negative charges on the 2-VP and -SH group, respectively. However, deuterated 2-VP is not commercially available and it has to be synthesized ad hoc.
Methods Mol Biol 2008
PMID:Isotope-coded two-dimensional maps: tagging with deuterated acrylamide and 2-vinylpyridine. 1836 55

1,N6-Ethenoadenine (epsilonA) is generated endogenously by lipid peroxidation and exogenously by tumorigenic industrial agents, vinyl chloride, and vinyl carbamate. epsilonA detected in human tissues causes mutation and is implicated in liver, colon and lung cancers. N-methyl purine DNA-glycosylase (MPG) is the only enzyme known so far to repair epsilonA. However, the mechanism of in vivo repair of epsilonA and the role of MPG remain enigmatic. Moreover, previous in vivo repair studies for DNA lesions, including epsilonA, focused only on the step of the removal of the base lesion without further insight into the completion of the repair process. This may be in part due to the unavailability of an appropriate in vivo quantitative method to evaluate complete BER process at the basal level. Our newly developed in vivo method is highly sensitive and involves phagemid M13mp18, containing epsilonA at a defined position. The complete repair events have been estimated by plaque assay in E. coli with the phagemids recovered from the human cells after cellular processing. We found that the detectable complete (removal and replacement of epsilonA with adenine) repair was observed only 18% in 16 h, but with the repair nearing completion within 24 h in colon cancer, HCT-116, cells. Moreover, MPG is the predominant enzyme for the BER process to remove epsilonA in mammalian cells. Although, the epsilonA is fairly a bulky adduct compared to other small BER substrate lesions, NER pathway is not involved in repair of this adduct. Furthermore, the epsilonA repair in vivo and in vitro is predominant in the G0/G1 phase of the cell cycle.
Mol Cell Biochem 2008 Jun
PMID:Evidence of complete cellular repair of 1,N6-ethenoadenine, a mutagenic and potential damage for human cancer, revealed by a novel method. 1837 35

The linear-dichroic infrared (IR-LD) spectroscopy of oriented solid samples as suspension in nematic liquid crystal have been carried out for experimental IR-band assignment and structural information of 2-{5,5-dimethyl-3-[2-(2,4,6-trimethoxyphenyl)vinyl]cyclohex-2-enylidene} malononitrile polymorphs. The last data have been compared with known crystallographic ones, thus determining the validity of IR-LD spectral conclusions as well as its possibility to determination of Davydov's splitting effect and separation of pairs of maxima corresponding to non-equivalent molecules included in the unit cell of given compound. The experimental structural and spectroscopic data in our case are supported with theoretical DFT ones, obtaining both the electronic structure and vibrational frequencies in gas phase.
Spectrochim Acta A Mol Biomol Spectrosc 2008 Dec 01
PMID:Monoclinic and triclinic polymorphs of 2-{5,5-dimethyl-3-[2-(2,4,6-trimethoxyphenyl)vinyl]cyclohex-2-enylidene}malononitrile-solid-state linear-polarized IR-spectroscopy, DFT calculations and vibrational analysis. 1839 97

FTIR and FT-Raman spectra of four generations of phosphorus-containing dendrons with terminal aldehyde or PCl groups have been recorded and analyzed. Their spectral patterns are determined by the ratio T/R (T, the number of terminal groups; R, the number of repeated units). Bands assigned to the core, repeated units and terminal groups were separated by the difference spectroscopy method. The optimized geometry, frequencies and intensity of IR bands of G(1v) generation dendron with terminal aldehyde groups were obtained by the density functional theory (DFT). It was found that the internal skeleton of molecules exists in a single stable conformation with planar O-C(6)H(4)-CHN-N(CH(3))-P(S) fragments, but terminal groups may adopt the t,g,g- and t,-g,g-rotational isomers. The t,-g,g-conformer is 0.74 kcal/mol less stable compared to the t,g,g-conformer. The bond length and bond angles obtained by DFT show the best agreement with experimental data. Relying on DFT calculations a complete assignment of vibrations is proposed for different parts of the studied dendrons. The calculated frequencies and intensity of IR bands of the t,g,g- and t,-g,g-conformers of G(1v) are found to be in reasonable agreement with the experimental results. The most reactive site in dendron is the core function and vinyl group is preferred for nucleophilic attack. In dendrimer the most reactive are the terminal groups.
Spectrochim Acta A Mol Biomol Spectrosc 2008 Dec 01
PMID:FTIR and FT-Raman spectra and DFT vibrational analysis of phosphorus-containing dendrons. 1847 60

Plasmalogens represent a unique type of phospholipids characterized by the presence of a vinyl-ether bond at the sn-1 position of the glycerol backbone. Peroxisomes are essential in their biosynthesis. Their suggested functions include protection against oxidative stress, participation in signal transduction, membrane fusion events, cholesterol transport and membrane trafficking, processes known to be disturbed in sphingolipidoses. We here report on red blood cell membrane plasmalogen levels in Gaucher disease patients. Plasmalogen levels were measured as their dimethylacetal derivatives (DMA) by gas chromatography in lipid extracts of erythrocytes from 15 patients. Their relative amount was estimated as the ratio between C18:0 DMA and methylstearate (C18:0), as well as C16:0 DMA and methylpalmitate (C16:0). Statistically significant lower levels of both plasmalogen species were observed in Gaucher disease patients compared to normal individuals. Furthermore, a negative correlation between plasmalogen levels and chitotriosidase was observed in the patients, which was statistically significant for the C18:0 species. Upon therapy, a significant rise of plasmalogen levels and fall in chitotriosidase activity was observed. However, C18:0 DMA/C18:0 was still significantly lower in Gaucher disease patients compared to controls and the negative correlation to chitotriosidase persisted. At both time points there was no indication of an overt peroxisomal dysfunction, very long chain fatty acid, phytanate and pristanate levels being normal. In conclusion, reduced plasmalogen levels that show a significant rise following treatment and a negative correlation to total disease burden, as expressed by chitotriosidase activity, are observed in Gaucher disease.
Blood Cells Mol Dis
PMID:Plasmalogen levels in Gaucher disease. 1850 47

Density functional theory (DFT) calculations at the B3LYP/6-31G(d) level were carried out for 47 vinyl monomers with structures C(1)H2 = C(2)HR3, and the calculated quantum chemical descriptors were used to construct quantitative structure-property relationship (QSPR) models of the reactivity parameters of monomers Q and e. Stepwise multiple linear regression analysis (MLRA) and artificial neural networks (ANN) were adopted to generate the models. Simulated with the final optimum back-propagation (BP) neural networks, the results show that predicted lnQ and e values are in good agreement with experimental data, with test sets possessing correlation coefficients of 0.982 for lnQ and 0.943 for e. The proposed ANN models have better prediction ability than existing models.
J Mol Model 2008 Nov
PMID:DFT-based theoretical QSPR models of Q-e parameters for the prediction of reactivity in free-radical copolymerizations. 1865 Nov 85

Using pseudobioaffinity ligand L-histidine immobilized to poly(ethylene vinyl alcohol) hollow fiber membrane is an interesting approach for the purification of total IgG and its subclasses from untreated serum in a single step. Gentle adsorption and elution conditions of this chromatography system allow efficient recovery of the protein in its native form. This approach was employed for the recovery and molecular study of rheumatoid factor (RF), an anti-IgG autoantibody (AAb) that form immune complexes with autologous IgG Abs in the sera. The purity of the recovered molecule was analyzed on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), revealed a 150-kDa IgG band and an additional approximately 300 kDa band which may be RF bound IgG complex. Since RF is an AAb, the purified protein was studied for its catalytic functions like peptide, DNA, and RNA hydrolyzing activities. The substrate Pro-Phe-Arg-4-methyl-coumaryl-7-amide (PFR-MCA) hydrolyzing activity by total IgG from different patient sera was found to be greater than healthy controls. In an effort to identify the subclass specificity for the proteolytic function, the pre-purified total IgG fractions from rheumatoid arthritis (RA) sera were subjected to rechromatography using a discriminating buffer. In this experiment, the activity was found in the non-retained fractions suggesting IgG2 specificity for the catalytic function. A comparative study between different catalytic functions was performed for IgG separated from individual patient.
J Mol Recognit
PMID:Molecular studies of rheumatoid factor using pseudobioaffinity membrane chromatography. 1882 80

Colloidal dispersions of solid lipids are under intensive investigation as drug delivery systems. In the present study, poly(vinyl alcohol) (PVA) was tested as an alternative stabilizer for triglyceride nanoparticles. The dispersions contained 10% triglyceride (trimyristin or tristearin) and 5% PVA and were prepared by high pressure melt homogenization. The nanoparticle dispersions were investigated for their thermal behavior and storage stability with special regard to the polymorphic transitions of the triglyceride matrix, including effects of storage temperature and the incorporation of model drugs (diazepam, ubidecarenone) using photon correlation spectroscopy, differential scanning calorimetry, X-ray diffraction, and transmission electron microscopy. The release of the model drug diazepam from a selected nanoparticle dispersion was investigated with differential pulse polarography. Triglyceride nanoparticles prepared with PVA displayed an unusually high stability of the metastable alpha-modification depending on the type of triglyceride and the storage conditions. In tristearin nanoparticles, the alpha-polymorph was stable for at least 9 months at refrigerator temperature and the particles exhibited a spherical shape in electron microscopic investigations. Moreover, the alpha-form in PVA-stabilized tristearin nanoparticles seemed to be highly disordered, as it did not lead to a pronounced small-angle X-ray reflection. Storage at higher temperatures led to a transformation of the particles into the beta-modification, which usually was accompanied by an increase in particle size. Incorporation of the two model drugs did not change the crystal modification of the particle matrix to a large extent. After dilution into a large volume of release medium, a large fraction of the model drug diazepam was released immediately but there was no further release over several hours. The high stability of PVA-stabilized tristearin nanoparticles with regard to particle size and alpha-modification makes them suitable as a model for investigations on the influence of the polymorphic form (e.g., in comparison with nanoparticles in the more stable beta-modification) on pharmaceutically important parameters such as drug load and drug release.
Mol Pharm
PMID:Poly(vinyl alcohol) as emulsifier stabilizes solid triglyceride drug carrier nanoparticles in the alpha-modification. 1904 18

Triacetoxyvinylsilane (TAVS) has been used as a precursor to prepare sol-gel under aqueous conditions. The sol-gel product has been applied for the surface treatment of aluminum. Infrared and Raman spectra have been collected for TAVS and for TAVS sol-gel, xerogel and sol-gel-coated aluminum. Vibrational analyses have been suggested for the recorded spectra based essentially on the group frequencies and the spectral variation with the change of the sol-gel product states and the vibrational assignments of similar molecules. From the recorded infrared and Raman spectra of the sol-gel and xerogel, it is found that the sol-gel produced in the process with TAVS is essentially the same as that prepared from vinyltriethoxysilane. Thermo-gravimetric analysis (TGA) of TAVS xerogel has been conducted, and an explanation has been given in coordination with the results obtained from IR spectroscopic study of the xerogels cured at different temperatures. The study has demonstrated the thermal effect on the condensation of the sol-gel process and on the vinyl decomposition of TAVS xerogel.
Spectrochim Acta A Mol Biomol Spectrosc 2009 Apr
PMID:Infrared and Raman spectra of triacetoxyvinylsilane, aqueous sol-gel and xerogel. 1911 Apr 64


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