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PubMed2002

Proteomic profiling of mechanistically distinct enzyme classes using a common chemotype.

Proteomics research requires methods to characterize the expression and function of proteins in complex mixtures. Toward this end, chemical probes that incorporate known affinity labeling agents have facilitated the activity-based profiling of certain enzyme families. To accelerate the discovery of proteomics probes for enzyme classes lacking cognate affinity labels, we describe here a combinatorial strategy. Members of a probe library bearing a sulfonate ester chemotype were screened against complex proteomes for activity-dependent protein reactivity, resulting in the labeling of at least six mechanistically distinct enzyme classes. Surprisingly, none of these enzymes represented targets of previously described proteomics probes. The sulfonate library was used to identify an omega-class glutathione S-transferase whose activity was upregulated in invasive human breast cancer lines. These results indicate that activity-based probes compatible with whole-proteome analysis can be developed for numerous enzyme classes and applied to identify enzymes associated with discrete pathological states.

Affinity Labels↗

PubMed1998

Acid promoted transformations of fluorescent luminarosine and its 2'-modified analogues.

The susceptibility of highly fluorescent luminarine nucleosides to acid promoted anomerization reactions has been studied in order to select a derivative with suitable properties for chemical synthesis of luminarine-labeled oligo(deoxy)ribonucleotides. Both O-acetylated derivatives Ia-c and parent luminarosine IIa, as well as 2'-O-methylluminarosine IIb, and 2'-deoxyluminarosine IIc undergo anomerization at pH = 4 however, at considerably different velocities. In the case of O-protected nucleosides (Ia-c), the anomerization leads to an equilibrium mixture of respective beta and alpha furanosides, the rate and extent of anomerization decreasing in the following order: Ic >> Ia > Ib. Parent nucleosides (IIa-c) bearing free hydroxyls are generally more susceptible to anomerization than the O-acetylated derivatives but a similar order of reactivity (IIc >> IIa > IIb) is observed. In each case, a complex mixture containing both beta and alpha ribopyranosyl and -furanosyl forms is formed. Their structure and anomeric configuration have been proved by 1H and 13C NMR spectroscopy. The results point to 2'-O-methylluminarosine as the fluorophore of choice for further derivatization and chemical introduction into oligo(deoxy)ribonucleotides.

Chromatography, High Pressure Liquid↗

PubMed2000

Analysis of some commercial polysorbate formulations using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

Analyses of polysorbate formulations (Tween 20, Tween 40, Tween 60, and Tween 80) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) reveal a complex mixture of oligomers that include polyethylene glycols, polyethylene glycol esters, isosorbide polyethoxylates, sorbitan polyethoxylates, polysorbate monoesters, polysorbate diesters, and sorbitol polyethoxylate esters. The MALDI-TOF mass spectra for these formulations show the presence of sodiated molecules in which the major signals are attributed to the presence of polyethylene glycols, isosorbide polyethoxylates, and sorbitan polyethoxylates. Additionally, the complexity of the spectra was correlated to the constituent fatty acid moieties in the polysorbate formulations. Thus Tween 20 showed the presence of polysorbate monolaurates, polysorbate monomyristates, and polysorbate monopalmitates. Tween 40 contained polysorbate mono- and dipalmitates. Tween 60 contained polysorbate monopalmitates and polysorbate monostearates. For the Tween 80, mass assignment for polysorbate monooleates and polysorbate dioleates was equivocal, because both of these oligomeric series have the same molecular weight as the sorbitan polyethoxylates, and thus the Tween 80 MALDI-TOF spectrum appeared to be the least complicated of the four commercial polysorbate formulations.

Journal Article↗

PubMed2005

Reduction of the concentration difference of proteins in biological liquids using a library of combinatorial ligands.

The discovery of polypeptides and proteins with relevance to a particular biological state is complicated by their vast number and concentration range in most biological mixtures. Depletion methodologies are frequently used to remove the most abundant species; however, this removal not only fails significantly to enrich trace proteins, it may also nonspecifically deplete them due to their interactions with the removed high-abundance proteins. Here we report a simple-to-use methodology that reduces the protein concentration range of a complex mixture like whole serum through the simultaneous dilution of high-abundance proteins and the concentration of low-abundance proteins. This methodology utilizes solid-phase ligand libraries of immense diversity, generated by "split, couple, recombine" combinatorial chemistry, that are used for affinity-based binding to the proteins of a given mixture. With a controlled sample-to-ligand ratio it is possible to modulate the relative concentration of proteins such that many peptides or proteins that are undetectable by classical analytical methods become easily accessible. The reduction in the dynamic range of unfractionated serum is specifically described along with treatment of other proteomes such as extracts from Escherichia coli, chicken egg white and cell culture supernatant. Mono- and bi-dimensional electrophoresis (1-DE and 2-DE respectively) and surface-enhanced laser desorption/ionization-mass spectrometry (SELDI-TOF-MS) technology demonstrate the reduction in protein concentration range. Combining this approach with additional fractionation methods further increased the number of detectable species.

Adsorption↗

PubMed1992

Radiation-induced syntheses in cometary simulated models.

The behavior of an aqueous-dominant multicomponent cometary model is examined at high doses of ionizing radiation. The system is composed of a water mixture of HCN (0.2 mol dm-3), CH3CN (0.04 mol dm-3), C2H5CN (0.02 mol dm-3), CH3OH (0.12 mol dm-3) and HCO2H (0.01 mol dm-3. It was exposed to gamma rays at doses up to 18.5 MGy. The chemical kinetic database used in the computer treatment of experimental data consists of 79 reactions. A complex mixture of products has been synthesized: gases, amino acids, carboxylic acids and polymeric material. The results suggest that the pristine material in cometary nuclei may have been chemically altered by the action of cosmic rays and embedded radionuclides.

Amino Acids↗

PubMed2000

Laser-induced dispersed fluorescence detection of polycyclic aromatic compounds in soil extracts separated by capillary electrochromatography.

Polycyclic aromatic hydrocarbons (PAHs) and nitrogen containing aromatic compounds (NCACs) are characterized in soil extracts and laboratory standards by capillary electrochromatography (CEC) with laser-induced dispersed fluorescence (LIDF) detection using a liquid-nitrogen cooled charge-coupled device detector. The LIDF detection technique provides information on compound identity and, when coupled with the high separation efficiencies of the CEC technique, proves useful in the analysis of complex mixtures. Differences in fluorescence spectra also provide a means of identifying co-eluting compounds by using deconvolution algorithms. Detection limits range from 0.5 to 96x10(-10) M for selected PAHs and 0.9-3.7x10(-10) M for selected NCACs. Soil extracts are also injected onto the CEC column to evaluate chromatographic method performance with respect to complex samples and the ability to withstand exposure to environmental samples.

Chromatography, Micellar Electrokinetic Capillary↗

PubMed2002

Sister chromatid exchange and proliferative rate index in the longitudinal risk assessment of occupational exposure to pesticides.

At present, there are more than 1,000 chemicals classified as pesticides and many reports have shown that some of them have genotoxic properties. In the present longitudinal study, possible genetic damage on a population of workers occupationally exposed to a mixture of pesticides by using sister chromatid exchange (SCE) analysis has been evaluated. As an additional cytogenetic parameter, the proportion of lymphocytes that undergo one, two or three cell divisions as well as proliferative rate index have been determined. This study was performed on the exposed group of workers employed in pesticide production, simultaneously exposed to a complex mixture of pesticides (atrazine, alachlor, cyanazine, 2,4-dichlorophenoxyacetic acid, and malathion). The blood samples of the exposed subjects were collected in three different periods: before the beginning of the new pesticide production period, after 8 months of everyday work in the pesticide production, and 8 months after the removal of subjects out of the production. In all three samplings, the mean value of SCE and number of cells with high sister chromatid exchange frequency (HFC) in the exposed group was significantly higher in the comparison with the control group. There were no differences in the proliferative rate index (PRI) between the control and exposed group, regardless of the sampling period. In both groups examined, the majority of lymphocytes were found in the second cell division, following cultivation. These results suggest that the increase in the number of SCE found in the exposed subjects is not the result of either cytotoxic or epigenetic action of pesticide mixture, but chronic occupational exposure to mixture of pesticides.

Adult↗

PubMed2000

Evaluation of 24-color multifluor-fluorescence in-situ hybridization (M-FISH) karyotyping by comparison with reverse chromosome painting of the human breast cancer cell line T-47D.

Multifluor-fluorescence in-situ hybridization (M-FISH) chromosome paints for all the chromosomes in the human complement labeled with different combinations of fluorochromes is a recent technological development enabling assignment of chromosomal material to rearranged chromosomes. Little data is available on the accuracy and limitations of the approach to the analysis of complex karyotypes, which are characteristic of many malignant diseases. Here we compare M-FISH analysis of the breast-cancer-derived cell line T-47D with a previous analysis by reverse chromosome painting analysis of flow-sorted chromosomes from the same material. This demonstrated a high degree of concordance. It also illustrated the limitations of M-FISH analysis, including difficulties identifying small regions of chromosomal material and intrachromosomal rearrangements. Confirmation of selected aberrations using less-complex mixtures of painting probes and further definition of abnormalities using single copy markers may be required. The detailed karyotype description possible by M-FISH analysis contrasts with the definition in the original G-banding analysis. This and the level of concordance with reverse FISH painting supports the utility of the approach in the definition of complex karyotypes.

Breast Neoplasms↗

PubMed1994

Nevirapine resistance mutations of human immunodeficiency virus type 1 selected during therapy.

Drug susceptibility and mutations in the reverse transcriptase (RT) gene were analyzed with 167 virus isolates from 38 patients treated with nevirapine, a potent nonnucleoside inhibitor of human immunodeficiency virus type 1 (HIV-1) RT. Resistant isolates emerged quickly and uniformly in all patients administered nevirapine either as monotherapy or in combination with zidovudine (AZT). Resistance developed as early as 1 week, indicating rapid turnover of the virus population. The development of resistance was associated with the loss of antiviral drug activity as measured by CD4 lymphocyte counts and levels of HIV p24 antigen and RNA in serum. In addition to mutations at amino acid residues 103, 106, and 181 that had been identified by selection in cell culture, mutations at residues 108, 188, and 190 were also found in the patient isolates. Sequences from patient clones documented cocirculating mixtures of populations of different mutants. The most common mutation with monotherapy, tyrosine to cysteine at residue 181, was prevented from emerging by coadministration of AZT, which resulted in the selection of alternative mutations. The observations documented that, under selective drug pressure, the circulating virus population can change rapidly, and many alternative mutants can emerge, often in complex mixtures. The addition of a second RT inhibitor, AZT, significantly altered the pattern of mutations in the circulating population of HIV.

Antiviral Agents↗

PubMedDate not supplied

[Epstein-Barr virus].

Epstein-Barr Virus (EBV) is the prototype member of the human herpesvirus subfamily Gammaherpesviridae. EBV establishes a latent infection in lymphoïd cell and replicates in epithelial cells. Infection of individuals with EBV is widespread in all human populations, as shown by the high proportion of individual with specific antibodies in their serum. EBV is the etiological agent of the infectious mononucleosis and has been implicated in the pathogenesis of an increasing number of human malignancies, the best characterized being endemic Burkitt's lymphomas, nasopharyngeal carcinomas (NPC), and polyclonal lymphomas in immunocompromised patients. EBV infection in vivo is a complex mixture of latent, reactivated, transforming, or replicative type of infection. EBV infection is characterized by sporadic viral excretion in the oropharynx and persistent latent infection in the bone marrow and peripheral blood lymphocytes. EBV infection includes an intense immune response. During primary infection, the humoral response is primarily directed toward antigens of the lytic cycle, membrane antigen complex, early antigen (EA), viral capsid antigen (VCA) while the antibodies response to EBNAs is delayed. The cell mediated response controls the proliferation of EBV-infected lymphocytes through two classes of cytotoxic cells, namely, natural killer and T8 cytotoxic cells. Laboratory diagnosis of EBV infection is recently based upon molecular biology techniques which provides a useful tool for direct identification of EBV and may allow to better understand the role of the virus in the pathogenesis of EBV associated disorders.

Antibody Formation↗

PubMed2002

Polymer characterization by combining liquid chromatography with MALDI and ESI mass spectrometry.

High-performance polymers are complex mixtures of materials of different size and chemical composition and with different end groups and architecture. To determine the molecular heterogeneity of such systems, hyphenation of several techniques is required. The value of coupling mass spectrometry (MS) with separation techniques has already been recognized - such methods have proved to be among the most powerful for molecular characterization of complex polymer systems. The review focuses on matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) MS coupled with liquid chromatography (LC). Such hyphenation has been used for most polymer analysis by mass spectrometry coupled with separation techniques. The advantages and/or limitations of these techniques for polymer characterization are discussed. Future prospects are briefly outlined.

Journal Article↗

PubMed1995

New promise in combinatorial chemistry: synthesis, characterization, and screening of small-molecule libraries in solution.

BACKGROUND: The increasing interest in combinatorial chemistry as a tool for the development of therapeutics has led to many new methods of creating molecular libraries of potential lead compounds. Current methods have made it possible to develop libraries of several million compounds. As a result, the limiting factor in the screening of libraries has become the identification and characterization of active species. We have recently described a method for generating libraries of water-soluble compounds containing mixtures of 10(4) to 10(5) different small organic molecules by using generally applicable solution phase chemistry. We set out to develop new methods to characterize and decode these libraries. RESULTS: Libraries were generated by condensing a multi-acid-chloride core molecule with various amines, producing molecules with functional groups about a rigid backbone. Composition and complexity of the libraries was evaluated using electrospray mass spectrometry to analyze model libraries containing up to 55 different molecules. The number of peaks obtained in mass spectrometry is directly correlated with the complexity of the library, and we were therefore able to deduce which of the expected compounds had in fact been formed in the library, and which of the building blocks in the library were not efficiently used. An iterative selection procedure was developed using this information, which allowed the screening of libraries of up to 50,000 chemical species to produce a competitive inhibitor of the enzyme trypsin. CONCLUSIONS: Our strategy for the identification of active species should be broadly applicable to other methods of generating complex libraries of small molecules. The selection from the library of a compound with desired biological properties augurs well for the potential value of generating and screening complex mixtures of small molecules in solution.

Amines↗

PubMed2004

Chromatographic analysis and sequencing approach of heparin oligosaccharides using cetyltrimethylammonium dynamically coated stationary phases.

C(18) and C(8) bonded stationary phases dynamically coated with cetyltrimethylammonium (CTA) and strong anion exchange (SAX) were developed to obtain separations of oligosaccharide mixtures resulting from chemical or enzymatic depolymerization of heparin. With this method, the retention of sulfated oligosaccharides is directly adjustable depending on the amount of CTA adsorbed into the column. Oligosaccharides containing up to 20 sulfates were separated with a resolving power superior to that of conventional SAX analysis. The stability of the column coating enables hundreds of injections. Using ammonium methane sulfonate aqueous solutions as ultraviolet transparent mobile phases, it was possible to set up double detection, including selective detection of acetylated oligosaccharides. Analytical gel permeation chromatography was directly coupled to CTA-SAX, obtaining a two-dimensional profile of analyzed oligosaccharidic mixtures. A sequencing method of heparin oligosaccharides using partial depolymerization by heparinases according to their size and sulfation pattern and digest analysis by CTA-SAX was developed. A direct application of this method to the analysis of oligosaccharide mixtures obtained by complete digestion of heparins by heparinases I, II, and III was done. It allowed a reliable quantification of heparin building blocks. We also focused our attention on di- and tetrasaccharidic species containing the 3-O-sulfated glucosamines taken as markers of the active sites for antithrombin III. The method was also applied to more complex mixtures resulting from porcine heparin partially depolymerized with heparinase I. The specificity of the reaction was studied up to decasaccharidic fractions.

Animals↗

PubMed1995

Developmental effects of dioxins.

The potent developmental toxicity of dioxin in multiple species has been known for a number of years. However, recent studies have indicated that dioxin also induces functional developmental defects, many of which are delayed. Subtle structural deficits, not detectable at birth, have also been described in multiple species and in both sexes. Certain defects have been reported not only in animals but also in children prenatally exposed to complex mixtures containing dioxinlike compounds. None of the effects can be attributed to modulation of any one endocrine system. For example, dioxin does not bind to the estrogen receptor, but it can cause effects that are both estrogenic and antiestrogenic. However, viewing dioxin and related compounds as endocrine disruptors that may alter multiple pathways sheds some light on the complexities of this potent class of growth dysregulators.

Animals↗

PubMed2002

The identification of protein-protein interactions of the nuclear pore complex of Saccharomyces cerevisiae using high throughput matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry.

Mass spectrometry has become the technology of choice for detailed identification of proteins in complex mixtures. Although electrophoretic separation, proteolytic digestion, mass spectrometric analysis of unseparated digests, and database searching have become standard methods in widespread use, peptide sequence information obtained by collision-induced dissociation and tandem mass spectrometry is required to establish the most comprehensive and reliable results. Most tandem mass spectrometers in current use employ electrospray ionization. In this work a novel tandem mass spectrometer employing matrix-assisted laser desorption ionization-time-of-flight/time-of-flight operating at 200 Hz has been used to identify proteins interacting with known nucleoporins in the nuclear pore complex of Saccharomyces cerevisiae. Proteins interacting with recombinant proteins as bait were purified from yeast extracts and then separated by one-dimensional SDS-PAGE. Although peptide mass fingerprinting is sometimes sufficient to identify proteins, this study shows the importance of employing tandem mass spectrometry for identifying proteins in mixtures or as covalently modified forms. The rules for incorporating these features into MS-Tag are presented. In addition to providing an evaluation of the sensitivity and overall quality of collision-induced dissociation spectra obtained, standard conditions for ionization and fragmentation have been selected that would allow automatic data collection and analysis, without the need to adjust parameters in a sample-specific fashion. Other considerations essential for successful high throughput protein analysis are discussed.

Amino Acid Sequence↗

PubMed2004

A thin chip microsprayer system coupled to Fourier transform ion cyclotron resonance mass spectrometry for glycopeptide screening.

A thin polymer microchip was coupled with a Fourier transform ion cyclotron resonance (FTICR) 9.4 T mass spectrometer and the method was optimized in negative ion mode for glycopeptide screening. The interface between the polymer microchip and FTICR mass spectrometer consists of an in-laboratory conceived and designed mounting system that exhibits robust and controllable alignment of the chip toward the inlet of the mass spectrometer. The particular attribute of the polymer chip coupled to the FTICR mass spectrometer, to achieve an increase in ionization efficiency and sensitivity under the premise of high mass accuracy of detection, is highlighted by the large number of major and minor glycopeptide structures detected and identified in highly heterogeneous mixtures obtained from urine matrices. Glycoforms expressing various saccharide chain lengths ranging from tri- to dodecasaccharide, bearing up to three sialic acid moieties, could be detected and assigned based on the accuracy of the mass measurement (average mass deviation below 6 ppm) of their molecular ions. -Thin chipESI-FTICRMS is a potent novel system for glycomic screening of complex mixtures, as demonstrated for identification of singly sialylated O-glycosylated amino acids and peptides from urine matrices, and could be considered for general applicability in the glycoanalytical field.

Amino Acid Sequence↗

PubMed1999

Lipid analysis by matrix-assisted laser desorption and ionization mass spectrometry: A methodological approach.

Whereas matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has gained high importance in the field of protein analysis, surprisingly few studies were published about the use of MALDI for lipid analysis. Lipids, however, are well-suited for MALDI since all experiments can be performed in a sole organic phase and, thus, extremely homogeneous matrix/analyte mixtures are formed. We report here for the first time the application of MALDI-TOF-MS for the analysis of diacylglycerols, phosphatidylcholines, and (poly)phosphoinositides. It is shown that in a matrix of 2,5-dihydroxybenzoic acid the molecular ions (M + 1) of phosphatidylcholines as well as the corresponding adducts of different phosphoinositides are easily detected even in complex mixtures, and thus, detailed data on the fatty acid composition are provided. In contrast, diacylglycerols are mainly detected as the corresponding sodium or potassium adducts, but not as the protonated forms. Fragmentation reactions of fatty acids on the double bonds and on the polar lipid head group are observed to a minor extent in the spectra of all investigated lipids. Generally, choline derivatives are most sensitive toward further fragmentation reactions. Due to its very high sensitivity (up to picomolar concentrations) MALDI-TOF-MS can be used for the direct investigation of biologically relevant lipid mixtures occurring, e.g. , in cell membranes. The analysis of the lipid composition of neutrophilic granulocytes is given as a representative example for future applications.

Diglycerides↗

PubMed2003

In vitro evaluation of the efficacy of skin barrier creams and protective gloves on percutaneous absorption of industrial solvents.

OBJECTIVES: The aim of the experiments was to evaluate the efficacy of skin barrier creams (SBCs) and protective gloves and its potential for reduction of percutaneous absorption of industrial solvents. METHODS: We assessed percutaneous absorption of ethylene glycol (EG), isopropyl alcohol (IA) and 1,2,4-trimethylbenzene (TMB), using static diffusion cells. These solvents were applied neat (EG, TMB) as well as in 10% and 50% aqueous solution (EG, IA) or in 10% and 50% ethanol-diluted solution (TMB). Furthermore, we tested the percutaneous absorption of IA mixed in one cleaning agent (CA), used in newspaper printing shops to clean the rollers of printing machines. Additionally, the penetration behaviour of 10% and 50% solutions of EG, IA and TMB was tested. The experiments were carried out on untreated and on SBC-treated excised human skin from one donor, and on protective gloves. Saline was used as receptor fluid for EG and IA, and neat ethanol for TMB. RESULTS: The penetration of 50% EG, IA and TMB solutions through SBC-treated skin was higher than in untreated skin (factor 3.9 for EG, 0.32 for IA and 0.06 for TMB). The penetration of IA in the IA-CA mixture was five-times higher through untreated skin as for the single compound in 10% aqueous solution. In skin, treated with SBC, we found a 17-fold penetration enhancement of IA in the IA-CA mixture. No appreciable penetration of EG and IA was observed through nitrile rubber gloves. CONCLUSIONS: Our in vitro experiments could not demonstrate an efficacy of SBC to protect skin penetration for the tested solvents. The percutaneous absorption of all solvents in 50% solution was increased through skin treated with SBCs. Furthermore, SBCs enhance the penetration rates of solvents from complex mixtures compared with the single solvents. The tested gloves showed sufficient protection for the hydrophilic solvents, but not for TMB.

2-Propanol↗