Two-dimensional database of mouse liver proteins: changes in hepatic protein levels following treatment with acetaminophen or its nontoxic regioisomer 3-acetamidophenol

Overdose of acetaminophen (APAP) causes acute hepatotoxicity in rodents and man. The mechanism underlying APAP-induced liver injury remains unclear, but experimental evidence strongly suggests that activation of APAP and subsequent formation of protein adducts are involved in hepatotoxicity. Using proteomics technologies, we constructed a two-dimensional protein database for mouse liver, comprising 256 different gene products and investigated the proteins affected after APAP-induced hepatotoxicity. Adult male mice received a single dose of APAP (100 or 300 mg/kg) or its nontoxic regioisomer 3-acetamidophenol (AMAP, 300 mg/kg). The extent of liver damage was assessed 8 h after administration by increased liver enzyme release and histopathology. Changes in the protein level were studied by comparison of the intensities of the corresponding spots on two-dimensional (2-D) gels. The expression level of about 35 of the identified proteins was modified due to treatment with APAP or AMAP. The observed changes were usually in the order of 10-50% of the control value and were more marked in the high- than in the low-dose of APAP-treated animals. Most of the changes caused by AMAP occurred in a subset of the proteins modified by APAP. Many of the proteins showing changed expression levels are either known targets for covalent modification by N-acetyl-p-benzoquinoneimine (NAPQI) or involved in the regulation of mechanisms that are believed to drive APAP-induced hepatotoxicity.     

Study of Burkitt lymphoma cell line proteins by high resolution two-dimensional gel electrophoresis and nanoelectrospray mass spectrometry

We paper describe a mass spectrometric approach generally applicable for the rapid identification and characterization of proteins isolated by two-dimensional gel electrophoresis (2-DE). The highly sensitive nanoflow-electrospray mass spectrometry employing a quadrupole-time of flight mass spectrometer was used for the direct identification of proteins from the peptide mixture generated from only one high resolution 2-DE gel without high performance liquid chromatography (HPLC) separation or Edman sequencing. Due to the high sensitivity and high mass accuracy of the instrument employed, this technique proved to be a powerful tool for the identification of proteins from femtomole amounts of materials. We applied the technique for the investigation of Burkitt lymphoma BL60 cell proteins. This cell line has been used as a model to assign apoptosis-associated proteins by subtractive analysis of normal and apoptotic cells. From the nuclear fraction of these cells, 36 protein spots were examined, from only one micropreparative Coomassie Brilliant Blue R-250 stained gel, after proteolytic digestion by matrix assisted laser desorption ionization (MALDI) and nanospray mass spectrometry (MS). In combination with database searches, of 33 proteins were successfully identified by nanospray-MS/MS-sequencing of up to eight peptides per protein. Three proteins were new proteins not listed in any of the available databases. Some of the identified proteins are known to be involved in apoptosis processes, the others were common proteins in the eukaryotic cell. The given technique and the protein data are the basis for construction of a database to compare normal and apoptosis-induced cells and, further, to enable fast screening of drug impact in apoptosis-associated processes.     

Proteomic analysis of the human colon carcinoma cell line (LIM 1215): development of a membrane protein database

The proteomic definition of plasma membrane proteins is an important initial step in searching for novel tumor marker proteins expressed during the different stages of cancer progression. However, due to the charge heterogeneity and poor solubility of membrane-associated proteins this subsection of the cell's proteome is often refractory to two-dimensional electrophoresis (2-DE), the current paradigm technology for studying protein expression profiles. Here, we describe a non-2-DE method for identifying membrane proteins. Proteins from an enriched membrane preparation of the human colorectal carcinoma cell line LIM1215 were initially fractionated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE, 4-20%). The unstained gel was cut into 16 x 3 mm slices, and peptide mixtures resulting from in-gel tryptic digestion of each slice were individually subjected to capillary-column reversed phase-high performance liquid chromatography (RP-HPLC) coupled with electrospray ionization-ion trap-mass spectrometry (ESI-IT-MS). Interrogation of genomic databases with the resulting collision-induced dissociation (CID) generated peptide ion fragment data was used to identify the proteins in each gel slice. Over 284 proteins (including 92 membrane proteins) were identified, including many integral membrane proteins not previously identified by 2-DE, many proteins seen at the genomic level only, as well as several proteins identified by expressed sequence tags (ESTs) only. Additionally, a number of peptides, identified by de novo MS sequence analysis, have not been described in the databases. Further, a "targeted" ion approach was used to unambiguously identify known low-abundance plasma membrane proteins, using the membrane-associated A33 antigen, a gastrointestinal-specific epithelial cell protein, as an example. Following localization of the A33 antigen in the gel by immunoblotting, ions corresponding to the theoretical A33 antigen tryptic peptide masses were selected using an "inclusion" mass list for automated sequence analysis. Six peptides corresponding to the A33 antigen, present at levels well below those accessible using the standard automated "nontargeted" approach, were identified. The membrane protein database may be accessed via the World Wide Web (WWW) at http://www.ludwig. edu.au/jpsl/jpslhome.html.     

Ricinus communis toxin-mediated inhibition of protein synthesis in cell-free extracts of a toxin-resistant variant mouse lymphoma cell line.

Ricinus communis agglutinin II (RCAII, ricin, toxin) at low concentrations inhibits protein synthesis in cell-free extracts, but not in intact cells, of an RCAII-resistant mouse lymphoma variant cell line. The concentration dependence of the inhibition by RCAII was the same in cell-free extracts of both RCAII-resistant variant and RCAII-sensitive parental cells, while intact parental cells are 250 times more sensitive to RCAII toxicity. The onset of RCAII inhibition of cell-free protein synthesis was extremely rapid in both cases, being complete in a few minutes. Under these conditions RCAII inhibits protein synthesis in intact RCAII-sensitive parental cells, but maximal inhibition requires several hours to occur. These results support our previous electron microscopic observations that the variant cells are defective in the uptake of RCAII by endocytosis at low toxin concentrations.     

Two-dimensional gel electrophoresis, protein electroblotting and microsequencing: a direct link between proteins and genes.

We have used two-dimensional gel electrophoresis as a general "preparative" method to purify proteins for microsequencing analysis. In the first experiments, proteins derived from a total extract of Nicotiana tabacum leaf tissue were directly blotted from the gel onto poly(4-vinyl-N-methylpyridinium iodide)-coated glass fiber sheets. The major spots were excised and subjected to NH2-terminal sequence analysis, which made it possible to identify five of the eight selected proteins, while two more were recognized by generated internal sequences. In a second set of experiments, proteins of human origin were separated on multiple two-dimensional gels and the Coomassie Brilliant Blue-stained spots were excised from the gels. The combined spots were re-eluted and concentrated in a new gel and blotted on Immobilon. They were fragmented by in situ proteolysis and the generated peptides were separated by reverse phase-high performance liquid chromatography and sequenced. At the average, the internal sequences that were obtained covered 35 residues per protein and allowed unambiguous identification of 13 of the 23 proteins analyzed so far. The sequence information obtained of the unidentified proteins is sufficient for further cloning. These results demonstrate that systematic sequence analysis of the major proteins seen in two-dimensional gels is within the reach of current technologies. This offers a unique opportunity to link information contained in protein databases with known or forthcoming DNA sequence data.     

Two-dimensional electrophoresis of cat sera: protein identification by cross reacting antibodies against human serum proteins.

After two-dimensional electrophoresis of cat serum, individual proteins were identified by means of cross reacting antibodies against the human protein homologues. Testing by cross reactivities seemed the method of choice because immunoreagents for cat proteins are not easily available.     

Two-dimensional molecular pattern in the structure of a calcium(II) complex with pyrazine-2,3-dicarboxylate and water ligands

The structure of di(aquo-O)(pyrazine-2,3-dicarboxylato-N,O; -O′,O′′) calcium(II) hydrate [Ca(2,3-PZDC)(H₂O)₂·;H₂O] contains molecular sheets in which Ca(II) ions are bridged by the carboxylate groups of the ligand molecules. Two bridging paths are evident. In the first, an N,O-bonding moiety formed by a hetero-ring nitrogen atom and the carboxylate oxygen atom nearest to it and both oxygen atoms of the second carboxylic group are active. The second path is formed by the other oxygen atom from the carboxylic group involved in the N,O-bonding moiety and an oxygen atom from the second carboxylic group. The latter atom is bidentate. A two-dimensional molecular pattern is formed. Each Ca(II) ion is also coordinated by two water oxygen atoms, making the number of coordinated atoms eight. The coordination polyhedron is a distorted pentagonal bipyramid with an oxygen atom at the apex on one side of the equatorial plane and two oxygen atoms forming the apices on the other side.     

The master two-dimensional gel database of human AMA cell proteins: towards linking protein and genome sequence and mapping information (update 1991).

The master two-dimensional gel database of human AMA cells currently lists 3801 cellular and secreted proteins, of which 371 cellular polypeptides (306 IEF; 65 NEPHGE) were added to the master images during the last 10 months. These include: (i) very basic and acidic proteins that do not focus under normal running conditions and (ii) low-abundant proteins that can only be detected after prolonged gel exposure. Annotation categories updated in this version include "protein name", "antibody against protein", "cellular localization", and "microsequenced proteins". New entries include "human autoantigens" and "cDNAs". For convenience we have included an alphabetical list of all known proteins recorded in this database. In the long run, the main goal of this database is to link protein and DNA sequencing and mapping information (Human Genome Program) and to provide an integrated picture of the expression levels and properties of the thousands of proteins that orchestrate various cellular functions both under physiological and abnormal conditions.     

Anticancer activity of lanthanum (III) and europium (III) 5-fluorouracil complexes on Caco-2 cell line

Lanthanide complexes are of increasing importance in cancer diagnosis and therapy. In the present study 1:1 and 1:3 solid complexes of La (III)–5-FU (5-fluorouracil) were prepared and characterized. In solution, the formation of 1:1 La (III) and Eu (III) complexes enabled the enhancement of 5-FU's effectiveness. Binding constants of the 1:1 complexes of both metals were estimated using spectrophotometry and HPLC with fluorescence detection methods. The thermodynamic parameters ΔG ^° , ΔH ^° and ΔS ^° were calculated using differential scanning calorimetry. Evaluation of the cytotoxic activity of the 1:1 La (III)- and Eu (III)–5-FU complexes was performed through two methodologies, trypan blue for cell viability where La (III)- and Eu (III)–5-FU complexes were found to have 52,000 and 80,000 dead cells, respectively, and via flow cytometric analysis to measure the apoptotic values, which were found to be 59.87 and 86.86% respectively.     

Genetic polymorphism of a lymphocyte protein (p75) with six different alleles studied by two-dimensional electrophoresis: qualitative and quantitative data

The genetic polymorphism of a human lymphocyte protein (p75) was studied by two-dimensional electrophoresis within 17 families and, in addition, 22 unrelated individuals from Southern Germany, resulting in a total of approximately 100 individuals. The cytosolic and membrane proteins from cell lysates of phytohemagglutinin stimulated and [3H]leucine labeled lymphocytes were separated by two-dimensional electrophoresis. The p75 protein with an approximate molecular weight of 75,000 occurred in six variants with slightly different isoelectric points and/or apparent molecular weights. Three common variants (a, b, and c) and three rare variants (d, e and f) could be distinguished. Among the approximately 100 individuals studied we observed 15 different phenotypes, three homozygous (p75-a, -b, -c) and 12 heterozygous (p75-ab, -ac, -bc, -ad, -ae, -be, -bf, -cd, -ce, -cf, -de, -df) phenotypes. The genetics of the p75 protein variations was ascertained by family studies and quantitative computer analysis. We were able to show a Mendelian mode of inheritance of the variants within the families and a gene-dosage dependence of the protein spots in homozygous and heterozygous phenotypes. The data allowed us to assume a polymorphic protein p75 determined by six alleles on a autosomal gene locus. The allele frequencies were calculated from the phenotype distribution within 56 unrelated individuals. The gene frequencies of the three common alleles ranged between 0.38 and 0.22 and the gene frequencies of the three rare alleles ranged between 0.01 and 0.07.     

Toxicity reduction of 2-(5-nitrofuryl)acrylic acid following Fenton reaction treatment

Monitoring the enforcement of an EU-wide ban of nitrofuran antibiotics in the food production chain is a challenging task, given the nature of nitrofuran compounds. The original and modified Fenton reactions are advanced oxidation processes that can eliminate the toxicity of nitrofurans. 2-(5-Nitrofuryl)acrylic acid (I) was degraded as a model compound by the original Fenton reaction with ferrous sulphate, by Mohr’s salt at pH 3 and 7, and finally by advanced Fenton process (AFP) (Fe⁰/H₂O₂/H₂SO₄). In addition, the growth inhibition of Escherichia coli, a G⁻ bacterium, was tested both before and after AFP treatment. The results showed that a small degradation efficiency of this treatment process led to the toxicity changes and that the toxicity of I after AFP treatment process decreased. It seems that the treatment of polluted water using the Fenton reaction and its modifications would be a suitable method for degradation of nitrofuran derivatives in polluted water.     

Serum protein profiles of patients with pancreatic cancer and chronic pancreatitis: searching for a diagnostic protein pattern.

In this study, 13 sera from patients with pancreatic cancer, 9 from chronic pancreatitis and 10 from healthy subjects were analyzed by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The MALDI mass spectra revealed the presence of several low molecular weight peptides, among which some were detected only in the sera from both pathological conditions. On the other hand many peptides were observed only in control sera, and were absent in the sera from the two diseases. Therefore, MALDI analysis of the low molecular weight fraction (<10 000 Da) of sera from patients with pancreatic diseases enabled us to identify the presence of some disease-related signals and also some signals characteristic of normal subjects.     

Two-dimensional electrophoresis with immobilized pH gradients of leaf proteins from barley (Hordeum vulgare): method, reproducibility and genetic aspects

Leaf proteins from 14 barley cultivars (Hordeum vulgare) were analyzed by two-dimensional electrophoresis with immobilized pH gradients (IPG 4-7 and IPG 6-10) in the first dimension. Highly reproducible two-dimensional patterns were obtained, owing to constant spot positions along the isoelectric focusing axis. A number of variety-specific protein spots were detected, allowing us to discriminate barley cultivars not only into main groups but into individual cultivars.     

Quinone Imines with a Fused Azine Ring: II. Reaction of 5-(p-Tolylsulfonylimino)quinoline-8(5H)-ones with Sodium p-Toluenesulfinate

Depending on the substituent in the 7-position, 5-(p-tolylsulfonylimino)quinoline-8(5H)-ones react with sodium p-toluenesulfinate in acetic acid along three different pathways: 1,4- or 6,1-addition or nucleophilic substitution.     

Photochemical reactions. 75. The UV-irradiation of 3 beta-acetoxy-18-dimethoxy-20-oxo-delta(16)-5 alpha-pregnene

On UV.-irradiation in i-octane the α,β-unsaturated ketone 14 is transformed into a mixture of 15 and 16 .     

The human keratinocyte two-dimensional gel protein database (update 1992): towards an integrated approach to the study of cell proliferation, differentiation and skin diseases.

The master two-dimensional gel database of human keratinocytes currently lists 2980 cellular proteins (2098 isoelectric focusing, IEF; and 882 nonequilibrium pH gradient electrophoresis, NEPHGE) many of which correspond to posttranslational modifications. About 20% of all recorded proteins have been identified (protein name, organelle components, etc.) and they are listed in alphabetical order together with their M(r), pI, cellular localization and credit to the investigator(s) that aided in the identification. Also, we have listed 145 microsequenced proteins that are recorded in this database. As an aid in localizing the polypeptides we have included blow-ups of the master images (IEF, NEPHGE) displaying all the protein numbers. In the long run, the master keratinocyte database is expected to link protein and DNA sequencing and mapping information (Human Genome Program) and to provide an integrated picture of the expression levels and properties of the thousands of proteins that orchestrate various keratinocyte functions both in health and disease.