Depletion of the high-abundance plasma proteins.

Body fluids, like plasma and urine, are comparatively easy to obtain and are useful for the detection of novel diagnostic markers by applying new technologies, like proteomics. However, in plasma, several high-abundance proteins are dominant and repress the signals of the lower-abundance proteins, which then become undetectable either by two-dimensional gels or chromatography. Therefore, depletion of the abundant proteins is a prerequisite for the detection of the low-abundance components. We applied affinity chromatography on blue matrix and Protein G and removed the most abundant human plasma proteins, albumin and the immunoglobulin chains. The plasma proteins, prior to albumin and immunoglobulin depletion, as well the eluates from the two chromatography steps were analyzed by two-dimensional electrophoresis and the proteins were identified by MALDI-TOF-MS. The analysis resulted in the identification of 83 different gene products in the untreated plasma. Removal of the high-abundance proteins resulted in the visualization of new protein signals. In the eluate of the two affinity steps, mostly albumin and immunoglobulin spots were detected but also spots representing several other abundant plasma proteins. The methodology is easy to perform and is useful as a first step in the detection of diagnostic markers in body fluids by applying proteomics technologies.

Two-dimensional database of mouse liver proteins. An update.

We updated the two-dimensional protein database for mouse liver. Microsomal and cytosolic fractions of the liver proteins from male mice were separated by two-dimensional electrophoresis. The proteins were identified by Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) on the basis of peptide mass fingerprinting, following in-gel digestion with trypsin and matching with the theoretical peptide masses of all known proteins from all species. Approximately 5800 spots, excised from 14 two-dimensional gels, were analyzed which resulted in the identification of about 2500 proteins that were the products of 328 different genes. The database includes 112 newly identified gene products. The fractionation prior to two-dimensional electrophoresis was essential for the detection of the new proteins, 55% of which were found in the microsomal and 35% in the cytosolic fraction. The more frequently identified proteins in the various gels were heat shock proteins, house-keeping enzymes, such as ATP synthase chains, disulfide isomerase, and structural proteins, such as tropomyosin. About 45% of the identified proteins were detected 1-3 times, 45% 4-9 times, and the rest 10 or more times. Most proteins were represented by many spots. In average, about 18-20 spots were detected per gene product.

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.

Two-dimensional map of the proteome of Haemophilus influenzae.

We have constructed a two-dimensional database of the proteome of Haemophilus influenzae, a bacterium of medical interest of which the complete genome, comprising about 1742 open reading frames, has been sequenced. The soluble protein fraction of the microorganism was analyzed by two-dimensional electrophoresis, using immobilized pH gradient strips of various pH regions, gels with different acrylamide concentrations and buffers with different trailing ions. In order to visualize low-copy-number gene products, we employed a series of protein extraction and sample application approaches and several chromatographic steps, including heparin chromatography, chromatofocusing and hydrophobic interaction chromatography. We have also analyzed the cell envelope-bound protein fraction using either immobilized pH gradient strips or a two-detergent system with a cationic detergent in the first and an anionic detergent in the second-dimensional separation. Different proteins (502) were identified by matrix-assisted laser desorption/ionization mass spectrometry and amino acid composition analysis. This is at present one of the largest two-dimensional proteome databases.

Identification of beta-secretase-like activity using a mass spectrometry-based assay system.

We describe an assay system for the identification of site-specific proteases. The assay is based on a protein substrate that is immobilized on ceramic beads. After incubation with cell homogenates, the beads are washed and digested with endoproteinase Lys-C to liberate a defined set of peptides. The peptide fragments are identified by mass spectrometry. The assay was used to screen for beta-secretase, the protease that cleaves amyloid precursor protein (APP) at the beta-site. Cathepsin D was identified as the enzyme responsible for beta-secretase-like activity in two cell lines. Subsequent analysis of the related aspartic protease, cathepsin E, revealed almost identical cleavage specificity. Both enzymes are efficient in cleaving Swedish mutant APP at the beta-site but show almost no reactivity with wild-type APP. Treatment of cell lines with pepstatin inhibited the production of amyloid peptide (Abeta) when they were transfected with a construct bearing the Swedish APP mutant. However, when the cells were transfected with wild-type APP, the generation of Abeta was increased. This suggests that more than one enzyme is capable of generating Abeta in vivo and that an aspartic protease is involved in the processing of Swedish mutant APP.

Reliable automatic protein identification from matrix-assisted laser desorption/ionization mass spectrometric peptide fingerprints.

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry of protein samples from two-dimensional (2-D) gels in conjunction with protein sequence database searches is frequently used to identify proteins. Moreover, the automatic analysis of complete 2-D gels with hundreds and even thousands of protein spots ("proteome analysis") is possible, without human intervention, with the availability of highly accurate mass spectrometry instruments, and high-throughput facilities for preparation and handling of protein samples from 2-D gels. However, the lack of software for precise automatic analysis and annotation of mass spectra, as well as software for in-batch sequence database queries, is increasingly becoming a significant bottleneck for the proteomics work flow. In the present paper we outline an algorithm for reliable, accurate, and automatic evaluation of mass spectrometric data and database searches. We show here that simply selecting from the sequence database the protein that has the most matching fragment masses often leads to false-positive results. Reliable protein identification is dependent on several parameters: the accuracy of fragment mass determination, the number of masses submitted for query, the mass distribution of query masses, the number of masses matching between sample and database protein, the size of the sequence database, and the kind and number of modifications considered. Using these parameters, we derive a simple statistical estimation that can be used to calculate the probability of true-positive protein identification.

Rat brain proteins: two-dimensional protein database and variations in the expression level.

A two-dimensional database of rat brain proteins was constructed. Brain samples from newborn animals were analyzed by two-dimensional electrophoresis and the proteins were identified by matrix-assisted laser desorption/ionization mass spectrometry. The database comprises 210 different proteins, the majority of which are structural components, heat shock proteins and enzymes with various catalytic activities. Several minor differences in the expression level were detected, mainly of quantitative nature, which most likely represent allelic differences. The map may be useful in studies of neurological disorders in animal models of human diseases.

Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite chromatography.

Visualization of low-copy-number gene products is essential for the detection of novel drug targets by differential protein expression studies. We investigated the enrichment of low-abundance proteins of Escherichia coli by hydroxyapatite chromatography. The proteins of the various pools collected from a ceramic hydroxyapatite column were analyzed by two-dimensional electrophoresis and identified by matrix-assisted laser desorption ionization mass spectrometry. Approximately 800 spots corresponding to 296 different proteins were identified in the hydroxyapatite eluate. About 130 proteins that had not been detected in the two-dimensional gels of the total extract were identified. Hydroxyapatite chromatography enriched low-abundance but also major components of the E. coli protein extract. In particular, it enriched many low-molecular-mass proteins, such as cold-shock proteins. The proteins bound to the hydroxyapatite matrix belong to several classes, including enzymes with various catalytic activities, heat- and cold-shock proteins and many hypothetical and novel proteins with yet unknown functions. The results include a list of the proteins enriched by hydroxyapatite chromatography and a two-dimensional map of the enriched proteins. They may be useful in the design of protein purification pathways using master purification steps and in the search for novel drug targets.

Two-dimensional map of human brain proteins.

Samples of human brain from the parietal cortex lobe were analyzed by two-dimensional gel electrophoresis, using immobilized pH gradient strips covering the various pH regions. The protein spots were visualized with colloidal Coomassie blue stain and identified by matrix-assisted laser desorption/ionization mass spectrometry. Approximately 400 spots were identified, corresponding to 180 different brain proteins. The list of identified proteins includes a large number of structural proteins and of enzymes or enzyme subunits with various catalytic activities. The majority of proteins are localized in the cytoplasma and in mitochondria. The two-dimensional map may be useful as a reference database to study changes in the protein level caused by various disorders, such as Alzheimer's disease, major depression and schizophrenia.

Reduced aldehyde dehydrogenase levels in the brain of patients with Down syndrome.

Aldehyde dehydrogenase (ALDH) is a key enzyme in fructose, acetaldehyde and oxalate metabolism and represents a major detoxification system for reactive carbonyls and aldehydes. In the brain, ALDH exerts a major function in the metabolism of biogenic aldehydes, norepinephrine, dopamine and diamines and gamma-aminobutyric acid. Subtractive hybridization studies in Down Syndrome (DS) fetal brain showed that mRNA for ALDH are downregulated. Here we studied the protein levels in the brain of adult patients. The proteins from five brain regions of 9 aged patients with DS and 9 controls were analyzed by two-dimensional (2-D) gel electrophoresis and identified by matrix-assisted laser desorption ionization mass spectrometry. ALDH levels were reduced in the brain regions of at least half of the patients with Down Syndrome, as compared to controls. The decreased ALDH levels in the DS brain may result in accumulation of aldehydes which can lead to the formation of plaques and tangles reflecting abnormally cross-linked, insoluble and modified proteins, found in aged DS brain. Furthermore, we constructed a 2-Dmap including approximately 120 identified human brain proteins.

Reference map of the low molecular mass proteins of Haemophilus influenzae.

Analysis of the proteome of Haemophilus influenzae by two-dimensional polyacrylamide gel electrophoresis on conventional Tris-glycine gels does not usually result in efficient separation of the proteins in the 5-20 kDa range, which are mainly accumulated in the lower acidic and basic regions. In order to improve the separation of the low molecular mass proteins, we used homogeneous Tricine gels of two urea concentrations in the second-dimensional separation. The Tricine gel systems allowed the efficient and reproducible separation of the proteins of the microorganism with masses between 5 and 20 kDa, however, no proteins with masses below 5 kDa could be visualized. Approximately 80 proteins migrating in the 5-25 kDa region were identified by matrix assisted laser desorption/ionization - mass spectrometry, of which 40 identified for the first time. The digestion of the low mass proteins often produced only few peptides, which were insufficient for confident identification by mass spectrometry. Therefore, the identification was occasionally achieved by a sequential digestion with two proteases, trypsin or endoproteinase Lys-C as first and carboxypeptidase P as second enzyme. The gel system described may be useful for the efficient separation of low molecular mass proteins from other organisms to construct standard maps.

[Colonic diverticulitis. Primary clinical and ultrasound diagnosis--report of 47 cases from general practice]. / Kolondivertikulitis. Diagnosestellung primär klinisch und sonographisch-Bericht über 47 Fälle aus der Praxis.

Clinical and sonographic diagnosis-Report on 47 cases From 1993 to 1996, 47 patients with/after acute diverticulitis were examined in our practice by abdominal ultrasound. In all 36 cases with acute diverticulitis, a dolent non-echous wall thickening of descendent/sigmoid colon was seen. In five cases, we found other sonographic signs suspicious of penetration. Elevation of CRP and sometimes leukocytosis assisted the diagnosis in acute cases. In 39 of the 47 patients, colonoscopy was performed in the practice mostly during intermissions. Diverticula were confirmed in 31 patients whereas sigmoid stenosis from chronic diverticulitis could not be passed in 6 cases. 32 patients were treated with antibiotics and 10-including those with stenosis-underwent surgery. Except in one particular case (tubar abscess involving the sigmoid), operation confirmed sonographic findings of severe inflammation (stenosis and sealed perforation, respectively, in five cases). In patients presenting with pain in the left lower quadrant of the abdomen, colonic diverticulitis has to be considered especially if signs of inflammation are present. After clinical examination the first diagnostic measures should be venopuncture (CRP, leukocytes) and at the same time abdominal ultrasound by an experienced clinician. Due to its high accuracy, abdominal ultrasound is sufficient for primary diagnosis and evaluation of the course of colonic diverticulitis. Colonoscopy and barium enema follow after resolution of acute inflammation.

Large-scale identification of proteins of Haemophilus influenzae by amino acid composition analysis.

Two-dimensional protein maps of microorganisms are useful tools for elucidation and detection of target proteins, a process essential in the development of new pharmaceutical products. We applied amino acid composition analysis, following separation by two-dimensional gel electrophoresis, for large-scale identification of proteins of Haemophilus influenzae. H. influenzae is a bacterium of pharmaceutical interest of which the entire genome, comprising approximately 1700 open reading frames, has been sequenced. For amino acid analysis, we used both precolumn derivatization of amino acids followed by reversed-phase chromatography of the derivatized residues and post-column derivatization of the residues previously separated on an ion exchanger. The composition analyses derived from both methods allowed the identification of 110 protein spots. The proteins were identified using the AACompldent software on the ExPASy server accessible via the World Wide Web with a success rate of 52%. In some cases, introduction of the analysis data of 12 residues was sufficient for a correct identification. Proteins which contained an unusually high percentage of one residue could be unambiguously identified. Amino acid composition analysis proved to be an error-robust, efficient method for protein identification. The method can be practically established in every biochemical laboratory and, complementary to mass spectrometry, represents an important analytical tool for the mapping of the proteomes of organisms of interest.

[Evaluation of the bioequivalence of two fast-releasing iron(II) sulfate formulations]. / Prüfung der Bioäquivalenz von zwei schnellfreisetzenden Eisen(II)-Sulfat-Formulierungen.

Bioequivalence of a new oral iron formulation (A: FE(II)SO4.H2O, capsule with 100 mg Fe++, Eryfer 100, CAS 7782-63-0) with the standard formulation (B: Fe(II)SO4.H2O, capsule with 50 mg Fe++, Eryfer) was demonstrated after administration of 100 mg Fe++ in a single-dose two-way cross-over design to 16 normal female volunteers. Iron concentrations were monitored from 24 h before (basal) to 24 h post application. The area under concentration difference curve AUC(diff) and the maximal concentration difference Cmax(diff) were calculated subtracting the basal from the time-corresponding postabsorptive concentrations. AUC(diff) (A: 170 nmol/ml. h, B: 168 nmol/ml.h) and Cmax(diff) (A: 23.3 nmol/ml, B: 21.8 nmol/ml) showed but minor differences between formulations. The AUC(diff) and Cmax ratio (A/B) and the corresponding 90% confidence intervals, 102% (74-129%) and 107% (91-123%), were included by the acceptance range of 70-130% as stated in the study protocol. Hence, both formulations were bioequivalent with respect to rate and extent. The ANOVA coefficient of variation of Cmax(diff) was considerably smaller than that of AUC(diff) (26% versus 44%). The characteristics based on the postabsorptive iron increase (post-absorptive concentrations minus concentration preceding immediately application) AUC(pad) (ratio 99% (83-114%) and Cmax(pad) (ratio 104% (95-112%) exhibited smaller ANOVA-CVs (25% and 14%, respectively) as compared with AUC(diff) and Cmax(diff). All these characteristics appeared to be rather normal than log-normal distributed. It was concluded that the study design was selective to demonstrate an adequate bioavailability of iron formulations.

[Comparison of the pharmacokinetics of a quick-release bezafibrate formulation with a sustained-release formulation. 2. Multiple-dose administration and chronopharmacokinetics]. / Vergleich der Pharmakokinetik einer schnellfreisetzenden Bezafibrat-Formulierung mit einer Retard-Formulierung. 2. Mitteilung: Multiple-dose-Applikation und Chronopharmakokinetik.

The pharmacokinetic profile of a 300 mg immediate release formulation (A) was compared to a 400 mg sustained release formulation (B) of the lipid lowering drug bezafibrate (CAS 41859-67-0). Preparation A was applied twice a day whereas B was applied once a day in the evening. The means of Cmax (12.5 micrograms/ml) and AUC (66.8 micrograms/ml.h) for preparation A were considerably higher than for B (Cmax: 6.6 micrograms/ml, AUC: 39.8 micrograms/ml.h), whereas no differences were found regarding Tcav (A: 8.9 h, B: 8.3 h) and PTF (A: 4.6, B; 4.1). An AUC ratio for A/B of 119% (CI90%: 108-132%) was determined after dose correction. For A an AUC/AUEC ratio of 110% was found when comparing multiple versus single-dose application, whereas this ratio with 136% appeared to be considerably higher for B. Slight chronopharmacological effects were found for preparation A, which was applied twice a day in the evening and in the morning. During night-time the AUC was (insignificantly) 12% higher than during day-time, whereas the apparent elimination halflife time was 40% longer at night (p < 0.025), which corresponded to an extended tmax of median 3 h during night-time as compared to 1.75 h at day-time.

[Comparison of the bioequivalence of two allopurinol preparations]. / Zum Nachweis der Bioäquivalenz von zwei Allopurinol-Präparaten.

Allopurinol generally is considered to be a problematic substance as to its bioavailability. To prove the quality, the in-vivo bioequivalence of an allopurinol (CAS 315-30-0) preparation (Cellidrin 300) in comparison to the standard preparation has been investigated. Both products were bioequivalent with regard to all relevant parameters such as AUC, tmax and Cmax.

Cytochrome P-450LM2 oligomers in proteoliposomes.

The effects of bifunctional cross-linking reagents on the purified hexameric cytochrome P-450LM2 in an aqueous medium and on the proteoliposomal cytochrome P-450LM2 have been compared. In both cases, cross-linking is shown to result in the appearance of a range of additional protein bands in SDS electrophoretograms. The number and the positions of these bands seem to be similar in the solubilized and in the proteoliposomal cytochromes. No additional bands appear when the purified cytochrome P-450 was pretreated with 0.2%. Emulgen 913, which decomposes cytochrome P-450LM2 hexamers. The results indicate that the membrane-bound cytochrome P-450 can exist in the oligomeric (presumably hexameric) form.

Immobilized cytochrome P-450LM2. Dissociation and reassociation of oligomers.

Subunit interactions in the purified hexameric cytochrome P-450LM2 have been studied using covalent binding of one of the 6 promoters to an insoluble matrix. High ionic strength, large-scale pH changes, guanidine chloride and sodium cholate taken at membrane-solubilizing concentrations, had no effect on the aggregation state of the immobilized hemoprotein. SDS caused a 6-fold decrease in the amount of the bound cytochrome. Non-ionic detergents (Emulgen 913, octylglucoside, Tritons) induced hexamer dissociation. In the presence of Emulgen 913 (greater than 0.2%), monomers and immobilized dimers were obtained as cytochrome P-450 was studied in an aqueous medium and in the immobilized state, respectively. Immobilized dimers could be reconstituted to hexamers by treatment with an excess of solubilized monomers after removal of the detergent. In the presence of various phospholipids, which increased the immobilized cytochrome P-450LM2 demethylase activity and induced characteristic spectral changes, no hexamer dissociation was shown. The data obtained are thus in agreement with the suggestion that hexameric arrangement is inherent in the cytochrome P-450 when it is bound to the native membranes.

[Study of the structural organization of cytochrome P-450 oligomers using immobilized isoenzyme LM2]. / Issledovanie strukturnoi organizatsii oligomerov tsitokhroma P-450 s ispol'zovaniem immobilizovannoi izoformy LM2.

Subunit interactions of highly purified hexameric cytochrome P-450 LM 2 has been studied using covalent binding of one of the six protomers to an insoluble matrix. Immobilized cytochrome was catalytically active in monooxygenase reactions and retained the spectral characteristics of cytochrome P-450 LM 2. High ionic strength, large scale pH changes and addition of guanidine chloride were without effect on the aggregation state of the immobilized hemoprotein. However, several detergents induced hexamer dissociation. The crucial role of hydrophobic forces in hexamer subunit interaction was demonstrated. Incubation of the immobilized cytochrome P-450 LM 2 with sonicated liposomes composed of various phospholipids did not result in oligomer dissociation and protein translocation from the matrix to the lipid phase, although the catalytic activity of the immobilized cytochrome significantly increased in the presence of liposomes. The data suggest that cytochrome P-450 LM 2 may be of hexameric structure in the native membranes.

[Cytochrome P-450 in proteoliposomes: oligomeric structure of the LM2 isoform]. / Tsitokhrom P-450 v proteoliposomakh: oligomernaia struktura izoformy LM2.

Crosslinking of protein molecules with bifunctional reagents and subsequent electrophoresis of the modified proteins revealed the presence of cytochrome P-450 LM 2 oligomers in proteoliposome membranes obtained in different ways and differing in their phospholipid composition. Data from a comparative analysis of cytochrome P-450 oligomeric structures in solution and in membrane are suggestive of the hexameric organization of cytochrome P-450 LM 2 within proteoliposome membranes.