Differentiation of protein species of alpha-2u-globulin according to database entries: A half-theoretical approach.

The alpha-2u-globulin protein, the main subject of this study, is the most abundant protein in adult male rat urine. In this investigation there are 19 spots identified as alpha-2u-globulin by 2-DE and MALDI-TOF/TOF-MS. All of them are in the low molecular weight region, at approximately 15-25kDa. Searches within both, SwissProt and NCBI databases gave different from each other, but on the majority the same database entry as the highest ranked result for all spots. For this half-theoretical approach all entries from the NCBI database for the protein alpha-2u-globulin were considered in more detail. The sequences and the masses of the theoretically resulting tryptic peptides were compared with the PMF spectra of the spots identified as alpha-2u-globulin. This study presents a trial to distinguish between different protein species of that protein, only on the amino acid level. Other modifications like phosphorylation, glycosylation or any other group modification could not be considered here. Different protein species can be predicted for groups of closer positioned spots. Statements about which spot contains which peptide variant can be done, too. But it was found that several spots contain more than one protein species. BIOLOGICAL SIGNIFICANCE: In this investigation a half-theoretically approach was shown to differentiate between protein species of different spots identified as the same protein. Different positions of spots in 2-DE gels mean different contents of protein species. Here, peptide masses from sequences of protein database entries were searched in the PMF spectra of alpha-2u-globulin. Different peptide variants could be assigned to different spots. It was also found that several spots contain more than one peptide variant and therefore more than one protein species. In addition, the insufficiency of the database has been demonstrated.

Structural changes in plasma circulating fibrinogen after moderate beer consumption as determined by electrophoresis and spectroscopy.

The effects of short-term moderate beer consumption (MBC) on plasma circulating fibrinogen (PCF) in patients suffering from coronary atherosclerosis were investigated by use of 2-dimensional electrophoresis (2-DE), circular dichroism (CD), and Fourier transform infrared spectroscopy (FT-IR). Forty-eight volunteers after coronary bypass surgery were divided into experimental (EG) and control (CG) groups, each of 24. Patients of the EG group consumed 330 mL of beer/day (about 20 g of alcohol) for 30 consecutive days, and CG volunteers drank mineral water instead of beer. Blood samples were collected before and after the experiment. In 21 out of 24 patients after beer consumption the plasma circulating fibrinogen was compromised: changes in its secondary structure were found. These changes were expressed in relatively low electrophoretic mobility and charge heterogeneity, decrease in alpha-helix and increase in beta-sheet, and in slight shift of amide I and II bands. Our findings indicate that one of the positive benefits of moderate beer consumption is to diminish the production of fibrinogen and its stability, which reduces the potential risk exerted by this protein. Thus, in most of beer-consuming patients some qualitative structural changes in plasma circulating fibrinogen were detected.

An iterative calibration method with prediction of post-translational modifications for the construction of a two-dimensional electrophoresis database of mouse mammary gland proteins.

Protein databases serve as general reference resources providing an orientation on two-dimensional electrophoresis (2-DE) patterns of interest. The intention behind constructing a 2-DE database of the water soluble proteins from wild-type mouse mammary gland tissue was to create a reference before going on to investigate cancer-associated protein variations. This database shall be deemed to be a model system for mouse tissue, which is open for transgenic or knockout experiments. Proteins were separated and characterized in terms of their molecular weight (M(r)) and isoelectric point (pI) by high resolution 2-DE. The proteins were identified using prevalent proteomics methods. One method was peptide mass fingerprinting by matrix-assisted laser desorption/ionization-mass spectrometry. Another method was N-terminal sequencing by Edman degradation. By N-terminal sequencing M(r) and pI values were specified more accurately and so the calibration of the master gel was obtained more systematically and exactly. This permits the prediction of possible post-translational modifications of some proteins. The mouse mammary gland 2-DE protein database created presently contains 66 identified protein spots, which are clickable on the gel pattern. This relational database is accessible on the WWW under the URL: http://www.mpiib-berlin.mpg.de/2D-PAGE.

Proteome analysis of secreted proteins of the gastric pathogen Helicobacter pylori.

Secreted proteins (the secretome) of the human pathogen Helicobacter pylori may mediate important pathogen-host interactions, but such proteins are technically difficult to analyze. Here, we report on a comprehensive secretome analysis that uses protein-free culture conditions to minimize autolysis, an efficient recovery method for extracellular proteins, and two-dimensional gel electrophoresis followed by peptide mass fingerprinting for protein resolution and identification. Twenty-six of the 33 separated secreted proteins were identified. Among them were six putative oxidoreductases that may be involved in the modification of protein-disulfide bonds, three flagellar proteins, three defined fragments of the vacuolating toxin VacA, the serine protease HtrA, and eight proteins of unknown function. A cleavage site for the amino-terminal passenger domain of VacA between amino acids 991 and 992 was determined by collision-induced dissociation mass spectrometry. Several of the secreted proteins are interesting targets for antimicrobial chemotherapy and vaccine development.