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The development of procedures for retrospective detection and quantitation of exposure to phosgene, based on adducts to hemoglobin and albumin, is described. Upon incubation of human blood with [14C]phosgene (0-750 μM), a significant part of radioactivity (0-13%) became associated with globin and albumin. Upon Pronase digestion of globin, one of the adducts was identified as the pentapeptide O=C-(V-L)-S-P-A, representing amino acid residues 1-5 of α-globin, with a hydantoin function between N-terminal valine and leucine. Micro-LC/tandem MS analyses of tryptic as well as V8 protease digests identified one of the adducts to albumin as a urea resulting from intramolecular bridging of lysine residues 195 and 199. The adducted tryptic fragment could be sensitively analyzed by means of micro-LC/tandem MS with multiple-reaction monitoring (MRM), enabling the detection in human blood of an in vitro exposure level of ≥ 1 μM phosgene.

Binding of components of the fibrinolytic system to fibrin is important for the regulation of fibrinolysis. In this study, decomposition of the fibrin network and binding of plasminogen and plasminogen activators (PAs) to fibrin during lysis of a plasma clot were investigated with confocal microscopy using fluorescein-labeled preparations of fibrinogen, plasminogen, tissue-type PA (t-PA), and two-chain urokinase-type PA (tcu-PA). Lysis induced by PAs present throughout the plasma clot was accompanied by a gradual loss of fibrin content of fibers and by accumulation of plasminogen onto the fibers. Two sequential phases could be distinguished: a phase of prelysis, during which the fibrin network remained immobile, and a phase of final lysis, during which fibers moved with a tendency to shrink and eventually disappeared. The two phases occurred simultaneously but in different locations when lysis was induced by PAs present in the plasma surrounding the clot. The zone of final lysis was located within a 5-8-μm superficial layer, where fibers were mobile, and surface-associated fibrin agglomerates appeared. Plasminogen accumulated in these agglomerates up to 30-fold as compared with its concentration in the outer plasma. t-PA was also highly concentrated in the agglomerates, and tcu-PA bound to them slightly. The zone of prelysis, where plasminogen was moderately accumulated on the immobile fibers, was located deeper in the clot. This zone was much thinner in the case of t-PA-induced lysis than in the case of tcu-PA-induced lysis, reflecting the difference in penetration of the two PAs into the clot. We conclude that under conditions of diffusional transport of fibrinolytic enzymes from outside a plasma clot, extensive lysis is spatially restricted to a zone not exceeding 5-8 μm from the clot surface. In this zone the structure of the fibrin network undergoes significant changes, and strikingly high accumulation of fibrinolytic components takes place.

Species from the genus Bacillus have the ability to form endospores, dormant cellular forms that are able to survive heat and acid preservation techniques commonly used in the food industry. Resistance characteristics of spores towards various environmental stresses are in part attributed to their coat proteins. Previously, 70 proteins have been assigned to the spore coat of Bacillus subtilis using SDS-PAGE, 2-DE gel approaches, protein localization studies and genome-wide transcriptome studies. Here, we present a "gel-free" protocol that is capable of comprehensive B. subtilis spore coat protein extraction and addresses the insoluble coat fraction. Using LC-MS/MS we identified 55 proteins from the insoluble B. subtilis spore coat protein fraction, of which 21 are putative novel spore coat proteins not assigned to the spore coat until now. Identification of spore coat proteins from a B. subtilis food-spoilage isolate corroborated a generic and "applied" use of our protocol. To develop specific and sensitive spore detection and/or purification systems from food stuff or patient material, suitable protein targets can be derived from our proteomic approach. Finally, the protocol can be extended to study cross-linking among the spore coat proteins as well as for their quantification. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Background: The mucus layer is an important dynamic component of the epithelial barrier. It contains mucin glycoproteins and other compounds secreted by the intestinal epithelium, such as secretory IgA. However, a standardized in vivo sampling technique of mucus in humans is not yet available. Aim: To assess the validity and feasibility of mucin and protein determinations in human colonic mucus collected under physiological conditions. Subjects and methods: Triplicate colonic mucus samples were collected in 11 healthy volunteers using cytology brushes during sigmoidoscopy. As an indication of the quantity of collected mucus, total protein and mucin concentrations were determined by measuring oligosaccharide equivalents and monosaccharides. Also secretory IgA and sialic acid concentrations were determined and proteomic analysis was performed using surface enhanced laser desorption/ionization-time of flight-mass spectrometry. Results: Mean values of secretory IgA and sialic acid corrected for the amount of mucus ranged from 0.16 to 1.81 g secretory IgA/mmol oligosaccharide equivalents and from 12.6 to 48.6 g sialic acid/mmol oligosaccharide equivalents. Proteomic analysis of mucus is feasible and cluster analysis showed subject specific profiles. Conclusion: Using cytology brushes, human colonic mucus can be sampled and under physiological conditions. These samples could give information on the composition and quality of the mucus layer. © 2009 Editrice Gastroenterologica Italiana S.r.l.

An aneurysm of the aorta is a common pathology characterized by segmentalweakeningof the artery.Althoughit isgenerally accepted that the vessel-wall weakening is caused by an impaired collagen metabolism, a clear association has been demonstrated only for rare syndromes such as the vascular type Ehlers-Danlos syndrome. Here we show that vessel-wall failure in growing aneurysms of patients who have aortic abdominal aneurysm (AAA) or Marfan syndrome is not related to a collagen defect at the molecular level. On the contrary our findings indicate similar (Marfan) or even higher collagen concentrations (AAA) and increased collagen cross-linking in the aneurysms. Using 3D confocal imaging we show that the two conditions are associated with profound defects in collagen microarchitecture. Reconstructions of normal vesselwall showthat adventitial collagen fibers are organized in a loose braiding of collagen ribbons. These ribbons encage the vessel, allowing the vessel to dilate easily but preventing overstretching. AAA and aneurysms in Marfan syndrome show dramatically altered collagen architectures with loss of the collagen knitting. Evaluations of the functional characteristics by atomic force microscopy showed that the wall has lost its ability to stretch easily and revealed a second defect: although vascular collagen in normal aorticwall behaves as a coherent network, inAAAand Marfan tissues it does not. As result, mechanical forces loaded on individual fibers are not distributed over the tissue. These studies demonstrate that the mechanical properties of tissue are strongly influenced by collagen microarchitecture and that perturbations in the collagen networks may lead to mechanical failure.

Background: The presence of fibrous tissue in poorly healing venous leg ulcers suggests abnormal collagen metabolism. The aim was to determine whether there were differences in collagen turnover and matrix metalloproteinase (MMP) activity between ulcers that healed, those that did not heal and normal skin. Methods: Biopsies were taken from the ulcers of 12 patients whose venous ulcers went on to heal and 15 patients whose ulcers failed to heal despite 12 months of compression bandaging. Biopsies were taken from 15 normal controls. Collagen turnover (collagen III N-terminal propeptide (PIIINP) and degraded collagen), and total MMP, MMP-1 and MMP-3 activities were measured. Results: PIIINP and degraded collagen levels were higher in ulcers that healed compared with lesions that failed to heal (P = 0.005 and P < 0.001 respectively) and normal skin (P = 0.003 and P < 0.001). MMP-1 activity was also higher in healing ulcers than resistant ulcers (P < 0.001) and normal skin (P < 0.001). Significantly more total MMP activity was present in all ulcers than in normal skin (P < 0.001), but there was no difference in total MMP (and MMP-3 activity) between ulcers that healed and those that did not. Conclusion: Rapidly healing venous leg ulcers had increased collagen turnover and MMP-1 activity, which appeared to differentiate them from those that failed to heal within 12 months. Copyright © 2008 British Journal of Surgery Society Ltd.

The aim of this work was to study the effect of the formation of more heat-stable conformers of chicken egg ovalbumin during incubation at basic pH (9.9) and elevated temperature (55°C) on the protein aggregation properties at neutral pH. Native ovalbumin (N-OVA) is converted on the hours time-scale into more heat-stable forms denoted I- (intermediate) and S-OVA, that have denaturation temperatures 4.8 and 8.4°C, respectively, higher than that of N-OVA. The conversions most likely proceed via I-OVA, but direct conversion of N-OVA into S-OVA with slower kinetics can not be excluded. It is demonstrated that both I- and S-OVA have similar denaturation characteristics to N-OVA, except that higher temperatures are required for denaturation. The presence of even small contributions of I-OVA does, however, reduce the Stokes radius of the aggregates formed upon heat treatment of the material at 90°C about 2-fold. This affects the gel network formation considerably. Since many (commercial) preparations of ovalbumin contain varying contributions of the more heat-stable forms mentioned, proper characterization or standardization of the isolation procedure of the material is essential to control or predict the industrial application of this protein. Chemicals/CAS: ovalbumin, 77466-29-6; Ovalbumin, 9006-59-1

Interfacial rheological properties and their suitability for foam production and stability of two vegetable proteins were studied and compared to β-casein. Proteins used ranged from flexible to rigid/globular in the order of β-casein, gliadin and soy glycinin. Experiments were performed at pH 6.7. Network forming properties were characterised by the surface dilational modulus (determined with the ring trough) and the critical falling film length (Lstill) at which a stagnant protein film will break. Gliadin had the highest dilational modulus, followed by glycinin and β-casein, whereas glycinin formed the strongest film against fracture in the overflowing cylinder. The rate of decrease in the surface tension was studied at the air-water (Wilhelmy plate method) and the oil-water interface (bursting membrane) and the dynamic surface tension during compression and expansion in the caterpillar. Gliadin had the lowest equilibrium interfacial tensions and β-casein the lowest dynamic surface tension during expansion. Hardly any foam could be formed at a concentration of 0.1 g/l by shaking. At a concentration of 1.4 g/l most foam was formed by β-casein, followed by gliadin and glycinin. It seems that in the first place the rate of adsorption is important for foam formation. For the vegetable proteins, adsorption was slow. This resulted in lower foamability, especially for glycinin. © 2003 Elsevier B.V. All rights reserved.

Heme-containing peroxidases from white rot basidiomycetes, in contrast to most proteins of fungal origin, are poorly produced in industrial filamentous fungal strains. Factors limiting peroxidase production are believed to operate at the posttranslational level. In particular, insufficient availability of the prosthetic group which is required for peroxidase biosynthesis has been proposed to be an important bottleneck. In this work, we analyzed the role of two components of the secretion pathway, the chaperones calnexin and binding protein (BiP), in the production of a fungal peroxidase. Expression of the Phanerochaete chrysosporium manganese peroxidase (MnP) in Aspergillus niger resulted in an increase in the expression level of the cLxA and bipA genes. In a heme-supplemented medium, where MnP was shown to be overproduced to higher levels, induction of clxA and bipA was also higher. Overexpression of these two chaperones in an MnP-producing strain was analyzed for its effect on MnP production. Whereas bipA overexpression seriously reduced MnP production, overexpression of calnexin resulted in a four- to fivefold increase in the extracellular MnP levels. However, when additional heme was provided in the culture medium, calnexin overexpression had no synergistic effect on MnP production. The possible function of these two chaperones in MnP maturation and production is discussed. Chemicals/CAS: BipA protein, Aspergillus; Calcium-Binding Proteins; Calnexin, 139873-08-8; Culture Media; Fungal Proteins; Heme, 14875-96-8; HSP70 Heat-Shock Proteins; manganese peroxidase, EC 1.11.1.13; Peroxidases, EC 1.11.1.-

Systems biology has developed in recent years from a technology-driven enterprise to a new strategic tool in Life Sciences, particularly for innovative drug discovery and drug development. Combining the ultimate in systems phenotyping with in-depth investigations of biomolecular mechanisms will enable a revolution in our understanding of disease pathology and will advance translational medicine, combination therapies, integrative medicine, and personalized medicine. A prerequisite for deriving the benefits of such a systems approach is a reliable and well-validated bioanalytical platform across complementary measurement modalities, especially transcriptomics, proteomics, and metabolomics, that operates in concert with a megavariate integrative biostatistical/bioinformatics platform. The applicable bioanalytical methodologies must undergo an intense development trajectory to reach an optimal level of reliable performance and quantitative reproducibility in daily practice. Moreover, to generate such enabling systems information, it is essential to design experiments based on an understanding of the complexity and statistical characteristics of the large data sets created. Novel insights into biology and system science can be obtained by evaluating the molecular connectivity within a system through correlation networks, by monitoring the dynamics of a system, or by measuring the system responses to perturbations such as drug administration or challenge tests. In addition, cross-compartment communication and control/feed-back mechanisms can be studied via correlation network analyses. All these data analyses depend critically upon the generation of high-quality bioanalytical platform data sets. The emphasis of this paper is on the characteristics of a bioanalytical platform that we have developed to generate such data sets. The broad applicability of Systems Biology in pharmaceutical research and development is discussed with examples in disease biomarker research, in pharmacology using system response monitoring, and in cross-compartment system toxicology assessment. © 2007 American Chemical Society.

Filamentous growth of Aspergillus oryzae on solid cereal substrates involves secretion of substrate converting enzymes and a solid substrate specific polarised hyphal growth phenotype. To identify proteins produced under these specific conditions, the extracts of A. oryzae grown on wheat-based media were analysed using N-terminal sequence analysis. In a submerged wheat-based growth medium of A. oryzae, besides α-amylase, also an arabinosidase and xylanase were abundantly produced. In the extracts of A. oryzae grown on wheat-based solid substrate besides α-amylase and chitinase, two new proteins of 16 and 27 kDa were identified. These hypothetical proteins showed only close homologies to filamentous fungal proteins. © 2005 Elsevier B.V. All rights reserved.

The gelling characteristics of two vicilin fractions from pea (Pisum sativum L.) were compared over a range of pH and salt conditions after preliminary results showed that despite having equal opportunity to unfold, and expose hydrophobic residues, they had different minimum gelling concentrations (at pH 7.6). Furthermore, at this pH one fraction formed turbid gels and the other formed transparent gels. The fraction that formed transparent gels contained a substantial amount of the 70 kDa α-subunits of vicilin, and thus it was hypothesized that the highly charged N-terminal extension region on these 70 kDa subunits hinders gelation of this vicilin fraction at pH 7.6 and I = 0.2 due to repulsion of the net negative charge. The experiments designed to test this hypothesis are presented and discussed in this paper and prove that the hypothesis was true, which offers the possibility to control or modify the gelation behavior of vicilin on the basis of information of its subunit composition.

In the current paper we show that exposure of human callus to isocyanates leads to covalent modifications within keratin proteins. Mass spectrometric analyses of pronase digests of keratin isolated from exposed callus show that both mono- and di-adducts (for di-isocyanates) are predominantly formed on the ε-amino group of lysine. In addition, numerous modified tryptic keratin fragments were identified, demonstrating rather random lysine modification. Interestingly, preliminary experiments demonstrate that in case of MDI a similar lysine di-adduct was formed with lung elastin. Our data support the hypothesis that skin sensitization through antigenic modifications of skin proteins by isocyanates could play a role in occupational isocyanate-induced asthma. It is further envisaged that the elucidated adducts will also have great potential for use as biomarkers to assess skin exposure to isocyanates. Advantageously, the various lysine adducts display the presence of a characteristic daughter fragment at m/z 173.1 [lysine-NCO]+, enabling generic and rapid screening for exposure to isocyanates. © 2015 Elsevier Ireland Ltd. All rights reserved.

It was studied how protein-protein and protein-membrane interactions influence the filtration performance during the ultrafiltration of protein solutions over polymeric membranes. This was done by measuring flux, streaming potential, and protein transmission during filtration of bovine serum albumin (BSA) solutions at various pH values using various membranes with different cut-off values. It was found that protein-membrane interactions influence the fouling behaviour in the initial stages of filtration. In the high-fouling regime (later stages of filtration), protein-protein interactions dictate the overall performance. AFM images of the membrane surfaces taken after the filtration experiments showed that the membranes were totally covered by a protein fouling layer. The structure of this fouling layer depended strongly on pH. In particular, very open structures with high permeabilities were found at low pH (below the iso-electric point of the protein). These induced high values of flux and protein transmission. (C) 2000 Elsevier Science B.V. It was studied how protein-protein and protein-membrane interactions influence the filtration performance during the ultrafiltration of protein solutions over polymeric membranes. This was done by measuring flux, streaming potential, and protein transmission during filtration of bovine serum albumin (BSA) solutions at various pH values using various membranes with different cut-off values. It was found that protein-membrane interactions influence the fouling behaviour in the initial stages of filtration. In the high-fouling regime (later stages of filtration), protein-protein interactions dictate the overall performance. AFM images of the membrane surfaces taken after the filtration experiments showed that the membranes were totally covered by a protein fouling layer. The structure of this fouling layer depended strongly on pH. In particular, very open structures with high permeabilities were found at low pH (below the iso-electric point of the protein). These induced high values of flux and protein transmission.

ACA-DC 0040 produced an antimicrobial agent, which was named thermophilin T, active against several lactic acid bacteria strains of different species and food spoilage bacteria, such as Clostridium sporogenes C22/10 and Cl. tyrobutyricum NCDO-1754. The crude antimicrobial compound is sensitive to proteolytic enzymes and α-amylase, heat-stable (100 °C for 30 min), resistant to pH exposure at pH 1-12 and demonstrates a bactericidal mode of action against the sensitive strain Lactococcus cremoris CNRZ-117. The production of bacteriocin was optimized approximately 10-fold in an aerobic fermenter held at constant pH 5.8 and 6.2. Ultrafiltration experiments with culture supernatant fluids containing the bacteriocin, and further estimation of molecular weight with gel filtration chromatography, revealed that bacteriocin in the native form has a molecular weight in excess of 300 kDa. SDS-gel electrophoresis of partially purified thermophilin T showed that bacteriocin activity was associated with a protein band of approximately 2.5 kDa molecular mass.

A study was carried out to obtain more insight into the parameters that determine the secretion of heterologous proteins from filamentous fungi. A strategy was chosen in which the mRNA levels and protein levels of a number of heterologous genes of different origins were compared. All genes were under control of the Aspergillus awamori 1,4-β-endoxylanase A (exlA) expression signals and were integrated in a single copy at the A. awamori pyrG locus. A Northern (RNA) analysis showed that large differences occurred in the steady-state mRNA levels obtained with the various genes; those levels varied from high values for genes of fungal origin (A. awamori 1,4-β- endoxylanase A, Aspergillus niger glucoamylase, and Thermomyces lanuginosa lipase) to low values for genes of nonfungal origin (human interleukin 6 and Cyamopsis tetragonoloba [guar] α-galactosidase). With the C. tetragonoloba α-galactosidase wild-type gene full-length mRNA was even undetectable. Surprisingly, small amounts of full-length mRNA could be detected when a C. tetragonoloba α-galactosidase gene with an optimized Saccharomyces cerevisiae codon preference was expressed. In all cases except human interleukin 6, the protein levels corresponded to the amounts expected on basis of the mRNA levels. For human interleukin 6, very low protein levels were observed, whereas relatively high steady-state mRNA levels were obtained. Our data suggest that intracellular protein degradation is the most likely explanation for the low levels of secreted human interleukin 6.

Elucidation of noncholinesterase protein targets of organophosphates, and nerve agents in particular, may reveal additional mechanisms for their high toxicity as well as clues for novel therapeutic approaches toward intoxications with these agents. Within this framework, we here describe the synthesis of the activity-based probe 3, which contains a phosphonofluoridate moiety, a P-Me moiety, and a biotinylated O-alkyl group, and its use in activity-based protein profiling with two relevant biological samples, that is, rhesus monkey liver and cultured human A549 lung cells. In this way, we have unearthed eight serine hydrolases (fatty acid synthase, acylpeptide hydrolase, dipeptidyl peptidase 9, prolyl oligopeptidase, carboxylesterase, long-chain acyl coenzyme A thioesterase, PAF acetylhydrolase 1b, and esterase D/S-formyl glutathione hydrolase) as targets that are modified by the nerve agent sarin. It is also shown that the newly developed probe 3 might find its way into the development of alternative, less laborious purification protocols for human butyrylcholinesterase, a potent bioscavenger currently under clinical investigation as a prophylactic/therapeutic for nerve agent intoxications. © 2009 American Chemical Society.

A full length cDNA sequence for a barley grain lipoxygenase was obtained. It includes a 5' untranslated region of 69 nucleotides, an open reading frame of 2586 nucleotides encoding a protein of 862 amino acid residues and a 3' untranslated region of 142 nucleotides. The molecular mass of the encoded polypeptide was calculated to be 96.392. Its amino acid sequence shows a high homology with that of other plant lipoxygenases identified to date.