Multiplex detection and identification of proteins on a PVDF membrane blocked with a synthetic polymer-based reagent

2-DE is one of the most powerful methods for analyzing proteins expressed in cells and tissues. Immunodetection of proteins blotted on a polymer membrane is the method of choice for detecting specific proteins in 2-D gels. To precisely locate spots of immunoreactive proteins in 2-D gels, both dye staining and immunodetection were performed on the same PVDF membrane. Prior to immunodetection, nonspecific adsorption of the antibodies to the membrane was blocked with a synthetic polymer-based reagent (N-102) after protein transfer. The protein was then stained with colloidal gold or CBB followed by protein spot identification by LC-MS. Described herein is a method for multiplex analysis of proteins transferred to a PVDF membrane. Proteins that were phosphorylated at tyrosine in the phosphoproteome of rice callus or human ovarian cancer cells were detected by immunoblotting and subsequently identified with high precision.     

Enhanced immunodetection of blotted house dust mite protein allergens on nitrocellulose following blocking with Tween 20

The effect of blocking nitrocellulose membranes with the nonionic detergent Tween 20 on the detection, by protein blotting, of IgE-binding to house dust mite Dermatophagoides pteronyssinus allergens has been investigated. Tween blocking led to enhanced immunodetection of allergens despite removal of proteins from the membrane when compared to protein blocking agents which did not displace transferred components. The enhancement varied with the different mite components and, for one in particular, antigen Der p II, an increase of more than 100-fold in IgE antibody binding occurred despite a concurrent loss of more than 90% of Der p II from the membrane. Both the enhancement of binding and loss of components from the membrane were dependent upon the time course of blocking and the concentration of Tween used.     

A novel multiplex method for the simultaneous detection and relative quantitation of pollen allergens

Standardization of pollen protein extracts is essential in order to ensure efficiency and safety in allergy diagnosis and immunotherapy. In this paper, we have optimized a multiplex Western blotting method for the simultaneous detection of four olive pollen allergens (Ole e 1, Ole e 2, Ole e 5, and Ole e 9) on a single blot using a monoclonal antibody from mouse and three polyclonal antibodies raised in rabbit. We utilized unconjugated Fab antibody fragments for blocking rabbit primary antibodies, and fluorescence-based detection. These changes allowed an accurate and reliable comparative quantitation of these allergens among pollen-protein samples from six olive cultivars. In addition, we also tested the IgE-binding capacity of these pollen extracts by reprobing the same blot with a pool of sera from eight patients allergic to olive and detection with enzyme conjugated antibodies. A noticeable variability regarding allergen content and IgE-reactivity was found among the olive cultivars analyzed. Moreover, we could easily confirm the identity of some of the IgE-binding proteins by simply overlapping both fluorescence and chemiluminescence images. This method is versatile since it can be applied to other allergogenic plant species and extended to other allergens.     

The proteome of maize leaves: use of gene sequences and expressed sequence tag data for identification of proteins with peptide mass fingerprints.

As a first step in establishing a proteome database for maize, we have embarked on the identification of the leaf proteins resolved on two-dimensional (2-D) gels. We detected nearly 900 spots on the gels with a pH 4-7 gradient and over 200 spots on the gels with a pH 6-11 gradient when the proteins were visualized with colloidal Coomassie blue. Peptide mass fingerprints for 300 protein spots were obtained with matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometer and 149 protein spots were identified using the protein databases. We also searched the pdbEST databases to identify the leaf proteins and verified 66% of the protein spots that had been identified using the protein databases. Sixty-seven additional protein spots were identified from expressed sequence tags (ESTs). Many abundant leaf proteins are present in multiple spots. Functions of over 50% of the abundant leaf proteins are either unknown or hypothetical. Our results show that EST databases in conjunction with peptide mass fingerprints can be used for identifying proteins from organisms with incomplete genome sequence information.     

Reduction and alkylation of proteins in preparation of two-dimensional map analysis: why, when, and how?

The standard procedure adopted up to the present in proteome analysis calls for just reduction prior to the isoelectric focusing/immobilized pH gradient (IEF/IPG) step, followed by a second reduction/alkylation step in between the first and second dimension, in preparation for the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) step. This protocol is far from being optimal. It is here demonstrated, by matrix assisted laser desorption/ionization-time of flight (MALDI-TOF)-mass spectrometry, that failure to reduce and alkylate proteins prior to any electrophoretic step (including the first dimension) results in a large number of spurious spots in the alkaline pH region, due to "scrambled" disulfide bridges among like and unlike chains. This series of artefactual spots comprises not only dimers, but an impressive series of oligomers (up to nonamers) in the case of simple polypeptides such as the human alpha- and beta-globin chains, which possess only one (alpha-) or two (beta-) -SH groups. As a result, misplaced spots are to be found in the resulting two-dimensional (2-D) map, if performed with the wrong protocol. The number of such artefactual spots can be impressively large. In the case of analysis of complex samples, such as human plasma, it is additionally shown that failure to alkylate proteins results in a substantial loss of spots in the alkaline gel region, possibly due to the fact that these proteins, at their pI, regenerate their disulfide bridges with concomitant formation of macroaggregates which become entangled with and trapped within the polyacrylamide gel fibers. This strongly quenches their transfer in the subsequent SDS-PAGE step.     

Glucose/Ribitol Dehydrogenase and 16.9 kDa Class I Heat Shock Protein 1 as Novel Wheat Allergens in Baker’s Respiratory Allergy

Wheat allergens are responsible for symptoms in 60–70% of bakers with work-related allergy, and knowledge, at the molecular level, of this disorder is progressively accumulating. The aim of the present study is to investigate the panel of wheat IgE positivity in allergic Italian bakers, evaluating a possible contribution of novel wheat allergens included in the water/salt soluble fraction. The water/salt-soluble wheat flour proteins from the Italian wheat cultivar Bolero were separated by using 1-DE and 2-DE gel electrophoresis. IgE-binding proteins were detected using the pooled sera of 26 wheat allergic bakers by immunoblotting and directly recognized in Coomassie stained gel. After a preparative electrophoretic step, two enriched fractions were furtherly separated in 2-DE allowing for detection, by Coomassie, of three different proteins in the range of 21–27 kDa that were recognized by the pooled baker’s IgE. Recovered spots were analyzed by nanoHPLC Chip tandem mass spectrometry (MS/MS). The immunodetected spots in 2D were subjected to mass spectrometry (MS) analysis identifying two new allergenic proteins: a glucose/ribitol dehydrogenase and a 16.9 kDa class I heat shock protein 1. Mass spectrometer testing of flour proteins of the wheat cultivars utilized by allergic bakers improves the identification of until now unknown occupational wheat allergens.     

Analysis of the mouse proteome. (I) Brain proteins: separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation

The total protein of the mouse brain was fractionated into three fractions, supernatant, pellet extract and rest pellet suspension, by a procedure that avoids any loss of groups or classes of proteins. The supernatant proteins were resolved to a maximum by large-gel two-dimensional electrophoresis. Two-dimensional patterns from ten individual mice of the commonly used inbred strain C57BL/6 (species: Mus musculus) were prepared. The master pattern was subjected to densitometry, computer-assisted image analysis and treatment with our spot detection program. The resulting two-dimensional pattern, a standard pattern for mouse brain supernatant proteins, was divided into 40 squares, calibrated, and specified by providing each spot with a number. The complete pattern and each of the 40 squares are shown in our homepage (http://www.charite.de/ humangenetik). The standard pattern comprises 8767 protein spots. To identify the proteins known so far in the brain fraction investigated, a first set of 200 spots was analyzed by matrix-assisted laser desorption/ionization - mass spectrometry (MALDI-MS) after in-gel digestion. By screening protein databases 115 spots were identified; by extending the analysis to selected, genetically variant protein spots, 166 spots (including some spot series) were identified in total. This number was increased to 331 by adding protein spots identified indirectly by a genetic approach. By comparing the two-dimensional patterns from C57BL/6 mice with those of another mouse species (Mus spretus), more than 1000 genetically variant spots were detected. The genetic analysis allowed us to recognize spot families, i.e., protein spots that represent the same protein but that are post-translationally modified. If some members of the family were identified, the whole family was considered as being identified. Spot families were investigated in more detail, and interpreted as the result of protein modification or degradation. Genetic analysis led to the interesting finding that the size of spot families, i.e., the extent of modification or degradation of a protein, can be genetically determined. The investigation presented is a first step towards a systematic analysis of the proteome of the mouse. Proteome analysis was shown to become more efficient, and, at the same time, linked to the genome, by combining protein analytical and genetic methods.     

Effectiveness of natural and synthetic blocking reagents and their application for detecting food allergens in enzyme-linked immunosorbent assays

Blocking is an important step before an enzyme-linked immunosorbent assay (ELISA) can be performed. It reduces non-specific binding to the microtiter plate to a minimum. For detecting food allergens by means of ELISA, the problem with protein blocking solutions is obvious. The blocker might interfere with the antibodies of the assay and leads to false positive results. Therefore, other blocking solutions are greatly needed. There are some alternatives like synthetic blockers or carbohydrates. Comparisons of these different blocking agents, namely proteins, carbohydrates, and synthetic blockers, were made at different reaction conditions. The incubation periods and temperatures were varied, as well as the pH. The best combinations were evaluated and compared, in respect of their blocking efficiency. The two best non-proteinaceous blockers, i.e. polyvinylalcohol and Ficoll, were subsequently applied to ELISA tests for the determination of α-casein and peanut. The study showed that Ficoll and PVA did as well as BSA in buffer solution. Therefore, they can be considered as alternative blocking reagents for ELISA, especially for the detection of food allergens.     

Western blot normalization: Time to choose a proper loading control seriously

Recent research has questioned the validity of housekeeping proteins in Western blot. Our present study proposed new ideas for Western blot normalization that improved the reproducibility of scientific research. We used the Gene Expression Omnibus (GEO) database and the web tool GEO2R to exclude unstable housekeeping genes quickly. In ischemic heart tissues, actin and tubulin changed significantly, whereas no statistically significant changes were observed in the expression of genes relative to glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Besides, the reliability of GAPDH was further examined by Western blot. Additionally, unstable housekeeping genes were found in other animal models of cardiovascular medicine. We also found that sodium dodecyl sulfate and temperature significantly impacted the results of Ponceau S staining. Membranes stained with Ponceau S after immunodetection could avoid this interference, and the coefficients of variation for post-immunodetection staining are lower than those produced by GAPDH immunodetection. Overall, we described a new use of differential gene expression analysis and proposed a modified Ponceau S staining method, which provided researchers with a proper loading control for Western blot and hence could improve reproducibility in research.     

Fluorescent labeling of proteins with nile red and 2-methoxy-2,4-diphenyl-3(2H)-furanone: physicochemical basis and application to the rapid staining of sodium dodecyl sulfate polyacrylamide gels and Western blots

The fluorescent hydrophobic dye Nile red allows the rapid, sensitive, and general staining of proteins in sodium dodecyl sulfate (SDS)-polyacrylamide gels. Nile red staining does not preclude further electroblotting of protein bands onto polyvinylidene difluoride (PVDF) membranes. The resulting Western blot can be stained with the covalent fluorescent dye 2-methoxy-2,4-diphenyl-3(2H)-furanone (MDPF) using a simple procedure. MDPF staining allows further N-terminal microsequencing and immunodetection of specific bands. This review considers the physicochemical, structural, and analytical studies that have led to the development of Nile red and MDPF staining methods. The usefulness of these procedures is discussed in comparison to other currently available fluorescent and nonfluorescent protein detection methods.     

A new multiphasic buffer system for sodium dodecyl sulfate-polyacrylamide gel electrophoresis of proteins and peptides with molecular masses 100,000-1000, and their detection with picomolar sensitivity.

A novel multiphasic buffer system for high resolution sodium dodecyl sulfate-polyacrylamide gel electrophoresis of dansylated and nondansylated proteins/peptides in the relative molecular mass (Mr) range of 100,000-1000 is described. The system, based on Jovin's theory of multiphasic zone electrophoresis, allows complete stacking and destacking of proteins/peptides within the above Mr range. The buffer system uses Bicine and sulfate as trailing and leading ion, respectively, and Bistris and Tris as counter ions in the stacking and separating phase, respectively. Through selection of two different counter ions--the characteristic feature of the present ionic system--the stacking limits of a multiphasic buffer system can be further widened, thus making it applicable to gel electrophoresis of a larger spectrum of rapidly migrating species, such as sodium dodecyl sulfate-proteins/peptides and nucleic acids, than has been possible previously. Highly sensitive detection methods for proteins as well as for polypeptides down to approximately Mr 1000 are described. Dansylated proteins/peptides were detected by their fluorescence either directly within the gel or following electroblotting into anion-exchange or polyvinylidene difluoride membranes. The latter procedure resulted in detection sensitivities of approximately 1 ng. Nondansylated proteins/peptides were either detected within the gel by colloidal Coomassie staining or by electroblotting into polyvinylidene difluoride membranes, followed by colloidal gold staining. Prior to both staining procedures the proteins/peptides were pretreated with glutardialdehyde in the presence of borate at near neutral pH values to generate protein/peptide polymers of poor solubility. For a given pH the efficiency of the latter procedure was significantly influenced by the nature of the buffer ion used in the fixation buffer. In contrast to conventional fixation procedures even small polypeptides (Mr 1000) were immobilized and approximately 15 ng and 0.75 ng could be detected after colloidal Coomassie and colloidal gold staining, respectively.     

Alkaline extraction of human plasma proteins from nondenaturing micro-2-D gels for protein/polypeptide mass measurement and peptide mass fingerprinting using MALDI-TOF MS

Previously, we have reported a high-efficiency method of protein extraction from CBB-stained polyacrylamide gels for molecular mass measurement with MALDI-TOF MS [1]. In the present work, the alkaline extraction method was applied to CBB-stained 2-DE gels on which human plasma proteins were separated in the absence of denaturant. In order to examine the performance of the method, ten spots with apparent molecular masses (MMapp) in the range of 65 to 1000 kDa were selected and the proteins were extracted from the gel pieces. The extracts were subjected to whole-mass measurement by MALDI-TOF MS, with and without DTT treatment. In addition, the extracts were subjected to in-solution trypsin digestion followed by MALDI-TOF MS and PMF analysis. Successful extraction of proteins from the ten spots, up to MMapp 1000 kDa, has been ascertained by the significant PMF assignment (MASCOT) with high sequence coverage of the respective proteins or polypeptides. When direct mass measurement of the extracted proteins was attempted, three spots in MMapp range 65-100 kDa provided mass peaks. Five spots in MMapp range 150-400 kDa did not give mass peaks of the intact proteins, but showed those of the constituent polypeptides after the DTT treatment. Extraction of proteins prior to trypsin digestion enabled the procedure of PMF analysis to be much simpler than the conventional in-gel digestion method, providing comparable protein scores and sequence coverage. The technique presented here suggests a new strategy for the characterization of proteins separated by nondenaturing 2-DE.     

Restricted access chromatographic sample preparation of low mass proteins expressed in human fibroblast cells for proteomics analysis

Two-dimensional electrophoresis and modern image analysis systems have made it possible to study protein expression and regulation of proteins in biological systems. Proteins in the molecular mass region of 20-120 kDa are well investigated and described. However, proteins with masses below 20 kDa are the least investigated as they are rarely seen on 2D-PAGE due to fast migrations in the electric field and lack of staining efficiency. This paper describes a technique that enriches proteins in the lower mass region using solid-phase extraction. The purification step is carried out using C18 functionalised "restricted access" affinity chromatography whereby simultaneous trace enrichment and sample clean up is achieved. In this study expression patterns of TGF-beta stimulated and non-stimulated fibroblasts were compared after the solid-phase fractionation procedure. An increased expression pattern was obtained whereby 400 protein spots could be detected by image analysis in the <20-kDa region. Out of these, specific regulations of 14 spots were found by quantitative image analysis and spots of interest were identified with MALDI TOF-MS. The regulated and identified proteins were triosephosphate isomerase, cofilin and heat shock 27-kDa protein.     

Investigation on the interaction between colloidal gold and human complement factor 4 at different pH by spectral methods

The interaction between colloidal gold and human complement factor 4 (human C4) at different pH was investigated by spectral methods, including absorption and resonance light-scattering spectrometry. According to the changes of color and absorption spectra of colloidal gold solution in presence of human C4, the interaction between colloidal gold and human C4 was quantitatively investigated using a semi-empirical "flocculation parameter". At the same time, the changes of resonance light-scattering spectra and transmission electron microscopy (TEM) images indicate that the aggregation of colloidal gold happens by electrostatic interaction in presence of human C4 in the pH range 5-6. However, the colloidal gold solution remains stable at pH >6 and pH <5 due to the repulsive electrostatic interaction between colloidal gold and human C4. The flocculation parameter is directly proportional to the concentration of human C4 in the range from 9.7 to 233.0 microgl(-1). In addition, the interactions between the colloidal gold and bovine serum albumin (BSA) as well as human serum albumin (HSA) were also investigated using the same methods. It was found that there was no aggregation of colloidal gold in presence of BSA and HSA in the pH range 5-6. However, when the pH of solution is 4, the aggregation of colloidal gold happens. Because BSA and HSA have different structure, the intensity of aggregation of colloidal gold in presence of BSA is greater than that in presence of HSA at pH 4.     

Analysis of blood plasma proteins in patients with Alzheimer's disease by two-dimensional electrophoresis, sequence homology and immunodetection

Blood plasma proteins of patients with Alzheimer's disease (AD; senile dementia) and non-AD-type dementia were resolved by two-dimensional electrophoresis and identified by migration position in the electrophoresis pattern, sequence homology, and immunodetection by using antibodies. For the control experiments, blood plasma proteins of a healthy young individual and non-dementia patients were examined in a manner similar to that of the plasma samples of AD patients. In the plasma sample of the healthy young individual, more than 350 spots of silver-stained proteins were observed and among these spots, 73 spots were identified. Blood plasma proteins of the AD and non-AD-type dementia patients were compared with those of the control and non-dementia patients. In the blood plasma samples of five AD patients, three patients had apolipoprotein E4, and another patient showed apolipoprotein L and complement factor H. For the AD-related proteins apolipoprotein E, tau-1, and presenilin 2, proteins were examined by immunostaining with antibodies, in both AD and non-AD patients. Among the three samples of non-AD-type dementia patients, one was distinguishable by amyloid A proteins, and the other by haptoglobin isoforms.     

Gram-scale synthesis of monodisperse gold colloids by the solvated metal atom dispersion method and digestive ripening and their organization into two- and three-dimensional structures

We describe a synthetic procedure for preparation of large quantities of monodisperse thiol-stabilized gold colloids in toluene solution. The method is based on the solvated metal atom dispersion technique (SMAD), which is very suitable for preparation of large amounts of metal colloidal solutions, as well as of metal sulfide, metal oxide, and other types of dispersed compounds in different solvents. A combination of two different solvents like acetone and toluene is used for the preparation of the gold colloids. The necessity of initially carrying out the SMAD reaction in acetone comes from its high degree of solvation of gold particles. Acetone acts as a preliminary stabilizing agent. After its removal from the system, the particles are stabilized by dodecanethiol molecules, which enable their very good dispersion in toluene solution. A digestive ripening procedure is carried out with the gold-toluene colloid, and for this purpose pure toluene as solvent is necessary. This has a dramatic effect on the narrowing of particle size distribution and almost monodisperse colloids are obtained (some discussion of the probable mechanism of this remarkable digestive ripening step is given). These colloidal solutions have a great tendency to organize in two- and three-dimensional structures (nanocrystal superlattices, NCSs). We believe that this procedure provides a real opportunity to synthesize large amounts of gold nanocrystals as well as NCSs.     

In situ immobilizing of gold nanoparticles onto the surface of alumina particles

In this work, gold nanoparticles (AuNPs) were attached to the surface of alumina particles by an in situ immobilizing method. This modified colloidal deposition method allowed the immobilization of AuNPs with a much greater loading amount compared to the conventional one.     

Dense aqueous colloidal gold nanoparticles prepared from highly concentrated precursor solution

Gold nanoparticles were fabricated by reduction of highly concentrated Au(III) ions (200 mM) with casein proteins from milk. The gold nanoparticles were converted to nanoparticle-powders after washing and subsequent vacuum drying without aggregation. The nanoparticle-powders completely re-dispersed in aqueous solution, and stable colloidal gold nanoparticles were obtained. UV-vis extinction spectra and dynamic light scattering (DLS) measurements revealed that large assemblies (size, ca. 3 μm) and subaggregates (size, <0.5 μm) composed of gold nanoparticle-casein protein chain-Au(III) ion were dynamically formed and disintegrated over the course of the growth of the gold nanoparticles. Fourier transform infrared (FT-IR) spectra indicated conformational changes of casein proteins induced by the interaction of casein protein-Au(III) ion and -gold nanoparticle. Finally, rapid, one-pot, and highly concentrated synthetic procedures of gold and silver nanoparticle powders protected by casein (mean diameters below 10 nm) were successfully developed using 3-amino-1-propanol aqueous solutions as reaction media. Dense colloidal gold (40 g L(-1)) and silver (22 g L(-1)) nanoparticle aqueous solutions were obtained by re-dispersing the metal nanoparticle powders.     

Novel and simple route to fabricate 2D ordered gold nanobowl arrays based on 3D colloidal crystals

In this study, we present a new method to fabricate large-area two-dimensionally (2D) ordered gold nanobowl arrays based on 3D colloidal crystals by wet chemosynthesis, which combines the advantages of a very simple preparation and an applicability to "real" nanomaterials. By combination of in situ growth of gold nanoshell (GNSs) arrays based on three-dimensional (3D) colloidal silica crystals, a monolayer ordered reversed GNS array (2D ordered GNS array) was conveniently manufactured by an acrylic ester modified biaxial oriented polypropylene (BOPP). 2D ordered gold nanobowl array with adjustable periodic holes, good stability, reproducibility, and repeatability could be obtained when the silica core was etched by HF solution. The surface-enhanced Raman scattering (SERS) enhancement factor (EF) of this 2D ordered gold nanobowl array could reach 1.27 × 10(7), which shows high SERS enhancing activity and can be used as a universal SERS substrate.     

Dynamics of Arabidopsis thaliana soluble proteome in response to different nutrient culture conditions

In an effort to determine the best extraction procedure compatible with the high-reproducible 2-DE, different methods of soluble protein extraction from Arabidopsis cell culture suspensions grown in Gamborg B5 medium were tested. A reference 2-DE map was established for this soluble extract revealing 1184 spots. The most abundant protein spots were excised, trypsin-digested, and mass spectra obtained via MALDI-TOF and/or LC coupled to ESI-MS. Three hundred and thirty one proteins were identified and their functions were defined based on sequence comparisons and classified in different protein families. In order to analyze the impact of culture medium on the Arabidopsis proteome, we performed the 2-DE map from Arabidopsis cell suspensions cultured in another growth medium Murashige and Skoog (M-S) and 327 major spots were identified. Using PDQuest imaging analysis, significant increases in the amount of several housekeeping enzymes, stress/defense proteins, and heat shock proteins were found in M-S medium. Modified expression of certain proteins and detection of new isoforms involved in nitrate assimilation, nitrogen, and sulfur metabolism were also observed in the M-S medium. This study provides the first 2-DE maps of the soluble proteome of Arabidopsis cell suspensions. The comparative analysis of the Arabidopsis proteome in respect to different nutrient supplies shows that the culture medium may significantly influence the expression pattern of major soluble proteins in Arabidopsis cells. This work also constitutes an important step for further proteomic analysis concerning cell responses to abiotic or biotic stresses.