Showing papers on "Gel electrophoresis published in 2009"

Detergent binding explains anomalous SDS-PAGE migration of membrane proteins

Abstract: Migration on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) that does not correlate with formula molecular weights, termed “gel shifting,” appears to be common for membrane proteins but has yet to be conclusively explained. In the present work, we investigate the anomalous gel mobility of helical membrane proteins using a library of wild-type and mutant helix-loop-helix (“hairpin”) sequences derived from transmembrane segments 3 and 4 of the human cystic fibrosis transmembrane conductance regulator (CFTR), including disease-phenotypic residue substitutions. We find that these hairpins migrate at rates of −10% to +30% vs. their actual formula weights on SDS-PAGE and load detergent at ratios ranging from 3.4–10 g SDS/g protein. We additionally demonstrate that mutant gel shifts strongly correlate with changes in hairpin SDS loading capacity (R2 = 0.8), and with hairpin helicity (R2 = 0.9), indicating that gel shift behavior originates in altered detergent binding. In some cases, this differential solvation by SDS may result from replacing protein-detergent contacts with protein-protein contacts, implying that detergent binding and folding are intimately linked. The CF-phenotypic V232D mutant included in our library may thus disrupt CFTR function via altered protein-lipid interactions. The observed interdependence between hairpin migration, SDS aggregation number, and conformation additionally suggests that detergent binding may provide a rapid and economical screen for identifying membrane proteins with robust tertiary and/or quaternary structures.

Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots

Abstract: White lupin (Lupinus albus L.) roots efficiently take up and accumulate (heavy) metals, adapt to phosphate deficiency by forming cluster roots, and secrete antimicrobial prenylated isoflavones during development. Genomic and proteomic approaches were applied to identify candidate genes and proteins involved in antimicrobial defense and (heavy) metal uptake and translocation. A cDNA library was constructed from roots of white lupin seedlings. Eight thousand clones were randomly sequenced and assembled into 2,455 unigenes, which were annotated based on homologous matches in the NCBInr protein database. A reference map of developing white lupin root proteins was established through 2-D gel electrophoresis and peptide mass fingerprinting. High quality peptide mass spectra were obtained for 170 proteins. Microsomal membrane proteins were separated by 1-D gel electrophoresis and identified by LC-MS/MS. A total of 74 proteins were putatively identified by the peptide mass fingerprinting and the LC-MS/MS methods. Genomic and proteomic analyses identified candidate genes and proteins encoding metal binding and/or transport proteins, transcription factors, ABC transporters and phenylpropanoid biosynthetic enzymes. The combined EST and protein datasets will facilitate the understanding of white lupin's response to biotic and abiotic stresses and its utility for phytoremediation. The root ESTs provided 82 perfect simple sequence repeat (SSR) markers with potential utility in breeding white lupin for enhanced agronomic traits.

Isolation and characterization of a tumor necrosis factor binding protein from urine.

Abstract: Tumor necrosis factor (TNF)/cachectin can produce both beneficial and harmful manifestations. Mechanisms may operate to counteract potentially harmful effects such as shock and cachexia. The TNF binding protein (TNF-BP), which is found at increased levels in serum and urine of patients with chronic renal failure, may play such a role. TNF-BP was purified 1,000,000-fold to homogeneity from urine of patients with chronic renal failure by use of ion exchange chromatography, affinity chromatography on TNF-Sepharose and reverse phase chromatography. The purified protein contained only one chain with an apparent Mr on sodium dodecyl sulfate-polyacrylamide gel electrophoresis of 30,000. The aminoterminal amino acid sequence D-S-V-X-P-Q-G-K-Y-I-H-P-Q-V-N-S-I-X-K-T revealed no significant homologies with previously described protein sequences. TNF-BP may act as a regulator of the bioactivities of TNF/cachectin.

Horizontal polyacrylamide gradient gel electrophoresis for the simultaneous phenotyping of transferrin, post-transferrin, albumin and post-albumin in the blood plasma of cattle.

Abstract: Summary A simple method of horizontal polyacrylamide gel electrophoresis was described for the simultaneous phenotyping of transferrin, post-transferrin, albumin and post-albumin in the blood plasma of cattle. A step gradient gel of 8, 4, 12 and 14 % acrylamide concentration was used. The method enabled the detection of a new protein polymorphism in the post-transferrin region. Two alleles were observed. The transferrin phenotypes involving D1 and D2 alleles were clearly separated. The resolution of the post-albumin fractions was also better than described by earlier methods.

Oxidative modifications of glyceraldehyde-3-phosphate dehydrogenase play a key role in its multiple cellular functions.

Abstract: Knowledge of the cellular targets of ROS (reactive oxygen species) and their regulation is an essential prerequisite for understanding ROS-mediated signalling. GAPDH (glyceraldehyde-3-phosphate dehydrogenase) is known as a major target protein in oxidative stresses and becomes thiolated in its active site. However, the molecular and functional changes of oxidized GAPDH, the inactive form, have not yet been characterized. To examine the modifications of GAPDH under oxidative stress, we separated the oxidation products by two-dimensional gel electrophoresis and identified them using nanoLC-ESI-q-TOF MS/MS (nano column liquid chromatography coupled to electrospray ionization quadrupole time-of-flight tandem MS). Intracellular GAPDH subjected to oxidative stress separated into multiple acidic spots on two-dimensional gel electrophoresis and were identified as cysteine disulfide and cysteic acids on Cys152 in the active site. We identified the interacting proteins of oxidized inactive GAPDH as p54nrb (54 kDa nuclear RNA-binding protein) and PSF (polypyrimidine tract-binding protein-associated splicing factor), both of which are known to exist as heterodimers and bind to RNA and DNA. Interaction between oxidized GAPDH and p54nrb was abolished upon expression of the GAPDH active site mutant C152S. The C-terminal of p54nrb binds to GAPDH in the cytosol in a manner dependent on the dose of hydrogen peroxide. The GAPDH-p54nrb complex enhances the intrinsic topoisomerase I activation by p54nrb-PSF binding. These results suggest that GAPDH exerts other functions beyond glycolysis, and that oxidatively modified GAPDH regulates its cellular functions by changing its interacting proteins, i.e. the RNA splicing by interacting with the p54nrb-PSF complex.

The calcium oxalate crystal growth inhibitor protein produced by mouse kidney cortical cells in culture is osteopontin.

Abstract: Urine contains proteins that inhibit the growth of calcium oxalate (CaOx) crystals and may prevent the formation of kidney stones. We have identified a potent crystal growth inhibitor in the conditioned media from primary cultures of mouse kidney cortical cells. Conditioned media, incubated with the kidney cells for 6-72 h, was assayed for crystal growth inhibition; inhibitory activity increased 15-fold by 24 h. Inhibitory activity was purified from serum-free media containing proteinase inhibitors using anion-exchange and gel-filtration chromatography. A single band of molecular weight 80,000 daltons was seen after SDS-polyacrylamide gel electrophoresis. The sequence of the N-terminal 21 amino acids of this protein matched that of osteopontin (OP), a phosphoprotein initially isolated from bone matrix. Antisera raised to fusion proteins produced by plasmids containing the N-terminal or C-terminal portions of OP cDNA also cross-reacted with the protein purified from cell culture media on western blots. The effect of the purified protein on the growth of CaOx crystals was measured using a constant composition assay. A 50% inhibition of growth occurred at a protein concentration of 0.85 micrograms/ml, and the dissociation constant of the protein with respect to CaOx crystal was 3.7 x 10(-8) M. The concentration of OP in mouse urine, measured using antibodies raised to the purified protein, was approximately 8 micrograms/ml. We conclude that OP is synthesized by kidney cortical tubule cells and functions as a crystal growth inhibitory protein in urine.

Membrane-associated, boron-interacting proteins isolated by boronate affinity chromatography.

Abstract: Boron deficiency symptoms point to a role for boron in plant membranes, but the molecular partners interacting with boron have not yet been identified. The objective of the present study was to isolate and identify membrane-associated proteins with an ability to interact with boron. Boron-interacting proteins were isolated from root microsomal preparations of arabidopsis (Arabidopsis thaliana) and maize (Zea mays) using phenylboronate affinity chromatography, subsequently separated by two-dimensional gel electrophoresis and identified using MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) peptide mass fingerprinting. Twenty-six boron-binding membrane-associated proteins were identified in A. thaliana, and nine in Z. mays roots. Additional unidentified proteins were also present. Common to both species were the beta-subunit of mitochondrial ATP synthase, several beta-glucosidases, a luminal-binding protein and fructose bisphosphate aldolase. In A. thaliana, binding of these proteins to boron was significantly reduced after 4 d of boron deprivation. The relatively high number of diverse proteins identified as boron interacting, many of which are usually enriched in membrane microdomains, supports the hypothesis that boron plays a role in plant membranes by cross-linking glycoproteins, and may be involved in their recruitment to membrane microdomains.

Proteomic Analysis of the Luteal Endometrial Secretome

Abstract: Endometrium attains a secretory architecture in preparation for embryo implantation, but the identity of most endometrial secretory products remains unknown. Our objective was to characterize the endometrial secretome and compare protein expression between prereceptive (luteinizing hormone [LH]+4) and receptive (LH+9) phase endometrium. Endometrial lavage was performed in 11 participants and analyzed by difference gel electrophoresis (DIGE). LH+4 and LH+9 specimens were labeled with cyanine fluorescent dyes Cy3 and Cy5 tags, respectively, and combined. Proteins were separated using 2-dimensional gel electrophoresis, isolated, trypsin-digested, and subjected to mass spectrometry. In all, 152 proteins were identified; 82 were differentially expressed. Most proteins with increased expression on LH+9 functioned in host defense, while proteins with decreased expression had many functions. A total of 14 proteins had changes suggesting altered posttranslational modification. This article describes the first application of proteomic analysis to endometrial secretions, allowing identification of novel endometrial proteins as well as those differentially secreted in prereceptive and receptive phases.

Power and limitations of electrophoretic separations in proteomics strategies

Abstract: Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed.

Denaturing Urea Polyacrylamide Gel Electrophoresis (Urea PAGE)

Abstract: Urea PAGE or denaturing urea polyacrylamide gel electrophoresis employs 6-8 M urea, which denatures secondary DNA or RNA structures and is used for their separation in a polyacrylamide gel matrix based on the molecular weight. Fragments between 2 to 500 bases, with length differences as small as a single nucleotide, can be separated using this method(1). The migration of the sample is dependent on the chosen acrylamide concentration. A higher percentage of polyacrylamide resolves lower molecular weight fragments. The combination of urea and temperatures of 45-55 degrees C during the gel run allows for the separation of unstructured DNA or RNA molecules. In general this method is required to analyze or purify single stranded DNA or RNA fragments, such as synthesized or labeled oligonucleotides or products from enzymatic cleavage reactions. In this video article we show how to prepare and run the denaturing urea polyacrylamide gels. Technical tips are included, in addition to the original protocol (1,2).

The proteome of the presynaptic active zone: from docked synaptic vesicles to adhesion molecules and maxi-channels.

Abstract: The presynaptic proteome controls neurotransmitter release and the short and long term structural and functional dynamics of the nerve terminal. Using a monoclonal antibody against synaptic vesicle protein 2 we immunopurified a presynaptic compartment containing the active zone with synaptic vesicles docked to the presynaptic plasma membrane as well as elements of the presynaptic cytomatrix. Individual protein bands separated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis were subjected to nanoscale-liquid chromatography electrospray ionization-tandem mass spectrometry. Combining this method with 2-dimensional benzyldimethyl-n-hexadecylammonium chloride/sodium dodecyl sulfate-polyacrylamide gel electrophoresis and matrix-assisted laser desorption ionization time of flight and immunodetection we identified 240 proteins comprising synaptic vesicle proteins, components of the presynaptic fusion and retrieval machinery, proteins involved in intracellular signal transduction, a large variety of adhesion molecules and proteins potentially involved in regulating the functional and structural dynamics of the pre-synapse. Four maxi-channels, three isoforms of voltage-dependent anion channels and the tweety homolog 1 were co-isolated with the docked synaptic vesicles. As revealed by in situ hybridization, tweety homolog 1 reveals a distinct expression pattern in the rodent brain. Our results add novel information to the proteome of the presynaptic active zone and suggest that in particular proteins potentially involved in the short and long term structural modulation of the mature presynaptic compartment deserve further detailed analysis.

Purification and characterization of eosinophil cationic protein from normal human eosinophils.

Abstract: ECP (eosinophil cationic protein) was purified in high yield from the granules of human buffy coat eosinophils obtained from healthy individuals. The separation procedure included gel filtration on Sephadex G-75, ion-exchange chromatography on Bio Rex 70, and chelating chromatography on zinc-chelate Sepharose 6B. The normal ECP is a single-chain, highly cationic glycoprotein which separates on SDS-polyacrylamide gel electrophoresis into at least 3 molecular weight forms, with molecular weights of 18.5, 20 and 22 kDa. A heterogeneity in charge was also observed, with the 18.5 kDa form being the most cationic one. The various molecular species of ECP exhibited antigenic identity, identical amino acid compositions, and identical amino-terminal amino acid sequences. The molecular heterogeneity was shown to be caused by differences in glycosylation of the protein.

Optimization and validation of multi-coloured capillary electrophoresis for genotyping of Plasmodium falciparum merozoite surface proteins (msp1 and 2).

Abstract: Genotyping of Plasmodium falciparum based on PCR amplification of the polymorphic genes encoding the merozoite surface proteins 1 and 2 (msp1 and msp2) is well established in the field of malaria research to determine the number and types of concurrent clones in an infection. Genotyping is regarded essential in anti-malarial drug trials to define treatment outcome, by distinguishing recrudescent parasites from new infections. Because of the limitations in specificity and resolution of gel electrophoresis used for fragment analysis in most genotyping assays it became necessary to improve the methodology. An alternative technique for fragment analysis is capillary electrophoresis (CE) performed using automated DNA sequencers. Here, one of the most widely-used protocols for genotyping of P. falciparum msp1 and msp2 has been adapted to the CE technique. The protocol and optimization process as well as the potentials and limitations of the technique in molecular epidemiology studies and anti-malarial drug trials are reported. The original genotyping assay was adapted by fluorescent labeling of the msp1 and msp2 allelic type specific primers in the nested PCR and analysis of the final PCR products in a DNA sequencer. A substantial optimization of the fluorescent assay was performed. The CE method was validated using known mixtures of laboratory lines and field samples from Ghana and Tanzania, and compared to the original PCR assay with gel electrophoresis. The CE-based method showed high precision and reproducibility in determining fragment size (< 1 bp). More genotypes were detected in mixtures of laboratory lines and blood samples from malaria infected children, compared to gel electrophoresis. The capacity to distinguish recrudescent parasites from new infections in an anti-malarial drug trial was similar by both methods, resulting in the same outcome classification, however with more precise determination by CE. The improved resolution and reproducibility of CE in fragment sizing allows for comparison of alleles between separate runs and determination of allele frequencies in a population. The more detailed characterization of individual msp1 and msp2 genotypes may contribute to improved assessments in anti-malarial drug trials and to a further understanding of the molecular epidemiology of these polymorphic P. falciparum antigens.

Microfluidic polyacrylamide gel electrophoresis with in situ immunoblotting for native protein analysis.

Abstract: We introduce an automated immunoblotting method that reports protein electrophoretic mobility and identity in a single streamlined microfluidic assay. Native polyacrylamide gel electrophoresis (PAGE) was integrated with subsequent in situ immunoblotting. Integration of three PA gel elements into a glass microfluidic chip achieved multiple functions, including (1) rapid protein separation via on-chip PAGE, (2) directed electrophoretic transfer of resolved protein peaks to an in-line blotting membrane, and (3) high-efficiency identification of the transferred proteins using antibody-functionalized blotting membranes. In-chip blotting membranes were photopatterned with biotinylated antibody using streptavidin polyacrylamide (PA) thus yielding postseparation sample analysis. No pressure driven flow or fluid valving was required, as the assay was operated by electrokinetically programmed control. A model sample of fluorescently labeled BSA (negative control), α-actinin, and prostate specific antigen (PSA) was ...

Tartrate-resistant acid phosphatase from human bone: Purification and development of an immunoassay

Abstract: Tartrate-resistant acid phosphatase (TRAP) was purified 20,000-fold to apparent homogeneity from human bone. The purified enzyme consisted of one 32 kd subunit, which was cleaved by β-mercaptoethanol into two subunits of 15 kd and 20 kd, as shown by sodium dodecyl sulfide-polyacrylamide gel electrophoresis (SDS-PAGE) and silver staining. The purified enzyme was identified by N-terminal amino acid sequencing, and it was shown to be homologous with previously purified TRAPs from other sources. We developed a polyclonal antiserum against the purified enzyme in mice. In immunohistochemistry, the antiserum recognized osteoclasts from human bone and alveolar macrophages from human lung tissue, but no cells from human spleen tissue. It also stained osteoclasts from rat bone cells cultured on bovine bone slices. Purified TRAP could be inhibited by vanadate and molybdate, but not by tartrate, and it was activated 2-fold by β-mercaptoethanol. The glycoprotein structure of human bone TRAP was analyzed, and it was shown to contain only high-mannose type carbohydrates. We used the polyclonal antibody to develop a competitive fluorescence immunoassay for measuring serum TRAP concentrations. According to the assay, children have higher serum TRAP concentrations than adults, and postmenopausal women have higher concentrations than premenopausal women. Postmenopausal women also have higher serum TRAP concentrations than postmenopausal women on estrogen replacement therapy.

Structural characterization of heat-induced protein particles in soy milk.

Abstract: This study analyzed the aggregation mode of polypeptides in protein particles of soy milk by using ultracentrifugation, gel filtration, and sodium dodecyl sulfate−polyacrylamide gel electrophoresis...

Developing rice embryo proteomics reveals essential role for embryonic proteins in regulation of seed germination.

Abstract: Two-dimensional gel electrophoresis (2-DGE) in conjunction with mass spectrometry was utilized to unravel the changes in embryo proteins of geminating rice seeds. For this purpose, the embryos were dissected at 1 and 2 days after imbibition and germination of mature dry seeds. Proteins were extracted and their expression patterns were analyzed by large-format 2-DGE. A total of 642 silver nitrate stained protein spots were detected on 2-D gels, subjected to image analysis using the ImageMaster 6.0 2D Platinum software, resulting in the identification of 109 differentially expressed protein spots compared with imbibed seeds. MALDI-TOF-MS analysis resulted in the identification of 60 proteins, including 6 redundant and 54 nonredundant proteins. The identified proteins were classified according to their functional groups: metabolism (15 spots), oxygen-detoxifying (11 spots), protein processing/degradation (8 spots), stress/defense (5 spots), and energy (3 spots). Northern blot analysis demonstrated a good cor...

Diamide Triggers Mainly S Thiolations in the Cytoplasmic Proteomes of Bacillus subtilis and Staphylococcus aureus

Abstract: Glutathione constitutes a key player in the thiol redox buffer in many organisms. However, the gram-positive bacteria Bacillus subtilis and Staphylococcus aureus lack this low-molecular-weight thiol. Recently, we identified S-cysteinylated proteins in B. subtilis after treatment of cells with the disulfide-generating electrophile diamide. S cysteinylation is thought to protect protein thiols against irreversible oxidation to sulfinic and sulfonic acids. Here we show that S thiolation occurs also in S. aureus proteins after exposure to diamide. We further analyzed the formation of inter- and intramolecular disulfide bonds in cytoplasmic proteins using diagonal nonreducing/reducing sodium dodecyl sulfate gel electrophoresis. However, only a few proteins were identified that form inter- or intramolecular disulfide bonds under control and diamide stress conditions in B. subtilis and S. aureus . Depletion of the cysteine pool was concomitantly measured in B. subtilis using a metabolomics approach. Thus, the majority of reversible thiol modifications that were previously detected by two-dimensional gel fluorescence-based thiol modification assay are most likely based on S thiolations. Finally, we found that a glutathione-producing B. subtilis strain which expresses the Listeria monocytogenes gshF gene did not show enhanced oxidative stress resistance compared to the wild type.

Specific adsorption of some complement activation proteins to polysulfone dialysis membranes during

Abstract: Dialyser bioincompatibility is an important factor contributing to complications of hemodialysis with well known systemic consequences. Here we studied the local processes that occur on dialysis membranes by eluting proteins adsorbed to the polysulfone dialyser membranes of 5 patients after 3 consecutive routine maintenance hemodialysis sessions. At the end of each procedure, a plasma sample was also collected. These eluates and their accompanying plasma samples were separated by 2-dimensional gel electrophoresis, and all proteins that were present in all patients were analyzed by tandem mass spectrometry and a ratio of the relative spot intensity of the eluate to plasma ratio was calculated. Out of 153 proteins detected, 84 were found in all patients, 57 of which were successfully identified by mass spectrometry as 38 components of 23 unique proteins. In 10 spots the relative eluate intensity differed significantly from that in the plasma implying preferential adsorption. These proteins included ficolin-2, clusterin, complement C3c fragment and apolipoprotein A1. Our finding of a selective binding of ficolin-2 to polysulfone membranes suggests a possible role of the lectin complement pathway in blood-dialyser interactions.

Characterization of a collagenous cementum-derived attachment protein

Abstract: We report further characterization of a cementum-derived protein that promotes the adhesion and spreading of periodontal cells. The cementum attachment protein (CAP) was extracted from bovine cementum, separated by diethylamino ethyl (DEAE)-cellulose chromatography, and purified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and C18 reverse phase high performance liquid chromatography. The purified preparation contained a single protein band migrating with M(r) 56,000. It did not cross-react with polyclonal antibodies to osteopontin, vitronectin, or other attachment proteins. The attachment activity was resistant to chondroitinase ABC digestion. An internal amino acid sequence of six peptides was determined by microsequencing, and the peptide sequences were not present in other attachment proteins described in cementum. Four sequences contained Gly-X-Y repeats typical of collagen helix. One 17 amino acid peptide had 82% homology with a type XII collagen domain. However, bovine type XII collagen did not promote fibroblast attachment. Although another 19-amino-acid-long peptide had 95% homology to bovine alpha 1 [I], two other peptides were only 74% and 68% homologous, and the CAP was not recognized by anti-type I collagen antibody. The attachment activity of CAP was susceptible to bacterial collagenase. The CAP did not cross-react with antibodies to type V, XII, and XIV collagens. These data and our previous immunostaining data indicate that the CAP is not related to other collagens or attachment proteins and that it is a collagenous attachment protein localized in cementum.

Specific cleavage of histidine-containing peptides by copper (II)

Abstract: Copper(II) cleaves with moderate specificity peptides containing Ser-His or Thr-His sequences, at the N-terminal side of the hydroxyaminoacyl residue. The reaction is slow, and is first-order in peptide: CuII complex, with a half-life of several hours at 62 degrees C in sodium bicarbonate buffer, pH 8. Cleavage of other histidine-containing peptides also occurs, at a rate around 10-100-fold less. EDTA completely quenches the cleavage. The reaction is stoichiometric in CuII and is inhibited by amine-containing buffer components; Tris at 19 mM inhibits cleavage by 50%. The reaction has a complex pH-dependence, being very slow below pH 5, and with rates increasing with pH from pH 7 to pH 9.5. Slower degradative side reactions do occur, with destruction of tyrosine residues, particularly in the presence of high concentrations of chloride ion, but the specific cleavage appears to be a hydrolysis, as determined by amino-acid analysis and mass spectrometry of the products. The cleavage is clearly different from the previously described oxidative degradation of proteins catalysed by copper ions. Cleavage of denatured IgG protein occurs with sufficient specificity to reveal distinct bands on SDS-polyacrylamide gel electrophoresis under reducing conditions.