Quantitation of electrophoretic eluted proteins

Quantitation of stained, electroeluted proteins by the classical Lowry and Bradford protein assay is not possible because of some different interferences. In particular we have found that the substance interfering in the Lowry method cannot be removed by trichloroacetic acid precipitation nor can be compensated for by the appropriate blank. Interferences in the Bradford protein assay are due to detergents and pH of the protein buffer as well as to Coomassie brilliant blue R250 electroeluted with the protein sample. However, while these interferences can be compensated for by appropriate blank and standard curves, others (probably due to acrylamide fines) cannot be corrected. All these problems can be overcome by concentration and dialysis of electroeluted samples which permit the removal of interfering substances and the use of Bradford and Lowry protein assay in the 1-20 micrograms range, respectively. Successful applications are described for electroeluted bovine serum albumin, human hexokinase and phosphoglucomutase.     

Mapping of fruit allergens by 2D electrophoresis and immunodetection

Proteomic analyses of fruits are confronted with a series of specific obstacles: a general low protein content in plant tissues, allergen extraction from highly complex matrices and protein determination in the presence of interfering compounds. Different methods are currently being introduced to achieve higher protein yields and a simultaneous removal of interfering substances, such as polyphenols and polysaccharides. However, no universal protocol suitable for protein purification from any given plant species is available. Protein profiling by 2DE-western blotting offers a powerful tool for the detection and characterization of known and novel plant allergens. Moreover, the detection of IgE-reactive proteins from fruits is improved by combining western blot and alternative visualization techniques. The recent developments in bioinformatics and databases facilitate the interpretation of profiling studies with regard to novel potential fruit allergens.     

Mapping of fruit allergens by 2D electrophoresis and immunodetection

Proteomic analyses of fruits are confronted with a series of specific obstacles: a general low protein content in plant tissues, allergen extraction from highly complex matrices and protein determination in the presence of interfering compounds. Different methods are currently being introduced to achieve higher protein yields and a simultaneous removal of interfering substances, such as polyphenols and polysaccharides. However, no universal protocol suitable for protein purification from any given plant species is available. Protein profiling by 2DE-western blotting offers a powerful tool for the detection and characterization of known and novel plant allergens. Moreover, the detection of IgE-reactive proteins from fruits is improved by combining western blot and alternative visualization techniques. The recent developments in bioinformatics and databases facilitate the interpretation of profiling studies with regard to novel potential fruit allergens.     

Peptide production from proteins separated by sodium dodecyl-sulfate polyacrylamide gel electrophoresis

The development of amino acid sequencers with subnanomolar sensitivities has increased the need for both selective and highly efficient methods for both protein and peptide isolation. In this paper, we describe a simple procedure that utilizes the high resolving capacity of polyacrylamide gel electrophoresis to isolate a single target polypeptide, which can subsequently be subjected to proteolytic digestion and sequencing. Polypeptides are visualized in polyacrylamide gels as dodecyl sulfate/protein complexes, which are passively diffused from gel slices. Free dodecyl sulfate eluted with the protein solution is removed by KCl precipitation, allowing protein digestion with small amounts of trypsin or other proteolytic enzymes. Following enzymatic digestion, the peptide solution is made 6 M guanidine-HCl to remove interfering contaminants and thereby improve resolution of the digest by reverse-phase high-performance liquid chromatography. The peptides generated by this method are suitable for amino acid sequencing with good overall yields, averaging 15-30% on a gas-phase sequenator. The method described is useful for obtaining multiple peptide sequences from a single polypeptide isolated from a complex protein mixture.     

Precipitation of dilute chromatographic samples (ng/ml) containing interfering substances for SDS-PAGE

SDS-PAGE of chromatographic fractions requires prior removal of salts, detergents, denaturants, or organic solvents which may perturb the electrophoretic separation. Likewise, to successfully visualize minute amounts of protein present in chromatographic fractions, they must often be concentrated before analysis by SDS-PAGE. In this study, we used a dye precipitation procedure for simultaneous removal of interfering substances and concentration of dilute samples (ng/ml) before analysis by SDS-PAGE. Nanogram amounts of protein (143 ng) were effectively precipitated with a pyrogallol red-molybdate reagent from commonly used chromatographic buffers containing various interfering solutes or solvents. Proteins were successfully precipitated from solution in the presence of organic solvents (acetonitrile, methanol, 2-propanol), chaotropic agents (6 M urea, 6 M guanidine-HCl), a protein stabilizer (40% sucrose), metal chelators (30 mM EDTA and 30 mM EGTA), or high salt (1.0 M NaCl). Detergents, at concentrations up to twice their critical micelle concentrations, from the nonionic class (Triton X-100, Tween 20) or from the zwitterionic class (3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate) did not inhibit protein precipitation. Some interference was observed when proteins were precipitated in the presence of ammonium sulfate (0. 5-2.0 M). Proteins did not precipitate in the presence of ionic detergents (SDS and cetyltrimethylammonium bromide). The sensitivity of the combined pyrogallol red-molybdate precipitation/SDS-PAGE procedure is approximately 7 ng. Two other methods of precipitating proteins (trichloroacetic acid and phenol-ether) both exhibited varying degrees of effectiveness, ranging from 714 to 7 ng/ml, in the precipitation of individual proteins. In summary, the pyrogallol red-molybdate protein precipitation procedure facilitates the SDS-PAGE analysis of dilute protein samples (ng/ml) from chromatographic fractions of various compositions. The method is useful for rapid pilot-scale protein fractionation and facilitates the ongoing propensity of researchers to work with minuscule amounts of protein.     

Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation

The mRNA-cleavage step of RNA interference is mediated by an endonuclease, Argonaute2 (Ago2), within the RNA-induced silencing complex (RISC). Ago2 uses one strand of the small interfering (si) RNA duplex as a guide to find messenger RNAs containing complementary sequences and cleaves the phosphodiester backbone at a specific site measured from the guide strand's 5' end. Here, we show that both strands of siRNA get loaded onto Ago2 protein in Drosophila S2 cell extracts. The anti-guide strand behaves as a RISC substrate and is cleaved by Ago2. This cleavage event is important for the removal of the anti-guide strand from Ago2 protein and activation of RISC.     

Specific measurement of DNA in nuclei and nucleic acids using diaminobenzoic acid

The diaminobenzoic acid (DABA) reaction with DNA, first described by Kissane and Robbins (J. M. Kissane and E. Robbins, 1958, J. Biol. Chem.233, 184–188) and variously modified, was reinvestigated and applied to the measurement of submicrogram quantities of DNA in nuclear fractions and nucleic acid preparations. The reaction conditions were optimized using a small volume of DABA. This method measures 0.1 μg of DNA with a fluorescence twice that of background and is linear to 10 μg of DNA. DABA yeilds a 1000-fold higher fluorescence with DNA compared with RNA, protein, and polysaccharides, and 0.1 μg of DNA is detectable in the presence of 200 μg of RNA or protein. The method is useful for detecting contaminating DNA in RNA preparations prior to hybridization. A simple procedure using ethanol precipitation was developed for removal of common interfering reagents such as sucrose, glycerol, salts, and Triton X-100. Nuclei isolated using detergents and assayed by this method are also free of measurable interfering lipids.     

橡胶树胶乳C-乳清双向电泳样品制备技术的建立及优化

在TCA/丙酮沉淀法的基础上,用乙醇和乙醚洗涤（称双乙法）沉淀获得橡胶树胶乳C-乳清蛋白样品,并在样品溶解时通过超声助溶进一步提高样品的溶解度。结果显示,利用改良后的样品制备方法（TCA/丙酮+双乙法+超声处理）所获得的C-乳清蛋白样品的溶解性大幅增加,蛋白得率高达8.47 mg/mL C-乳清,为传统TCA/丙酮法的1.6倍;同时降低了盐离子浓度,等电聚焦时升压顺利、聚焦完全,双向电泳的图谱质量明显改善,在银染2D胶上可获得1 206个蛋白点,为传统TCA/丙酮法的2.7倍。本文对胶乳C-乳清蛋白样品制备方法进行深入优化,获得了重现性较好的高质量双向电泳蛋白图谱,促进了橡胶树蛋白质组学研究。     

Development and optimization of two-dimensional-electrophoresis protocol ofLeptospirillum ferriphilum

Leptospirillum ferriphilum is important in bioleaching, in which process it is often under heavy stresses of heavy metal ions and high oxidation reduction potential (ORP). Two-dimensional-electrophoresis (2-DE) and comparative proteomic analysis are useful to investigate the responses ofL. ferriphilum to environmental stresses. But, 2-DE analysis forL. ferriphilum is not successful as the samples ofL. ferriphilum contain low protein concentration, complex composition, high salt concentration, and many other interfering components, which make it difficult for 2-DE analysis. In this research, optimizations on the sample preparation and purification methods, sample volume, sample loading methods for isoelectric focusing (IEF), and gel visualization methods were made. More than 629 Coomassie stained spots in single gel were obtained. The image quality and protein concentration in most of the spots met the requirements for both differential spots analysis and mass-spectrum analysis. The 2-DE protocol forL. ferriphilum was successfully developed for the first time.     

Assay of protein in the presence of high concentrations of sulfhydryl compounds

A simple procedure is described for removal of Triton X-100 from protein samples by adsorption of the detergent on a commercial copolymer in bead form. The concentration of detergent can be lowered to approximately 0.01% with no loss or dilution of protein.     

Protein assay in the microgram range: modifications of the Hiraoka-Glick method

A method is described for the accurate estimation of protein samples ranging in size from 1 to 100 μg. It is based on fluorescence quenching of eosin Y by protein and modifies a method originally published by Hiraoka and Glick. The modified method is convenient to use. It is carried out with a stabilized reagent in cuvettes of standard size and permits the estimation of 5 μg or less of protein with precision of ± 9%. The measurements are shown to be sensitive to slight variations in ambient temperature and these contribute at least 3% to the error term shown. A graphical manner of presenting the data has been devised that provides a linear relationship over nearly 50-fold range of protein concentrations. Quenching is unaffected by presence of glucose or urea and partially inhibited by glycine or mercaptoethanol only if these are present in better than 100-fold excess over protein. Different proteins show different degrees of quenching and the method is thus most suitable for comparing quantitatively protein mixtures of similar composition. The modified method should be useful not only where microgram quantities of protein must be measured, but also with automated equipment or in cases where the Folin-Ciocalteau method cannot be employed due to presence of interfering substances.     

Preparation of Solid-Phase Immunosorbents by Coupling Human Serum Proteins to Cyanogen Bromide-Activated Agarose

The method of preparing solid-phase immunosorbents by covalently attaching proteins from whole human serum to cyanogen bromide-activated agarose has been investigated to determine optimum concentrations of cyanogen bromide and protein, and the optimum pH for the maximum attachment of proteins from serum. Two systems in which the above immunosorbents have proved useful are described: the removal of antibodies to normal serum proteins from anti-hepatitis B serum and the removal of light chain antibodies from anti-human immunoglobulin M serum.     

A biological assay technique for the assessment and comparison of systemic insecticide residues

A technique is described using mortality of aphids on excised leaf samples to assess residual systemic insecticides within the leaf or on its surface. Residues in crops or soil can also be assessed by keeping aphids on leaf samples treated with solvent extracts of contaminated material. Little or no pre-treatment for the removal of potentially interfering materials co-extracted from the crop is required. Comparison of mortalities caused by unknown residues with mortalities caused by known amounts of insecticide enables the technique to be used quantitatively. The sensitivity of the technique varies with the toxicity of the compound being assayed. With most of the insecticides tested, extract solutions down to about 10 ppm may be assessed directly; weaker solutions must first be concentrated.     

Determination of protein in extracts containing interfering substances and in radioactive samples following scintillation counting.

A method is described for determination of protein in biological preparations containing various interfering substances normally present in extraction media. The main steps of the procedure consist in depositing the protein solution on filter paper strips and removing all small molecular weight substances by washing with a number of aqueous and nonaqueous solvents. The protein remaining on the paper is then determined by a modification of Lowry's colorimetric procedure. The method also permits the determination of protein in radioactive samples which have been previously counted using a liquid scintillation mixture such as Apuasol or toluene-POPOP.     

A solid-phase method for the quantitation of protein in the presence of sodium dodecyl sulfate and other interfering substances

We describe a simple assay for small amounts of protein that is insensitive to sodium dodecyl sulfate (SDS) or many common interfering substances including Tris and reducing sugars. For this reason, it is particularly useful in the analysis of protein content of samples prior to SDS electrophoresis. The assay consists of the following steps: (i) absorption of protein to nitrocellulose; (ii) fixation of the bound protein with methanol; (iii) staining of the bound protein with amido black; and (iv) elution and spectrophotometric measurement of the bound dye. The assay is sensitive to as little as 0.5 microgram of protein in 1 microliter of solution. Although SDS does not interfere appreciably with measurement, Nonidet-P40 does.     

A silver-binding assay for measuring nanogram amounts of protein in solution

We recently reported a highly sensitive assay for measuring protein in solution based on the capacity of glutaraldehyde-treated protein to bind silver. This assay has now been made more sensitive, with a lower limit of detection of 5 ng, and more reproducible by supplementing protein samples with sodium dodecyl sulfate (SDS) to reduce protein loss to glassware. Two procedures have been developed. In one, protein samples are supplemented with both SDS and Tween 20 to yield very steep protein dose-response curves, which allow for more precise protein determinations, and very stable color formation, permitting OD measurements to be made several hours after the assay has been completed. In the second procedure, protein samples are supplemented with SDS alone which results in a less steep dose-response curve and less stable color formation but makes the assay substantially more tolerant of interfering substances. Thus, proteins in most commonly used buffers can be assayed directly with the second procedure without the need for buffer exchange. The procedure of choice, therefore, depends on the type and concentration of interfering substance. Proteins in buffers totally incompatible with either assay procedure (e.g., those containing reducing agents) can be easily buffer exchanged by centrifugation through 0.2% SDS equilibrated, drained Bio-Gel P-2 beads. The clinical utility of this improved assay is demonstrated by the accurate quantitation of protein in 0.5 μl of samples of human cerebral spinal fluid. This assay should therefore prove especially useful when a limited amount of protein is available for quantitation.     

A simple and rapid procedure for removal of triton X-100 from protein solution

A simple and rapid procedure for removal of Triton X-100 from protein solutions is described. The procedure is based on the extraction of Triton X-100 with chloroform from the protein solution. By the addition of sodium dodecyl sulfate before the extraction, the procedure was improved effectively and the sample thus prepared was used directly in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. This method can be used for the removal of other nonionic detergents and for samples of larger size.     

Nitrogenase from Bacillus polymyxa. Purification and properties of the component proteins.

A purification procedure is described for the components of Bacillus polymyxa nitrogenase. The procedure requires the removal of interfering mucopolysaccharides before the two nitrogenase proteins can be purified by the methods used with other nitrogenase components. The highest specific activities obtained were 2750 nmol C2H4 formed . min-1 . mg-1 MoFe protein and 2521 nmol C2H4 formed . min-1 . mg-1 Fe protein. The MoFe protein has a molecular weight of 215 000 and contains 2 molybdenum atoms, 33 iron atoms and 21 atoms of acid-labile sulfur per protein molecule. The Fe protein contains 3.2 iron atoms and 3.6 acid-labile sulfur atoms per molecule of 55 500 molecular weight. Each Fe protein binds two ATP molecules. The EPR spectra are similar to those of other nitrogenase proteins. MgATP changes the EPR of the Fe protein from a rhombic to an axial-type signal.     

Analysis of protein fragmentation inhibition by an MMP-inhibitor in an in vivo model of heart failure using automated chromatography

Proteomic strategies have continued to demonstrate value in studying disease by exploiting new technologies that can develop significant numbers of measurements from single samples. However, using complex samples such as tissues or blood has continued to be problematic due to the presence of major interfering substances. In this study, a process is described that uses denaturing peptide extraction from whole tissue and automated chromatography in order to allow subsequent analysis of more than 1000 tissue-derived peptides per sample. The process was employed to identify cardiac proteins that were spared degradation by administration of a heart-protecting matrix metalloproteinase (MMP) inhibitor (compound SC-621) following experimental myocardial infarction (MI). HPLC peptide fingerprints were developed from rat heart left ventricles and the resultant integrated peak data was compared across experimental animals. Surprisingly, although protein fragmentation was generally increased in MI hearts, the effect of the MMP inhibitor was only observed on a few species. The results from this study demonstrated that whole-tissue sample enrichment and peptide analysis using HPLC could be linked in order to study the effects of new compounds on a disease state. The system is flexible and amenable to improvements such as incorporating detection by mass spectrometry.     

Protein quantitation at the picomole level: an O-phthaldialdehyde-preTSK column-derivatization assay

A fluorescent protein assay was described wherein an isocratic high-performance liquid chromatography system was used to separate the o-phthaldialdehyde-derivatized proteins from interfering components. Using a small TSK guard column equilibrated in 0.1% sodium dodecyl sulfate, it was demonstrated that all proteins and peptides examined, containing more than 22 residues, coelute in the excluded volume and were resolved from fluorescent signals contributed by commonly used reagents. The assay was linear over a useful range of 3 ng to 1 microgram of protein and required less than 15 microliter of sample.