Iron-regulated proteins in Phanerochaete chrysosporium and Lentinula edodes: differential analysis by sodium dodecyl sulfate polyacrylamide gel electrophoresis and two-dimensional polyacrylamide gel electrophoresis profiles

Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis (2-DE) were used to identify iron-responsive proteins in the white-rot species (Phanerochaete chrysosporium and Lentinula edodes), by comparing the differential patterns of cellular and membrane proteins obtained from iron-sufficient and iron-deficient mycelia. Six cellular proteins induced by iron restriction have been observed in SDS-PAGE for P. chrysosporium and twelve for L. edodes. In 2-DE, the numbers of iron-restricted induced proteins were 12 and 9, respectively, in a resolution range of 15-60 kDa and pI 4.5-8.1. SDS-PAGE for the plasma membrane protein did not show differences, whereas the outer-membrane protein profile showed 6 and 5 proteins induced by iron depletion in P. chrysosporium and L. edodes, respectively. The results presented here are important data to unravel mechanisms of biosynthesis and/or transport of the iron-complexing agents in ligninolytic fungi and to further correlate them to the ligninolytic processes.     

Identification of unknown protein complex members by radiolocalization and analysis of low-abundance complexes resolved using native polyacrylamide gel electrophoresis

Identification of unknown binding partners of a protein of interest can be a difficult process. Current strategies to determine protein binding partners result in a high amount of false-positives, requiring use of several different methods to confirm the accuracy of the apparent association. We have developed and utilized a method that is reliable and easily substantiated. Complexes are isolated from cell extract after exposure to the radiolabeled protein of interest, followed by resolution on a native polyacrylamide gel. Native conformations are preserved, allowing the complex members to maintain associations. By radiolabeling the protein of interest, the complex can be easily identified at detection levels below the threshold of Serva Blue, Coomassie, and silver stains. The visualized radioactive band is analyzed by MS to identify binding partners, which can be subsequently verified by antibody shift and immunoprecipitation of the complex. By using this method we have successfully identified binding partners of two proteins that reside in different locations of a cellular organelle.     

Determination of protein spots separated by two-dimensional polyacrylamide gel electrophoresis

A simple method for quantitating proteins in the spots on two-dimensional polyacrylamide gel electropherograms is described. The system consists in three steps: (1) O'Farrell's two-dimensional gel electrophoresis of the proteins to be analysed; (2) staining of the gels with Coomassie brilliant blue; and (3) determination of the area and integrated density of the stained spots by the Joyce Loebl Magiscan-1 image analysis system. The method can be used for the determination of proteins in the range 0.5-100 micrograms/cm2; the amount of protein involved in most spots detected by the staining method actually falls within this range. As the minimum spot diameter that can easily be handled by the method is about 2 mm, as much as 30 ng of protein in such a spot can be determined. The method can also be applied to autoradiograms.     

Electrospray mass spectra from protein electroeluted from sodium dodecylsulfate polyacrylamide gel electrophoresis gels

Electrospray ionization/tandem mass spectrometry of proteins separated on sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) gels is severely limited by the requirement that the protein be completely separated from the SDS. As shown here, the gaseous noncovalent SDS adducts of protonated proteins thus formed can be dissociated by infrared irradiation. ESI spectra from myoglobin in SDS-containing solutions show molecular ions adducted with up to 15 dodecyl sulfates, but ir irradiation of these ions causes complete dissociation to expel the SDS.     

An improved sodium dodecyl sulfate-polyacrylamide gel electrophoresis system for the analysis of membrane protein complexes

Membrane protein complexes such as the reaction center complexes of oxygenic photosynthesis or the complex I of mitochondira are composed of many subunit polypeptides. To analyze their polypeptide compositions by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), a wide range of molecular sizes has to be resolved, especially in the low molecular mass range. We have improved the traditional Tris/HCI buffer systems adopting a Tris/2-(N-morpholino)ethanesulfonic acid (MES) buffer system containing 6 M urea. This gel system was used with an 18-24% acrylamide gradient for the separation of polypeptides with molecular masses from below 5 kDa to over 100 kDa. This buffer system can also be applied to the usual uniform concentration of acrylamide gel and also to minislab gels.     

Simultaneous immunoblotting analysis with activity gel electrophoresis in a single polyacrylamide gel

We describe here that a simple diffusion blotting method can couple immunoblotting analysis with another biochemical technique in a single polyacrylamide gel. The efficiency of protein transfer was evaluated by serial dilutions of nephrosin, a metalloproteinase of the astacin family, and by immunodetection. It is estimated that diffusion blotting produces 25-50% of the signal intensity compared to the classical electrophoretic transfer method. However, with diffusion blotting it is possible to generate several replicas from a single gel. In addition, a protein blot can be obtained from a sodium dodecyl sulfate (SDS)-polyacrylamide gel for zymography assay or from a native polyacrylamide gel for electrophoretic mobility shift assay (EMSA). In this regard, a particular signal in zymography or EMSA can be confirmed by simultaneous immunoblotting analysis with a corresponding antiserum. Therefore, diffusion blotting allows a direct comparison of signals between gels and replicas in zymography assay and EMSA. These advantages make diffusion blotting desirable when partial loss of transfer efficiency can be tolerated or be compensated by a more sensitive immunodetection reaction using enhanced chemiluminescence substrates.     

Study of complexes between lysozyme and sodium alkyl sulfates in the solid state

Complexes between lysozyme and sodium alkyl sulfates (decyl, dodecyl, tetradecyl and hexadecyl) in the solid state were prepared by mixing aqueous solutions of lysozyme and of the surfactant, separating the precipitated complex and purifying it. The stoichiometry of the complexes was investigated by elemental analysis and was found to correspond to about 8ǃ alkyl sulfate ions per lysozyme. Low- and wide-angle X-ray scattering were used to investigate the structure of the complexes. The scattering curves showed one fairly large scattering maximum, revealing a low state of organization of the complexes. The characteristic length characterizing the complexes was calculated from the value of the wave vector corresponding to the maximum of the scattered intensity. This length increased by about 0.233 nm per additional methylene group in the surfactant alkyl chain. A model where spherical aggregates of alkyl sulfate ions are arranged in a disordered simple cubic structure, dispersed in a matrix of lysozyme, provides a possible explanation of the results.     

Sequence analysis of proteins separated by polyacrylamide gel electrophoresis: towards an integrated protein database

Improved technologies or the synergistic use of complementary methods enhance the efficiency of research and permit the exploration of new approaches for the investigation of complex problems. High sensitivity protein sequence analysis and polyacrylamide gel electrophoresis are such complementary methods. Here we summarize the current status of high sensitivity sequence analysis of proteins separated in polyacrylamide gels and discuss strategies by which this technology can enhance biological research by generating new approaches for the solution of complex, multifacetted problems. Finally, we outline imminent technological advances in the area of high sensitivity protein sequence analysis and argue that further technological developments will ultimately lead to the generation of an integrated protein database (containing structural and functional as well as physiological information in an easily accessible form) of all the proteins separated by high resolution two-dimensional gel electrophoresis.     

Computer analysis of proteins separated by polyacrylamide gradient pore gel electrophoresis

A method for measuring lymph-to-plasma (L/P) protein concentration ratios obtained from protein fractions separated by polyacrylamide gradient gel electrophoresis is presented. A curve-fitting technique is used to decompose lymph and plasma electropherograms containing multiple components into individual components, eliminating protein-protein overlap regions. This allows the concentration of each component in the mixture to be measured accurately, yielding more precise estimates of L/P ratios. This technique consists of three phases. Individual electropherograms are constructed for proteins of various sizes by taking a weighted average of measured electropherograms obtained from the two protein standards closest in size to the protein of interest. Using these generated standard curves, the multicomponent lymph and plasma curves are decomposed into the least number of equally spaced components that yield a good fit. A linear least-squares method is used to do this. Each protein fraction is multiplied by the total measured protein concentration to provide a concentration for each component. Finally, L/P concentration ratios of protein fractions with visible peaks were computed by applying an averaging technique to the equally spaced protein fractions. Plots of sheep lung L/P ratio versus protein size obtained in this manner were compared to L/P ratios obtained using a method of analysis which does not correct for protein overlap. The corrected L/P ratios showed less scatter than the uncorrected curves. Lung lymph data analyzed with the correction method indicated an increased lung microvascular permeability for large proteins following endotoxin infusion, whereas the uncorrected curves were too noisy to support this concept.     

Modification of the immobilized metal affinity electrophoresis using sodium dodecyl sulfate polyacrylamide gel electrophoresis

Modification to the original immobilized metal affinity electrophoresis (IMAEP) technique is presented. SDS-PAGE is used instead of native PAGE for improved extraction of phosphoproteins from a mixture of proteins. Protein samples treated with 2% w/v SDS instead of native sample buffer ensure that proteins are negatively charged. These negative charges on the proteins assure that the proteins migrate electrophoretically towards the anode regardless of their pI values and hence pass through the region embedded with the metal ions. Another benefit of treating proteins with SDS is that it unfolds the phosphoproteins exposing the phosphate groups to facilitate the metal-phosphate interactions. Phosphorylated ovalbumin can only be extracted after SDS sample buffer treatment. Data show that there is no detrimental effect upon SDS treatment on the extraction of phosphoproteins from a mixture of proteins. Electrophoretic migration of phosphoproteins ceases upon encounter with metal ions like Al+3, Ti+3, Fe+3, Fe+2, and Mn+2 whereas non-phosphorylated proteins migrate freely.     

Capillary electrophoresis/tandem mass spectrometry for analysis of proteins from two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis

Capillary electrophoresis/time-of-flight mass spectrometry(CE/TOFMS) has been used for analysis of in-gel digests of protein spots excised from two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (2-D SDS-PAGE). An off-line purification and preconcentration procedure with a Zip Tip is used before CE/TOFMS analysis which allows for detection of protein spots with <1 picomole of material from 2-D gels. The off-line procedure provides sufficient purification for analysis while maintaining the quality of the CE separation. Using this procedure, several proteins from Coomassie Blue and zinc negatively stained gels are identified by the peptide maps generated and database searching. CE/TOF tandem mass spectrometry is used for the confirmation of database searching results and structural analysis of peptides that do not match the expected peptide maps obtained from the database in order to identify structural modifications. Several modifications were pinpointed and identified by this method.     

High-throughput protein analysis by multiplexed sodium dodecyl sulfate capillary gel electrophoresis with UV absorption detection

We have developed a novel, high-throughput approach for molecular mass determination of proteins from 14 200 to 116 000 based upon multiplexed, absorbance-based capillary electrophoresis. Via capillary multiplexing, 96 samples were analyzed simultaneously within 30 min. Detection with ultraviolet light obviates the need for protein staining or derivatization. The detection limit of the system was estimated at 5 microg/ml bovine serum albumin (BSA) when sampled from 12.5 mM Tris-HCl. The linear dynamic range was over two orders of magnitude from 5 microg/ml to 1000 microg/ml for BSA. Better than 5% sizing accuracy for protein molecular mass determination and excellent run-to-run and day-to-day reproducibility was obtainable with the described method.     

High-throughput sodium dodecyl sulfate polyacrylamide gel electrophoresis by linking conventional gel plates with automated liquid handler via Gel Adaptor

The automation of SDS-PAGE required substantial investment. To lower this barrier, we devised a cost-effective, simple, and general method where samples are loaded on SDS-PAGE gels held by a newly devised "Gel Adaptor" on a general automated liquid handler. In this method, the liquid handler loads samples on the SDS-PAGE gels held at an angle of 80 degrees on the Gel Adaptor so that the samples can be vertically loaded on the narrow paths of the wells of the slanted gels. This method allows the automated liquid handler to load 144 samples on SDS-PAGE gels in approximately 10 min, greatly reducing the time and cost for high-throughput SDS-PAGE analyses.     

Structural analysis of recombinant proteins prepared by semi-dry electroblotting after sodium dodecyl sulfate-polyacrylamide gel electrophoresis

Proteins that were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis were electroblotted onto polyvinylidene difluoride membranes in procedures to prepare homogeneous recombinant proteins for direct N-terminal sequence analysis. A semi-dry blotting procedure was employed to immobilize protein bands on the membranes for subsequent sequence analysis. This method has been used routinely to evaluate the quality of recombinant proteins, which are present in crude cell extracts produced by different expression systems or under different expression conditions. N-Terminal processing, amino acid misincorporation, as well as the inefficient secretion of recombinant proteins can be detected by direct N-terminal sequence analysis of the purified electroblotted samples. Consequently, time-consuming chromatographic procedures can be eliminated. These procedures are also especially valuable for determining degradation sites of a purified recombinant protein, as well as evaluating multiple gene products expressed by isolated cluster genes.     

Investigation of humate-cetyltrimethylammonium complexes by small-angle X-ray scattering

The structural examination of the complexes formed between humic acid and cationic surfactants has environmental implications. A humic acid (HA) dissolved in 0.1 M NaOH (5 g/L) was reacted with a cationic surfactant (hexadecyltrimethylammonium bromide or CTAB) at initial solution concentrations of 1, 5, 10, 20, 30, 40 and 50 mM. The HA precipitated at CTAB concentrations of 20, 30, and 50 mM but the complexes were soluble at 40 mM and below 20 mM. The charge neutralization between humic acid anions and CTAB micelles and the subsequent charge reversal due to hydrophobic interactions explain the behavior of the HA-CTAB complexes. The HA solution (5 g/L), reaction products (supernatants and precipitates), and pure cationic surfactant solutions were studied by the small-angle X-ray scattering (SAXS) technique in order to determine the structure of HA-CTAB complexes. The scattering intensity (I(q)) of various HA-CTAB systems were recorded over a range of scattering vectors (q=0.053-4.0 nm(-1)). HA forms networks in an alkaline solution with a characterization length of 7.8 nm or greater. The HA-CTAB precipitates and the 50-mM CTAB solution gave d(100) and d(110) reflections of a hexagonal structure. The hexagonal array of cylindrical CTAB micelles has a lattice parameter of 5.01 nm in pure solution, and the parameter decreases in the order: 4.96, 4.91, and 4.85 nm for the precipitates of HA-CTAB (50, 30, and 20 mM, respectively), indicating that the structure of CTAB micelles was disturbed by the addition of HA. The molecular properties and behavior of HA in solution were discussed.     

The analysis of glycoproteins in cells and tissues by two-dimensional polyacrylamide gel electrophoresis

Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was used to identify and analyse subsets of proteins in cells and tissues. The combination of 2-D PAGE and [125I] concanavalin A overlay revealed an extraordinary complexity and diversity in the glycoprotein profiles of different cell types. However, the glycoproteins are not expressed idiosyncratically. Rather, their expression is closely linked to the state of differentiation of a particular cell type. Such glycoproteins can therefore be used to generate antibodies specific for differentiated cells. 2-D PAGE analyses of cellular glycoproteins also revealed a major common glycoprotein of 100 kDa. This was localised to the lumen of the endoplasmic reticulum and is referred to as endoplasmin. The combination of 2-D PAGE with electroblotting and 45Ca overlay revealed that endoplasmin and several other luminal endoplasmic reticulum proteins (reticuloplasmins) are high capacity, low affinity calcium binding proteins which could function as calcium storage proteins in the endoplasmic reticulum. One of these called calreticulin is also found in the sarcoplasmic reticulum. 2-D PAGE and 45Ca overlay has been used to demonstrate the presence of a calcium-binding protein (CP22/sorcin) in the cytosol of rodent multidrug resistant cells. Analyses of murine serum by 2-D PAGE revealed the presence of a novel stress protein serum amyloid P component. These studies illustrate the value of 2-D PAGE when used in combination with detection methods which select specific subsets of proteins such as glycoproteins.     

Fabric-reinforced ultrathin polyacrylamide gels for sodium dodecyl sulfate-polyacrylamide gel electrophoresis and isoelectric focusing

The suitability of four different fabric materials for the preparation of ultrathin rein-forced polyacrylamide gels was investigated. With all fabric-reinforced gels, a good separation of proteins by isoelectric focusing and sodium dodecyl sulfate-electrophoresis could be achieved. Semi-dry electrophoretic blotting of proteins was possible with all types of fabric-reinforced gels. Two polyester fabrics (a net and a fleece) were decidedly superior in handling and dimensional stability on drying to a nylon fabric and another polyester fleece material. Only gels prepared with the former materials withstood further treatment, such as fixation, staining, destaining, and drying. One of the polyester fleece fabrics had poor handling properties and the nylon fabric was unsuitable for direct staining procedures employing concentrated (20% w/v) trichloroacetic acid as fixative.     

Esophageal carcinoma-associated proteins detected by two-dimensional polyacrylamide gel electrophoresis

Patterns of proteins of five surgically resected esophageal carcinomas were studied by two-dimensional polyacrylamide gel electrophoresis with silver staining. The samples of normal esophageal mucosa and esophageal carcinoma from the same patient were compared. Each gel had ca. 300 protein spots and had a similar pattern of proteins. Four spots were observed in all of the esophageal carcinomas that were not present in any of the normal mucosae. The molecular weights and isoelectric points were 46,000 and 5.3, 46,000 and 5.2, 36,000 and 4.7 and 33,000 and 5.1, respectively. One spot was observed in all of the normal mucosae but not in any of the esophageal carcinomas. Its molecular weight and isoelectric point were 27,000 and 5.3, respectively.