Electrophoretic studies on the assembly of the nitrogenase molybdenum-iron protein from the Klebsiella pneumoniae nifD and nifK gene products.

The electrophoretic properties of the molybdenum-iron (MoFe) protein component of nitrogenase and an iron-molybdenum cofactor (FeMoco)-reactivatable apoMoFe protein from Klebsiella pneumoniae were examined under anaerobic ([O2] < 5 ppm), nondenaturing conditions. In wild type K. pneumoniae extracts, two immunoreactive species migrating more slowly than purified MoFe protein were detected using anti-MoFe protein antibodies. The uppermost species comigrates with the apoMoFe protein produced by a K. pneumoniae mutant unable to synthesize FeMoco (UN106) and by Escherichia coli harboring the plasmids pVL222+pVL15 (nifHDKTYUSWZM+A). In vitro FeMoco titration of the UN106 and pVL222+pVL15 extracts increases the electrophoretic mobility of the apoMoFe protein to that of purified MoFe protein in a two-step process giving rise to a species of intermediate mobility between the apo- and holoMoFe proteins. Two-dimensional gel electrophoresis showed that a 20-kDa peptide is associated with the apoMoFe protein and with the intermediate species, but not with the holoMoFe protein. N-terminal sequencing identified this associated peptide as the nifY gene product, which we propose is acting as a temporary enforcer of the apoMoFe protein structure required for cofactor binding that is released upon FeMoco activation. This FeMoco-induced mobility shift was used to characterize the mutant apoMoFe proteins produced in E. coli as a result of deleting the various nitrogen fixation (nif) genes from the plasmid pVL222. E. coli extracts bearing plasmids deleted in nifH, nifS, nifTYUM, or nifWZM exhibit less than 10% of the apoMoFe protein activity of derepressed UN106 and contain an immunoreactive species whose electrophoretic mobility is increased upon addition of FeMoco from that of apoMoFe protein to that of holoMoFe protein in a single step. Anaerobic nondenaturing gel electrophoresis of 55Fe-labeled E. coli extracts followed by autoradiography showed that these inactive apoMoFe species do not contain iron, indicating that the P-clusters are absent. We therefore propose that NifH, S, U, W, Z, and M are all involved, to varying degrees, in P-cluster assembly. In addition, the presence of the P-clusters does appear to be necessary for the two-step FeMoco activation of the apoMoFe protein to occur.     

Gamma globulin-derived standards for the determination of molecular weights, transfer, and immunodetection efficiencies in protein blotting procedures

Molecular weight markers which are detectable using labeled antispecies antibodies or labeled Protein A have been prepared for use as standards on protein blots. The standards were prepared by the controlled reduction followed by subsequent alkylation of gamma globulin. Separate sets of standards were prepared using gamma globulins derived from human, mouse, rabbit, and sheep species. Standards were also prepared using monoclonal-derived gamma globulins from human myeloma fluid and mouse ascites fluid. Standards produced from monoclonal-derived gamma globulins produced very sharp bands on sodium dodecyl sulfate-polyacrylamide gels and proved to be excellent standards for this technique alone. However, the markers were uniquely suitable for use as standards in protein blotting procedures because their detection was achieved by the procedure used to detect the transferred antigen(s). The detection of immunoglobulin G (IgG)-derived standards on protein blots from all the species listed above was demonstrated using appropriate horseradish peroxidase (HRP)-conjugated antispecies antibodies. The use of other detection systems (biotin-labeled antibody and subsequent detection with HRP-steptavidin, HRP-Protein A) was also validated with human IgG-derived standards. Furthermore, the standards were shown to be suitable for use on both nitrocellulose and cationized nylon-based supports and could be used when adjacent samples were run under reducing conditions. Hence the gamma globulin-derived standards serve as both a control to check the adequacy of transfer and immunodetection systems and as markers which enable the molecular weights of detected antigens to be calculated.     

An electrophoretic method for selection of conditions for production of electrophoretically uniform protein colloidal gold complexes

An electrophoretic method was developed to determine the conditions required for production of electrophoretically uniform protein-colloidal gold complexes from monodisperse colloidal gold (Au) and electrophoretically uniform protein. The method is based on the electrophoretic migration of protein-Au complexes in agarose. The results demonstrate that two variables, the pH of adsorption and the quantity of protein added, can be manipulated to vary the electrophoretic mobility of the resulting protein-Au complexes. Thus, agarose gel electrophoresis can be used to select the pH of adsorption and the quantity of protein required to produce electrophoretically uniform protein-Au complexes. This new electrophoretic mobility test can be used in place of or in addition to the classical procedure of Zsigmondy and its many variations, both visual and spectrophotometric. The procedure described is also useful for electrophoretic comparison of small quantities of various protein-Au samples.     

A simplified electrophoretic system for determining molecular weights of proteins.

Electrophoresis of 31 different proteins in commercially prepared polyacrylamide gradient gels, Gradipore, yields a linear relationship between a hypothetical limiting pore size (the reciprocal of a limiting gel concentration, GL) and the cube root of the mol.wt., over the range 13 500-9000 000. A regression analysis of these data reveals that 98.6% of all variability in 1/GL is explained by the molecular weight, and this degree of accuracy compares favourably with existing methods for the determination of molecular weight by retardation of mobility in polyacrylamide. This new procedure has the additional advantages that molecular-weight standards can be obtained from readily available body fluids or tissue extracts by localizing enzymes and other proteins by standard histochemical methods, and that the same electrophoretic system can be used in determining molecular weights as is used in routine surveys of populations for individual and species variation in protein heterogeneity.     

Photobiotin as a sensitive probe for protein labeling

A sensitive method for the nonisotopic in vitro labeling of proteins under physiological conditions using photobiotin, a compound originally developed for labeling nucleic acids (Forster et al. (1985) Nucleic Acids Res. 13, 745), has been developed. Using sheep brain tubulin as a model protein it was shown that labeling with photobiotin resulted in detection limits below 10 pg when avidin-alkaline phosphatase was used in the final step. No significant loss of tubulin polymerization, colchicine binding, recognition by antitubulin antibodies, or changes in electrophoretic behavior were observed. In addition, photobiotinylation of antitubulin antibodies did not affect their recognition of unlabeled tubulin. The use of photobiotin labeling with avidin-alkaline phosphatase detection for electrophoretic separations of molecular weight standards, crude protein supernatants, and tubulin gave a 64 to 1024-fold increase in sensitivity over Coomassie blue staining.     

Production of a monoclonal antibody directed against rat liver glutathione-insulin transhydrogenase

A hybridoma cell line secreting monoclonal antibody specific for glutathione-insulin transhydrogenase has been produced by fusing mouse myeloma cells with spleen cells from mice immunized to purified rat liver glutathione-insulin transhydrogenase. The secreted antibody isotypes were found to be: Ig gamma 1 heavy chains and kappa light chains. This monoclonal antibody has been used to screen glutathione-insulin transhydrogenase in various rat tissue extracts (liver, fat, heart, testis, spleen, lung and kidney) following separation on NaDodSO4/urea polyacrylamide disc-gel electrophoresis and electrophoretic transfer to nitrocellulose. Screening with the monoclonal antibody showed the presence of one immunoreactive protein band equal in molecular weight to that of purified rat liver GIT (Mr 53,000) in extracts of all tissues studied and a second immunoreactive protein band of lower molecular weight (Mr 49,000) in spleen and lung tissue extracts. Separation of these two proteins by HPLC using a TSK-DEAE column demonstrated that both proteins exhibit insulin degrading activity. These data indicate that GIT may occur in multiple forms in some tissues.     

Immunodetection of nitrocellulose-adhesive proteins at the nanogram level after trinitrophenyl modification

A method for protein detection on nitrocellulose membranes based on modification with 2,4,6-trinitrobenzenesulfonic acid and reaction with anti-trinitrophenyl (TNP) serum as first antibody followed by peroxidase-conjugated second antibody is described. Protein quantities between 1 and 3 ng can be detected in the dot test. This method was used in a double immunodetection procedure after electrophoretic transfer of proteins localizing first a distinct antigen with its specific antiserum followed by visualization of the complete protein pattern on the same blot by the TNP/anti-TNP method as described above. As only water-soluble reagents are employed no shrinkage of the membrane occurs. Furthermore, the method can be used in a simultaneous immunodetection procedure visualizing the specific antigen together with TNP marker proteins using a mixture of the specific antiserum and the anti-TNP serum as first antibody.     

Sodium dodecyl sulfate-gel electrophoresis: staining of polypeptides using heavy metal salts

Water-soluble salts of several heavy metals were examined for their ability to stain polypeptides resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Brief gel exposure (5 min or less) to cobaltous acetate or chlorides of copper, nickel, and zinc produced negatively stained protein patterns that were qualitatively indistinguishable from those of parallel gels stained with Coomassie blue R-250. Protein patterns could be visualized less than 1 min after treatment of gels with zinc chloride; the threshold of detection was estimated at about 10-12 ng protein on standard-size slab gels. Test samples including human erythrocyte membranes, sialoglycoprotein (glycophorin) extracts, and commercial molecular weight protein standards were used to establish the scope of these stains. Protein patterns visualized by the heavy metal salts were compared and contrasted with profiles seen with three widely used silver stains. Proteins from gels treated with copper or zinc chloride could be easily recovered by simple diffusion; this makes feasible both analytical and preparative electrophoretic applications of the staining procedure. A mechanism is proposed to explain the observed protein staining by heavy metal salts.     

Micromere-specific cell surface proteins of 16-cell stage sea urchin embryos

Evidence is presented of cell-type specificity of surface proteins from the 16-cell stage sea urchin embryo. The protein composition of the micromere cell surface has been examined by 125I labelling of intact cells followed by SDS-PAGE. In Arbacia punctulata, four high molecular weight (HMW) proteins are detected on the surface of isolated micromeres--but not on mesomere-macromere fractions. In Strongylocentrotus droebachiensis, a micromere-specific protein of 133 K molecular weight (MW) was identified. This 133 K protein binds to wheat germ agglutinin (WGA) but not to concanavalin A (conA). Lectin binding was studied using a new technique. The procedure involves the separation, by SDS-PAGE, of iodinated cell-surface proteins followed by their electrophoretic transfer to lectin-coated nitrocellulose membranes. Using this procedure, cell-type-specific surface proteins which are also lectin-binding-specific, were detected.     

A method for expression and purification of soluble, active Hsp47, a collagen-specific molecular chaperone

Hsp47 is regarded as a collagen-specific chaperone with several suggested roles in collagen biosynthesis under normal and disease conditions. We describe here a procedure for the expression and purification of Hsp47 in Escherichia coli using the IMPACT expression system (New England Biolabs) where the guest gene is fused to the adduct, intein, with a chitin-binding domain. Use of this system resulted in relatively high levels of soluble Hsp47 compared to other available protocols, especially when the bacterial cells were induced at 14 degrees C instead of 37 degrees C. The cell lysate was passed through a chitin-Sepharose affinity column and Hsp47 was cleaved from intein using beta-mercaptoethanol. Minor degradation products were subsequently removed using a hydroxylapatite column to yield milligram amounts of pure and active protein suitable for structural studies. Gel electrophoretic analysis of the purified protein indicated the presence of a small proportion of trimeric species when non-reducing conditions were used. The ability to form a trimer may be important for its role as a chaperone. The IMPACT system allows for radiolabelling of purified Hsp47 with (35)S for use in binding experiments. Illustrative data on collagen binding by (35)S-Hsp47 are shown.     

Anomalous behavior of the major avian myeloblastosis virus glycoprotein in the presence of sodium dodecyl sulfate.

The sodium dodecyl sulfate (SDS) complex of the major glycoprotein of avian myeloblastosis virus exhibited an anomalously low free electrophoretic mobility compared with those of non-glycosylated protein standards. The apparent molecular weight of the glycoprotein calculated from the relation between log molecular weight and electrophoretic mobility depended on the acrylamide concentration and reached a lower limit of 80,000. The molecular weight was also estimated from the retardation coefficients of protein standards and the viral glycoprotein. This method yielded a molecular weight of 64,000 for the avian myeloblastosis virus glycoprotein. When gel chromatography in SDS was used to determine the apparent molecular weight of the glycoprotein from its hydrodynamic properties alone, the estimated value was 50,000. The generally assigned value of 80,000 daltons for the avian myeloblastosis virus major glycoprotein, as determined by SDS electrophoresis, may be an overestimate due to its relatively low free electrophoretic mobility and peculiar conformation in SDS.     

Preparative electrophoretic method for the purification of a hydrophobic membrane protein: subunit c of the mitochondrial ATP synthase from rat liver.

A method is described for the purification of subunit c of ATP synthase from rat liver mitochondria. After sample preparation and solvent extraction, the protein was purified to homogeneity by a single-step preparative electrophoretic procedure, using aqueous buffer and containing lithium dodecyl sulfate. The subunit is an extremely hydrophobic and insoluble protein and all solubilization attempts, using a variety of detergents, were unsuccessful except for lithium dodecyl sulfate. Buffer exchange and FPLC gel filtration removed the detergent from the purified sample, leaving the protein in a soluble form. The mammalian protein is composed of 75 amino acid residues, with a molecular mass of 7602 Da and is classified as a proteolipid. Subunit c accounts for 25 and 85% of the intralysosomal accumulation, within neurons, of storage material in juvenile and late-infantile forms of Batten's disease, respectively. This purification procedure allows access to a continuous supply of pure subunit c from a conventional source such as rat liver and preserves precious autopsy materials. The protein could be used as substrate in future proteolytic studies involving pepstatin-insensitive lysosomal proteases and for raising of more specific antibodies. The procedure could also be adapted/modified and used as a model for purifying other extremely insoluble proteins.     

Chain length determination of small double- and single-stranded DNA molecules by polyacrylamide gel electrophoresis.

We describe the use of polyacrylamide gel electrophoresis to estimate chain lengths of double- and single-stranded DNA molecules in the size range 20-1000 base pairs (or nucleotides). Double-stranded DNA molecules of known length produced either by organic synthesis or by restriction endonuclease digestion of viral DNAs were used as standards. The relative electrophoretic mobilities of these standards were examined on both nondenaturing (aqueous) polyacrylamide gels and on denaturing gels containing 7 M urea or 98% formamide. Electrophoretic mobility of DNA is a linear function of the log of molecular weight if appropriate conditions are used, although exceptions are noted. Chain lengths can be conveniently estimated by using as standards bacteriophage gamma DNA restriction fragments or commercially available tracking dyes.     

Purification and biochemical characterization of two novel antigens from Leishmania major promastigotes

The identification and characterization of antigens that elicit human T cell responses is an important step toward understanding of Leishmania major infection and ultimately in the development of a vaccine. Micropreparative SDS-PAGE followed by electrotransfer to a PVDF membrane and elution of proteins from the PVDF, was used to separate 2 novel proteins from L. major promastigotes, which can induce antibodies of the IgG2a isotype in mice and also are recognized by antisera of recovered human cutaneous leishmaniasis subjects. Fractionation of the crude extract of L. major revealed that all detectable proteins of interest were present within the soluble Leishmania antigens (SLA). Quantitation of these proteins showed that their expression in promastigotes is relatively very low. Considering the molecular weight, immunoreactivity, chromatographic and electrophoretic behavior in reducing and non-reducing conditions, these proteins are probably 2 isoforms of a single protein. A digest of these proteins was resolved on Tricine-SDS-PAGE and immunoreactive fragments were identified by human sera. Two immunoreactive fragments (36.4 and 34.8 kDa) were only generated by endoproteinase Glu-C treatment. These immunoreactive fragments or their parent molecules may be ideal candidates for incorporation in a cocktail vaccine against cutaneous leishmaniasis.     

Monoclonal antibodies against rat saliva and salivary gland antigens

Hybridomas were produced by the fusion of NS1 myeloma cells with spleen cells of a BALB/c mouse immunized with rat submandibular saliva. Growth of hybridomas was evident in 60/96 wells, and colonies secreting antibodies against saliva components were identified in 20 wells by using a solid phase enzyme-linked immunoassay. Cloning of cells from 12 wells yielded originally 43 hybridoma cell lines secreting anti-saliva antibodies. After recloning, one hybridoma (4Cl3) was selected for further studies. The hybridoma (4Cl3) cells were grown as ascites tumors, and the antibodies were purified from the ascitic fluid by diethylaminoethyl Affi-gel Blue chromatography. The purified antibody (MA4), immunoglobulin G1, immunoprecipitated a 39K dalton protein from submandibular saliva, and also reacted with a protein of the same electrophoretic mobility on immunoblots. From extracts of submandibular gland slices, incubated with [3H]leucine, the antibody again immunoprecipitated a 39K protein, indicating that this protein is synthesized in the gland. MA4 was used for immunocytochemical stainings of submandibular glands of rats of different ages. In general, immunostaining was seen only in acinar cells. Thus, there was no staining in the glands of 1-day-old rats that lack differentiated acinar cells. In the glands of 1- to 4-week-old rats the number of immunoreactive cells and the extent of immunostaining paralleled the differentiation of the acinar cells. In the glands of adult rats a uniform staining of the secretory granules of the acinar cells was observed. The immunoreactive 39K protein seemed to be restricted to the acinar cells in the submandibular gland; there was no immunostaining in the parotid, sublingual, or lingual salivary glands, or in the pancreas, colon, and duodenum. Stimulation of saliva secretion by isoproterenol resulted in a virtual depletion of the antigen from the acinar cells. These results indicate the feasibility of producing mouse hybridomas that secrete antibodies against rat saliva components. The monoclonal antibody at hand will be useful in analyzing the differentiation of the acinar cells, and the factors that influence this differentiation process.     

Measurement of DNA length by gel electrophoresis II: Comparison of methods for relating mobility to fragment length

Relationships between DNA length and electrophoretic mobility in an agarose gel have been compared by estimating the lengths of known DNA polymer fragments, using other fragments in the series as standards. Global estimates were made using 10 fragments as standards; local estimates were made using the two closest fragments on either side of the unknown as standards. Most relationships were fitted by least squares. All the relationships gave more accurate local than global estimates. The most accurate results were obtained using the reciprocal relationship, where the maximum error in the local estimates was less than 0.1%. The semilog relationship gave the least accurate results, with a maximum error in the local estimates of almost 5%. The polymer fragments were also used as standards to estimate the lengths of λ DNA restriction fragments. Here the estimates were in error by up to 3%, indicating the influence of base composition and sequence on electrophoretic mobility.     

A colloidal silver staining--destaining method for precise assignment of immunoreactive spots in two-dimensional protein patterns

The characterization of protein expression patterns by two-dimensional gel electrophoresis depends on efficient and reliable identification strategies for target spots. In addition to sophisticated techniques, such as microsequencing and peptide mass spectrometry, immunodetection of membrane-immobilized proteins is a valuable method with which to identify the corresponding spots for a given set of candidate proteins. To precisely assign immunoreactive spots, this approach requires specific immunodetection and staining of total protein to be performed on the same membrane. Here, we describe a highly sensitive, colloidal silver-based method for the assignment of immunoreactive spots in two-dimensional protein patterns. This simple and rapid procedure involves a destaining step after staining of nitrocellulose-bound proteins with colloidal silver. We show that destaining of proteins is a prerequisite for subsequent immunodetection using enhanced chemiluminescence. Several types of antibodies were successfully employed for antigen detection after the staining-destaining procedure. Our results demonstrate that the colloidal silver-based method is generally applicable for the unambiguous identification of candidate proteins in complex two-dimensional patterns.     

Southwestern blotting in investigating transcriptional regulation

Southwestern blotting is used to investigate DNA-protein interactions. The advantage of this technique over other related methods such as electrophoretic mobility shift assay (EMSA) and DNA footprinting is that it provides information regarding the molecular weight of unknown protein factor. This method combines the features of Southern and Western blotting techniques; a denaturing SDS-PAGE is first employed to separate proteins electrophoretically based on size, and after transferring the proteins to a membrane support, the membrane-bound proteins are renatured and incubated with a (32)P-labeled double-stranded oligonucleotide probe of specific DNA sequence. The interaction of the probe with the protein(s) is later visualized by autoradiography. This technique could be combined with database searching (TransFac, http://www.gene-regulation.com/pub/databases.html#transfac), prediction of potential protein factors binding onto a target motif (e.g., Patch search), in vitro supershift EMSA and in vivo chromatin immunoprecipitation (ChIP) assays for effective identification of protein factors. The whole Southwestern blotting procedure takes approximately 4 d to complete. In this article, a commonly used protocol and expected results are described and discussed.     

DNA chain length markers and the influence of base composition on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamide-gels.

The specific influence of the four nucleobases on electrophoretic mobility of oligodeoxyribonucleotides in polyacrylamide-gels under denaturing and nondenaturing conditions has been investigated using homooligomers from the four deoxyribonucleotides as chain length standards. Homooligomers of same chain lengths exhibit remarkable differences in mobility. Specific retardation of any other oligonucleotide investigated was found to be mainly dependent on base composition but not on sequence. A simple procedure is presented for calculating mobilities relative to the standards on denaturing gels. This allows a reliable identification of oligonucleotides on acrylamide-gels by exact chain length determination with respect to base composition and furthermore a detailed interpretation of complex reaction mixtures. The homooligomers also show the same differences in mobility on nondenaturing gels. The significance of this effect for strand separation is discussed.     

Immunological analysis of aconitase in pumpkin cotyledons: the absence of aconitase in glyoxysomes

Aconitase (EC 4.2.1.3) was purified by column chromatography and SDS-PAGE. Specific antibodies for aconitase were prepared after affinity purification of the antiserum with purified aconitase. The antibodies reacted with purified pumpkin aconitase, and with the 98 kDa protein band after electrophoretic fractionation of extracts of pumpkin cotyledons. Immunoblot analysis revealed a protein with similar molecular mass in extracts of several plants. The intensity of the 98 kDa band increased as pumpkin cotyledons developed in darkness, and decreased thereafter upon illumination. Aconitase activity showed a similar pattern. Anion exchange chromatography of a homogenate of pumpkin cotyledons, followed by western blotting, displayed the presence of immunoreactive protein bands only in fractions showing aconitase activity. The results indicate that the antibodies were specific for aconitase. When we investigated the presence of immunoreactive bands after sucrose gradient fractionation, aconitase was detected in the supernatant fractions and in mitochondria, while a very low amount was found in glyoxysomes. These data provide additional proof that aconitase is not localized in glyoxysomes.