Use of Dimethyl Suberimidate, a Cross-Linking Reagent, in Studying the Subunit Structure of Oligomeric Proteins

Amidination of aldolase, glyceraldehyde-3-phosphate dehydrogenase, tryptophan synthetase B protein, L-arabinose isomerase, and the catalytic subunit of E. coli aspartate transcarbamylase with the bifunctional reagent dimethyl suberimidate produces cross-linked proteins, with reaction predominating within oligomers. Disc electrophoresis of a modified protein on polyacrylamide gel in the presence of sodium dodecyl sulfate resolves a set of species with molecular weights equal to integral multiples of the protomer molecular weight. For oligomers composed of identical protomers, the number of principal species observed is identical to the number of protomers in the oligomer. Application of the method to two proteins composed of dissimilar protomers, native aspartate transcarbamylase and tryptophan synthetase α₂β₂ complex of E. coli, revealed differences in the reactivities of the different kinds of protomer within each oligomer.     

Isolation of tryptic fragment of antigen from mitochondrial inner membrane proteins reacting with antimitochondrial antibody in sera of patients with primary biliary cirrhosis

Most of the sera from patients with primary biliary cirrhosis contains antimitochondrial antibodies, which react with four proteins of the mitochondrial inner membrane. We reported in a previous paper that when beef heart mitochondrial inner membrane proteins were digested by trypsin, a new reactive 36 kDa fragment with antimitochondrial antibody was obtained. This 36 kDa fragment derives from original 70 kDa protein because the monoclonal antibody specific to 70 kDa protein reacts with the 36 kDa band equivalent to 70 kDa band. The 36 kDa fragment was purified using an affinity column conjugated with an immunoglobulin-rich fraction of primary biliary cirrhosis serum containing antimitochondrial antibody, preparative electrophoresis and high-performance liquid chromatography using a reverse phase column. The final preparation showed a single band in sodium dodecyl sulfate polyacrylamide gel electrophoresis. Its amino acid composition is in good agreement with that of the subunit binding domain of the pyruvate dehydrogenase complex E2 from bovine heart.     

Stoichiometry and composition of an aminoacyl-tRNA synthetase complex from rat liver.

The particulate aminoacyl-tRNA synthetases of rat liver were copurified about 1000-fold with more than 20% yields for individual synthetase activities. Measurements of aminoacylation activities showed that lysyl-, arginyl-, leucyl-, isoleucyl-, and methionyl-tRNA synthetases in the purified complex cosedimented at 18 S. The molecular weight of the synthetase complex is about one million, as estimated by gel filtration. The stoichiometry of the synthetase in the complex was determined by active site titration with aminoacyl adenylates. Results indicate that the 18S synthetase complex contains one subunit of methionyl-tRNA synthetase and two subunits of lysyl-tRNA synthetase. Polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate showed that the 18S synthetase complex contains eight major protein bands. Proteins with subunit molecular weights of 104,000, 92,000, 69,000, and 67,000 are present in molar ratios of 1:1:2:2, while proteins with subunit molecular weights of amounts. These results suggest that the particulate aminoacyl-tRNA synthetases exist as a heterotypic multienzyme complex with defined structure.     

Reconstitution of the Escherichia coli pyruvate dehydrogenase complex.

The binding of pyruvate dehydrogenase and dihydrolipoyl dehydrogenase (flavoprotein) to dihydrolipoyl transacetylase, the core enzyme of the E. coli pyruvate dehydrogenase complex [EC 1.2.4.1:pyruvate:lipoate oxidoreductase (decaryboxylating and acceptor-acetylating)], has been studied using sedimentation equilibrium analysis and radioactive enzymes in conjunction with gel filtration chromatography. The results show that the transacetylase, which consists of 24 apparently identical polypeptide chains organized into a cube-like structure, has the potential to bind 24 pyruvate dehydrogenase dimers in the absence of flavoprotein and 24 flavoprotein dimers in the absence of pyruvate dehydrogenase. The results of reconstitution experiments, utilizing binding and activity measurements, indicate that the transacetylase can accommodate a total of only about 12 pyruvate dehydrogenase dimers and six flavoprotein dimers and that this stoichiometry, which is the same as that of the native pyruvate dehydrogenase complex, produces maximum activity. It appears that steric hindrance between the relatively bulky pyruvate dehydrogenase and flavoprotein molecules prevents the transacetylase from binding 24 molecules of each ligand. A structural model for the native and reconstituted pyruvate dehydrogenase complexes is proposed in which the 12 pyruvate dehydrogenase dimers are distributed symmetrically on the 12 edges of the transacetylase cube and the six flavoprotein dimers are distributed in the six faces of the cube.     

Purification and amino acid analysis of a human macrophage cytotoxicity-inducing factor (MCF)

Recently we have described a CD4+ human T-cell hybridoma Ft.F3 (ATCC HB 9713). This hybridoma produces two proteins having molecular weights of 29 kd (P29) and 14.7 kd (P14.7) that function as activators of human monocyte tumor cytotoxicity and interleukin 1 (IL-1) synthesis (macrophage cytotoxicity-inducing factors, MCFs). Both MCF species were purified to apparent homogeneity, as assessed by two-dimensional (2D) gel electrophoresis, by a combination of dye ligand, ion exchange, and hydrophobic interaction chromatography, and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Exhaustive treatment of P29 by endoglycosidase F, performic acid, and 40x molar excess 2-mercaptoethanol failed to generate P14.7 from P29. Antisera raised to P29 recognized only P29 in immunoblots of 2D gels of crude hybridoma supernatant. Amino acid composition analyses of both species are similar but not identical. These MCFs appear to be distinct but possibly related proteins important in the inflammatory response, whereas N-terminal analysis of P29 reveals it to be a previously undescribed cytokine.     

Murine Ia and human DR antigens: homology of amino-terminal sequences.

Murine Ia and human DR antigens were isolated and purified by immunoprecipitation and sodium dodecyl sulfate/polyacrylamide gel electrophoresis with allo- and xenoantisera, respectively. The I-A subregion antigen consists of two chains, designated Aalpha and Abeta, with molecular weights of 35,000 and 26,000, respectively. The I-C subregion antigen likewise consists of two chains, designated Calpha and Cbeta, with molecular weights of 32,000 and 29,000, respectively. Under nonreducing conditions, the Cbeta chain migrates appreciably more rapidly on sodium dodecyl sulfate/polyacrylamide gels than the reduced Cbeta chain, reflecting the presence of an intrachain disulfide bond. The human DR antigen is also a two-chain unit and contains DRalpha and DRbeta components with molecular weights of 34,000 and 28,000, respectively. The DRbeta chain migrates more rapidly before reduction than afterward, like the murine Cbeta chain. The DRbeta and Cbeta chains are also strikingly homologous if a single amino acid shift is imposed on one of those chains. Thus, human DR antigens strongly resemble the murine I-C subregion antigens.     

Eukaryote ribosomes possess a binding site for concanavalin A.

Ribosomes prepared from chicken liver or rabbit reticulocytes bound concanavalin A in a molar ratio of approximately 1:1. This binding is to the large subunit of the eukaryote ribosomes with a dissociation constant of 5 X 10(-7) M (0 degrees). The binding of concanavalin A to Escherichia coli ribosomes was much less. Binding to the RNA or to possible membrane contaminants was ruled out in control experiments. Chicken liver ribosomes were labeled in vivo with 3H-labeled amino acids, purified, and dissociated in sodium dodecyl sulfate. Affinity chromatography of this preparation made it possible to isolate the small proportion of the ribosomal proteins (about 1.5%) containing the concanavalin A binding site. This protein moved as a single band during electrophoresis on polyacrylamide gels containing sodium dodecyl sulfate and showed an apparent molecular weight of 31,000.     

Subunit structure of dihydrolipoyl transacetylase component of pyruvate dehydrogenase complex from Escherichia coli

Limited tryptic digestion of the pyruvate dehydrogenase complex of Escherichia coli or its dihydrolipoyl transacetylase core cleaves the trypsin-sensitive transacetylase subunits into two large fragments, A (lipoyl domain) and D (subunit binding domain). Release of fragments A from the complex does not significantly affect its sedimentation coefficient or its appearance in the electron microscope. Fragment A contains the lipoyl moieties ((3)H-labeled), is acidic with an apparent isoelectric point of about 4.0, has a M(r) of 31,600 as determined by sedimentation equilibrium analysis, and has a swollen or extended structure (f/f(o) = 1.78). Fragment A exhibits anomalous properties, probably due to its acidic nature. It is resistant to staining with Coomassie blue and it migrates on sodium dodecyl sulfate/polyacrylamide gels as if it had a M(r) of 46,000-48,000. Further tryptic digestion converts fragment A into a lipoyl-containing fragment of M(r) 20,000 (fragment B) and eventually into an apparently stable product of estimated M(r) about 10,000 (fragment C). Fragment D has a compact structure of M(r) about 29,600 as determined by sedimentation equilibrium analysis in 6 M guanidinium chloride, and it possesses the intersubunit binding sites of the transacetylase, the binding sites for pyruvate dehydrogenase and dihydrolipoyl dehydrogenase, and the catalytic site for transacetylation. The assemblage of fragments D is responsible for the cube-like appearance of the transacetylase in the electron microscope. High-resolution electron micrographs of the transacetylase show fiber-like extensions, apparently corresponding to tryptic fragment A, surrounding the cube-like core.     

Purification of human platelet-derived growth factor.

Human platelets contain a polypeptide growth factor that stimulates the proliferation of connective tissue cells. Purification of this platelet-derived growth factor (PDGF) was accomplished by heat (100 degrees C) treatment of washed platelets and subsequent ion-exchange chromatography, gel filtration in 1 M acetic acid, isoelectric focusing, and preparative sodium dodecyl sulfate/polyacrylamide gel electrophoresis. PDGF has an isoelectric point of 9.8 and a molecular weight ranging from 13,000 to 16,000 as judged by gel filtration in 1 M acetic acid or analytical sodium dodecyl sulfate gel electrophoresis under reducing conditions. The specific activity of the purified PDGF is 20 million times greater than that found in unfractionated human serum. Purified PDGF stimulates replicative DNA synthesis and cell proliferation in quiescent density-arrested cultures of BALB/c 3T3 cells at concentrations of 1 ng/ml (0.1 nM).     

Uroporphyrinogen I synthase from human erythrocytes: separation, purification, and properties of isoenzymes.

Uroporphyrinogen I synthase [porphobilinogen ammonia-lyase (polymerizing), EC 4.3.1.8] from human erythrocytes was separated into two active protein peaks (A and B on DEAE-cellulose, by ammonium sulfate fractionation, on Sephadex G-100, and on DEAE-Sephadex A-50 with a NaCl gradient. The final purification was 613 and 743 times for A and B, respectively. The corresponding yields were 2.2 and 3.4% Fraction A was separated further into two (A1 and A2) active protein bands and fraction B into three (B1, B2, and B3) on analytical polyacrylamide disc gel electrophoresis. Bands A1 and A2 were identical with B1 and B2; B3 represented a third isoenzyme. Molecular weights (mean +/- SEM), measured by gel filtration and sodium dodecyl sulfate/polyacrylamide gel electrophoresis, were 38,000 +/- 1000 for B1 and 40,000 +/- 1000 for B2 and B3. Isoelectric focusing on 4% polyacrylamide gel separated both fractions A and B into three active protein bands. Maximal activity of the enzyme was found in gel cuts (5-mm) at pH 5.6 for both fractions A and B.     

Evidence for the presence of two nonidentical subunits in NAD-dependent isocitrate dehydrogenase of pig heart

The NAD-dependent isocitrate dehydrogenase [threo-D(S)-isocitrate:NAD(+) oxidoreductase (decarboxylating); EC 1.1.1.41] from pig heart is a multisubunit enzyme with a molecular weight of approximately 340,000. Electrophoresis of the enzyme in 10% polyacrylamide gels containing sodium dodecyl sulfate reveals two discrete bands with molecular weights of 41,000 and 39,000. The two bands exhibit approximately equal intensity when stained with Coomassie Blue, Amido Black, and Bromophenol Blue, suggesting that these polypeptide chains are present in equimolar quantities in the native enzyme. The same two-band pattern is observed when the sulfhydryl groups of the enzyme are blocked by alkylation with iodoacetate prior to electrophoresis, indicating that sulfhydryl oxidation is not responsible for the observed heterogeneity. Each of the subunits appears as a single band when eluted from the gel and again subjected to electrophoresis under the same conditions. Isocitrate dehydrogenase contains a total of 41 lysine and arginine residues per average subunit of 40,000 daltons. The observation of approximately 80 peptides upon paper chromatography and high voltage electrophoresis of tryptic digests of the enzyme is consistent with the existence of two distinct polypeptide chains. Dansylation yields two NH(2)-terminal amino acid derivatives: dansyl-phenylalanine and dansyl-alanine. It is concluded that the NAD-specific isocitrate dehydrogenase is composed of equal numbers of two nonidentical subunits.     

Allergic Potency of Japanese Cedar Pollen Cry j 1 Is Reduced by a Low Concentration of Hypochlorous Acid Generated by Electolysis

BackgroundAlthough Japanese cedar (Cryptomeria japonica) pollinosis has developed into a health problem, few methods eradicate indoor allergens completely. In a recent study, however, the effectiveness of inactivation with sodium hypochlorite (NaOCl) treatment was revealed. Therefore, the present study aimed to elucidate the ability of chlorine bleach (NaOCl) to reduce the immunogenicity of the major allergenic protein of Japanese cedar (Cry j 1).MethodsSodium dodecyl sulfate polyacrylamide gel electrophoresis, Western blotting, enzyme-linked immunosorbant assay, and skin testing were carried out in 7 individuals.ResultsThe allergenic protein was undetectable using sodium dodecyl sulfate polyacrylamide gel electrophoresis and silver staining at a sodium hypochlorite/allergenic protein molar ratio of 457. Western blotting with human sera showed the same dose-dependent efficacy. The immunogenicity of the purified protein and cedar pollen was also demonstrated on enzyme-linked immunosorbant assay to be reduced by sodium hypochlorite treatment in a dose- and time-dependent manner. Moreover, sodium hypochlorite-treatment inhibited the skin test response to the protein in all 7 individuals.ConclusionsHypochlorous acid generated by electrolysis is an effective method for significantly reducing the immunogenicity of Cry j 1.     

Noncollagenous proteins in cartilage of normal subjects and patients with degenerative joint disease. a gel electrophoretic study

Normal articular cartilage from subjects of various ages and cartilage from patients with degenerative joint disease were extracted with 4M guanidinium chloride. After dialysis against 8M urea pH 6.8, a 0.2M NaCl fraction was obtained by ion exchange chromatography on DE-52 in 8M urea. This fraction was concentrated, reduced, and analyzed by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (7% gels). Six major noncollagenous protein bands (P₁–P₆) were found; 2 were identified as the link proteins. The approximate molecular weights of P₁–P₆ were: 87,000, 64,000, 56,000, 46,000, 41, 000, and 27,000. A similar sodium dodecyl sulfate–polyacrylamide gel electrophoresis pattern of P₁–P₆ was found in young baboons, in normal young and aged humans, and in patients with degenerative joint disease. Peaks corresponding to extracted collagen were decreased in older patients and increased in patients with degenerative joint disease, even those of advanced age.     

Purification and characterization of branched chain α-keto acid dehydrogenase complex of bovine kidney

A branched chain alpha-keto acid dehydrogenase-dihydrolipoyl transacylase complex was purified to apparent homogeneity from bovine kidney mitochondria. As usually isolated, the complex (s(20,w) = 40 S) contained little, if any, dihydrolipoyl dehydrogenase. When saturated with the latter enzyme the complex had a specific activity of about 12 mumol of alpha-ketoisovalerate oxidized per min per mg of protein at 30 degrees with NAD(+) as electron acceptor. In addition to alpha-ketoisovalerate, the complex also oxidized alpha-ketoisocaproate, alpha-keto-beta-methylvalerate, alpha-ketobutyrate, and pyruvate. The ratios of the specific activities were 2.0:1.5:1.0:1.0:0.4, and the apparent K(m) values were 40, 50, 37, 56, and 1000 muM. The complex was separated into its component enzymes. The branched chain alpha-keto acid dehydrogenase (6 S) consists of two different subunits with estimated molecular weights of 46,000 and 35,000. The dihydrolipoyl transacylase (20 S) contains apparently identical subunits of molecular weight about 52,000. In the electron microscope, the transacylase has the appearance of a cube, and the molecules of branched chain alpha-keto acid dehydrogenase appear to be distributed on the surface of the cube. In contrast to the pyruvate dehydrogenase complex of bovine kidney, the branched chain alpha-keto acid dehydrogenase complex apparently is not regulated by phosphorylation-dephosphorylation. Its activity, however, is subject to modulation by end-product inhibition.     

Purification and Properties of Two RNA Polymerases from Physarum polycephalum

Two RNA polymerases have been purified from the slime mold Physarum polycephalum, one sensitive and one resistant to alpha-amanitin. Both enzymes are more active with denatured DNA than native DNA as a template and prefer Mn(++) rather than Mg(++) as a divalent cation. The alpha-amanitin-sensitive enzyme shows maximum activity at 0.15 M KCl, whereas the resistant enzyme is most active at very low ionic strength. Analysis of the resistant enzyme on polyacrylamide gels containing sodium dodecyl sulfate shows two subunits present in a 1:1 ratio with molecular weights of 205,000 and 125,000.     

New Small Polypeptides Associated with DNA-Dependent RNA Polymerase of Escherichia coli after Infection with Bacteriophage T4

Four new small polypeptides are associated with DNA-dependent RNA polymerase from E. coli after infection with T4 phage. The new polypeptides are easily detected in RNA polymerase from E. coli cells labeled with amino acids after phage infection. Their molecular weights range from 10,000 to 22,000, as detected by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. All four polypeptides are found after infection with either wild-type T4 phage or T4 early amber mutants in genes 44, 42, 47, and 46. None of the polypeptides is labeled significantly before 5 min after infection at 30 degrees . When two maturation-defective amber mutants in gene 55 of T4 phage are used for infection, a polypeptide with a molecular weight of 22,000 is absent. When a maturation-defective amber mutant in gene 33 of T4 phage is used, another small protein is absent.     

Affinity alkylation labels two subunits of the reduced acetylcholine receptor from mammalian muscle.

The acetylcholine receptor from denervated rat skeletal muscle was purified by affinity chromatography and, after reduction, was treated with the affinity alkylating agent 4-(N-maleimido)benzyltri[3H]methylammonium iodide. The receptor specifically incorporated approximately 1 mol of alkylating agent per mol of 125I-labeled alpha-bungarotoxin bound. Analysis of the labeled receptor by polyacrylamide gel electrophoresis in sodium dodecyl sulfate showed that two subunits were labeled; their apparent molecular weights were 45,000 and 49,000. These results suggest that the affinity reagent labels a second site for acetylcholine binding in the muscle receptor that is not labeled in receptors from Electrophorus or Torpedo.     

Tumor antigen(s) in cells productively infected by wild-type polyoma virus and mutant NG-18

When isolated by means of an anti-polyoma tumor (T) antiserum, the major product from mouse cells productively infected by wild-type polyoma virus is a polypeptide of 100,000 apparent molecular weight as judged by sodium dodecyl sulfate/polyacrylamide gel electrophoresis. In cells infected by NG-18, an hr-t mutant carrying a deletion of about 150 base pairs in the early region of the viral DNA, a T antigen species appears that comigrates with that of the wild-type virus. Comparisons of peptides after partial proteolysis reveal no differences between mutant and wild-type products. Both wild-type and mutant 100,000 products can be labeled in vivo with [(32)P]orthophosphate. An independent and more reliable estimate of the molecular weight of this protein using guanidine/Sepharose chromatography yields a value of 81,000 for both mutant and wild-type species. The apparent identity of wild-type and mutant products indicates that the deletion in NG-18 lies outside of the region encoding this major T antigen species.Immunoprecipitates from wild-type infected cells shows four bands in addition to the "100,000" band; these have apparent molecular weights of 63,000, 56,000, 36,000, and 22,000 by sodium dodecyl sulfate/polyacrylamide gel electrophoresis; the 56,000 and 36,000 species are phosphorylated. All four of these lower molecular weight bands are absent or drastically reduced in the immunoprecipitates from NG-18-infected cells.     

Identification of the Essential Light Chains of Myosin

The molecular weights of light chains associated with adult and embryonic chick myosin have been determined by polyacrylamide gel electrophoresis in the presence of 0.1% sodium dodecyl sulfate. Adult muscle myosin contains three light chains with molecular weights averaging 27,700, 21,000, and 16,500, while the embryonic form contains only the two largest of these three. Recombination and hybridization experiments have been performed with these samples. The data clearly demonstrate that only two light chains are required for the expression of the full ATPase activity of myosin. The third light chain consistently is associated with adult myosin, but definitive evidence for its role is lacking.