High-sensitivity sequence determination of proteins quantitatively recovered from sodium dodecyl sulfate gels using an improved electrodialysis procedure

Preparative isolation of protein complexes and other bioparticles by elution from polyacrylamide gels

Due to its unmatched resolution, gel electrophoresis is an indispensable tool for the analysis of diverse biomolecules. By adaptation of the electrophoretic conditions, even fragile protein complexes as parts of intracellular networks migrate through the gel matrix under sustainment of their integrity. If the thickness of such native gels is significantly increased compared to the analytical version, also high sample loads can be processed. However, the cage-like network obstructs an in-depth analysis for deciphering structure and function of protein complexes and other species. Consequently, the biomolecules have to be removed from the gel matrix into solution. Several approaches summarized in this review tackle this problem. While passive elution relies on diffusion processes, electroelution employs an electric field to force biomolecules out of the gel. An alternative procedure requires a special electrophoresis setup, the continuous elution device. In this apparatus, molecules migrate in the electric field until they leave the gel and were collected in a buffer stream. Successful isolation of diverse protein complexes like photosystems, ATP-dependent enzymes or active respiratory supercomplexes and some other bioparticles demonstrates the versatility of preparative electrophoresis. After liberating particles out of the gel cage, numerous applications are feasible. They include elucidation of the individual components up to high resolution structures of protein complexes. Therefore, preparative electrophoresis can complement standard purification methods and is in some cases superior to them.

Sample preparation by in-gel digestion for mass spectrometry-based proteomics

The proteomic characterization of proteins and protein complexes from cells and cell organelles is the next challenge for investigation of the cell. After isolation of the cell compartment, three steps have to be performed in the laboratory to yield information about the proteins present. The protein mixtures must be separated into single species, broken down into peptides, and, finally, identified by mass spectrometry. Most scientists engaged in proteomics separate proteins by electrophoresis. For characterization and identification of proteomes, mass spectrometry of peptides is the method of choice. To combine electrophoresis and mass spectrometry, sample preparation by "in-gel digestion" has been developed. Many procedures are available for in-gel digestion, which inspired us to review in-gel digestion approaches.

Crystal structure of omega transcriptional repressor encoded by Streptococcus pyogenes plasmid pSM19035 at 1.5 A resolution

The 71 amino acid residue omega protein encoded by the Streptococcus pyogenes non-conjugative plasmid pSM19035 is a transcriptional repressor that regulates expression of genes for copy number control and stable maintenance of plasmids. The crystal structure of omega protein has been determined by multiple isomorphous replacement, including anomalous scattering and refined to an R-factor of 21.1 % (R(free)=23.2 %) at 1.5 A resolution. Two monomers related by a non-crystallographic 2-fold axis form a homodimer that occupies the asymmetric unit. Each polypeptide chain is folded into two alpha-helices and one beta-strand forming an antiparallel beta-ribbon in the homodimer. The N-terminal regions (1-23 and 1-22 in subunits I and II, respectively) are not defined in the electron density due to proteolysis of the N-terminal 20 amino acid residues during crystallisation and partial disorder. The omega protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognizing the major groove of operator DNA; according to a modelled omega protein-DNA complex, residues Arg31 and Arg31' on the beta-ribbon are in positions to interact with a nucleobase, especially guanine.

A comparative analysis of the differential spatial and temporal distributions of the large (aggrecan, versican) and small (decorin, biglycan, fibromodulin) proteoglycans of the intervertebral disc

This study provides a comparative analysis of the temporal and spatial distribution of 5 intervertebral disc (IVD) proteoglycans (PGs) in sheep. The main PGs in the 2 and 10 y old sheep groups were polydisperse chondroitin sulphate and keratan sulphate substituted species. Their proportions did not differ markedly either with spinal level or disc zone. In contrast, the fetal discs contained 2 slow migrating (by composite agarose polyacrylamide gel electrophoresis, CAPAGE), relatively monodisperse chondroitin sulphate-rich aggrecan species which were also identified by monoclonal antibody 7-D-4 to an atypical chondroitin sulphate isomer presentation previously found in chick limb bud, and shark cartilage. The main small PG detectable in the fetal discs was biglycan, whereas decorin predominated in the 2 and 10 y old IVD samples; its levels were highest in the outer annulus fibrosus (AF). Versican was most abundant in the AF of the fetal sheep group; it was significantly less abundant in the 2 and 10 y old groups. Furthermore, versican was immunolocalised between adjacent layers of annular lamellae suggesting that it may have some role in the provision of the viscoelastic properties to this tissue. Versican was also diffusely distributed throughout the nucleus pulposus of fetal IVDs, and its levels were significantly lower in adult IVD specimens. This is the first study to identify versican in ovine IVD tissue sections and confirmed an earlier study which demonstrated that ovine IVD cells synthesised versican in culture (Melrose et al. 2000). The variable distribution of the PGs identified in this study provides further evidence of differences in phenotypic expression of IVD cell populations during growth and development and further demonstrates the complexity of the PGs in this heterogeneous but intricately organised connective tissue.

Comprehensive two-dimensional high-performance liquid chromatography for the isolation of overexpressed proteins and proteome mapping

A two-dimensional liquid chromatographic system is described here which uses size-exclusion liquid chromatography (SEC) followed by reversed-phase liquid chromatography (RPLC) to separate the mixture of proteins resulting from the lysis of Escherichia coli cells and to isolate the proteins that they produce. The size-exclusion chromatography can be conducted under either denaturing or nondenaturing conditions. Peaks eluting from the first dimension are automatically subjected to reversed-phase chromatography to separate similarly sized proteins on the basis of their various hydrophobicities. The RPLC also serves to desalt the analytes so that they can be detected in the deep ultraviolet region at 215 nm regardless of the SEC mobile phase used. The two-dimensional (2D) chromatograms produced in this manner then strongly resemble the format of stained 2D gels, in that spots are displayed on a X-Y axis and intensity represents quantity of analyte. Following chromatographic separation, the analytes are deposited into six 96-well (576 total) polypropylene microtiter plates via a fraction collector. Interesting fractions are analyzed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/MS) or electrospray mass spectrometry (ESI/MS) depending on sample concentration, which both yield accurate (2 to 0.02%) molecular weight information on intact proteins without any additional sample preparation, electroblotting, destaining, etc. The remaining 97% of a fraction can then be used for other analyses, such Edman sequencing, amino acid analysis, or proteolytic digestion and sequencing by tandem mass spectrometry. This 2D HPLC protein purification and identification system was used to isolate the src homology (SH2) domain of the nonreceptor tyrosine kinase pp60c-src and beta-lactamase, both inserted into E. coli, as well as a number of native proteins comprising a small portion of the E. coli proteome.

Elongation factor Ts of Chlamydia trachomatis: structure of the gene and properties of the protein

A putative structural gene cluster containing four open reading frames (ORFs) located downstream of the omp1 gene of Chlamydia trachomatis mouse pneumonitis (MoPn) was cloned and sequenced. A GenBank survey indicated that the identified cluster is similar to the rpsB-tsf-pyrH(smbA)-frr region of Escherichia coli. The second ORF was 846 bp encoding a 282-amino-acid polypeptide with a calculated M(r) 30,824. Alignment of this deduced protein sequence and E. coli elongation factor Ts (EF-Ts, product of tsf) demonstrated 34% identity and an additional 14% similarity. The putative chlamydial tsf gene was expressed in E. coli as a nonfusion protein and as a 6x His-tagged fusion protein. By SDS-PAGE analysis, the molecular weights of the nonfusion recombinant protein and a protein of chlamydial elementary bodies (EBs), which was recognized by monoclonal antibodies derived from the nonfusion recombinant protein, are 34 kDa. The purified recombinant 6x His-tagged fusion protein increased the rate of GDP exchange with both Chlamydia and E. coli elongation factor Tu (EF-Tu). These data show that the second gene of the identified cluster is tsf. Unlike EF-Ts from any other species, its activity was comparable to that of E. coli EF-Ts in exchange reaction with E. coli EF-Tu.

The anion transporter and a 28 kDa protein are selectively photolabeled by p-azidobenzylphlorizin under conditions that alter RBC morphology, flexibility, and volume

Tritiated p-azidobenzylphlorizin (p-AzBPhz) was photoactivated in the presence of red blood cells under conditions previously found to alter morphology, flexibility and volume. When less than 0.25 million molecules were added per cell, only a 28 kDa peptide was photolabeled: at 1-2 million molecules added, band 3 also incorporated significant radioactivity. When using leaky ghosts, other proteins became labeled, including those limited to the cytoplasm. Protein N-deglycosylation caused a shift of radiolabeled band 3 to higher Rf values on SDS-PAGE gels but not for the 28 kDa band; the latter was, however, susceptible to enzymatic digestion by NANase (N-acetylneuraminidase) III but not by NANase II. Inhibition of photoincorporation into both receptors by unlabeled p-AzBPhz was dose-dependent. Mercuric chloride and p-CMBS selectively blocked 28 kDa peptide labeling. DIDS partially blocked at band 3; after 15% inhibition, greater DIDS concentrations caused increased incorporation into the 28 kDa peptide. These results, and a temperature-dependent labeling pattern, suggest that: (i) cellular changes occur when p-AzBPhz binds to the exofacial sides of the anion transporter and 28 kDa peptide; (ii) these proteins may be physically associated in the native membrane; (iii) they mediate ligand-induced changes in morphology, flexibility, and volume.

Purification and properties of alternanase, a novel endo-alpha-1,3-alpha-1,6-D-glucanase

A newly isolated soil bacterium strain NRRL B-21195, tentatively identified as a Bacillus species, was found to be a constitutive producer of a novel type of glycanase that hydrolyses in an endo-fashion the polysaccharide alternan, an alpha-1,3-alpha-1,6-D-glucan, referred to in the literature as B-1355 dextran (fraction S), synthesized from sucrose by alternansucrase of Leuconostoc mesenteroides. The glycanase, named alternanase, has been purified to homogeneity from a cell-free culture fluid of the bacillus grown in a liquid medium containing D-glucose, and has been characterized. The enzyme has a molecular mass of 110000 Da (SDS/PAGE) and an isoelectric point of approximately 4.0. Optimum activity occurs at pH 7 and at a temperature of 40 degrees C. The enzyme is stable up to 50 degrees C but loses activity rapidly at 60 degrees C. Its action is inhibited by EDTA and stimulated by Ca2+. The enzyme requires, for its action, D-glucan chains in which alpha-1,3-linkages alternate with alpha-1,6-linkages; i.e., it is specific for alternan. Monitoring of alternan hydrolysis by determination of liberated reducing sugars pointed to an unusually low extent of hydrolysis and a low specific activity of the enzyme. As shown in the accompanying paper [Côté, G. L. & Biely, P. (1994) Eur. J. Biochem. 226, 641-648] the reason for this finding is that the main hydrolytic products are non-reducing, novel types of cyclic oligosaccharides.

Immunological similarities among trichocyst secretory proteins of Paramecium caudatum, Paramecium tetraurelia and Pseudomicrothorax dubius

Secretory vesicles called trichocysts structurally show a body and a tip in Paramecium and a shaft and four arms in Pseudomicrothorax. Biochemical and immunological relationships between both trichocyst types were examined. Three polyclonal antibodies were produced against 3 groups of protein bands of isolated Pseudomicrothorax dubius trichocysts separated by one-dimensional gel electrophoresis: G 1 (30-31 kDa), G 2 (26-27 kDa) and G 3 (15-20 kDa). By indirect immunofluorescent binding assay, the three antisera label extended (i.e. discharged) and condensed (i.e. non-discharged) trichocysts of both Ps. dubius and Paramecium caudatum. By immunogold labeling on ultrathin sections, the three antisera label the trichocyst shaft of Ps. dubius and the trichocyst body of Pa. caudatum on both condensed and extended secretory vesicles. On two-dimensional immunoblots, remarkable antigenic similarities are shown by trichocysts of Ps. dubius, Paramecium tetraurelia nd6 and Pa. caudatum. Anti-G 1 serum detects proteins at 28-32 kDa, pI 5.0-5.7, in the three cells. Anti-G 3 serum labels one protein group at ~ 15-22 kDa and a second protein group at ~ 35-50 kDa in Ps. dubius, Pa. tetraurelia nd6 and Pa. caudatum. Anti-G 2 serum labels proteins at ~ 15-22 kDa, pI 4.7-5.2, in all three species. Anti-G 2 serum also detects bands at 24-28 kDa and 30-31 kDa, pI 4.7-6.1, in Ps. dubius. No equivalent M(r) proteins are observed in either Paramecium spp. Comparisons of immunoblots of proteins of entire cells with and without ejectable trichocysts allowed identification of non-ejectable trichocyst proteins, some of which may be precursors localized within pretrichocysts. Such proteins are at 41-47 kDa in Ps. dubius, and at ~ 45 kDa in Paramecium.

Identification and molecular characterization of E-MAP-115, a novel microtubule-associated protein predominantly expressed in epithelial cells

A novel microtubule-associated protein (MAP) of M(r) 115,000 has been identified by screening of a HeLa cell cDNA expression library with an anti-serum raised against microtubule-binding proteins from HeLa cells. Monoclonal and affinity-purified polyclonal antibodies were generated for the further characterization of this MAP. It is different from the microtubule-binding proteins of similar molecular weights, characterized so far, by its nucleotide-insensitive binding to microtubules and different sedimentation behavior. Since it is predominantly expressed in cells of epithelial origin (Caco-2, HeLa, MDCK), and rare (human skin, A72) or not detectable (Vero) in fibroblastic cells, we name it E-MAP-115 (epithelial MAP of 115 kD). In HeLa cells, E-MAP-115 is preferentially associated with subdomains or subsets of perinuclear microtubules. In Caco-2 cells, labeling for E-MAP-115 increases when they polarize and form blisters. The molecular characterization of E-MAP-115 reveals that it is a novel protein with no significant homologies to other known proteins. The secondary structure predicted from its sequence indicates two domains connected by a putative hinge region rich in proline and alanine (PAPA region). E-MAP-115 has two highly charged regions with predicted alpha-helical structure, one basic with a pI of 10.9 in the NH2-terminal domain and one neutral with a pI of 7.6 immediately following the PAPA region in the acidic COOH-terminal half of the molecule. A novel microtubule-binding site has been localized to the basic alpha-helical region in the NH2-terminal domain using in vitro microtubule-binding assays and expression of mutant polypeptides in vivo. Overexpression of this domain of E-MAP-115 by transfection of fibroblasts lacking significant levels of this protein with its cDNA renders microtubules stable to nocodazole. We conclude that E-MAP-115 is a microtubule-stabilizing protein that may play an important role during reorganization of microtubules during polarization and differentiation of epithelial cells.

Purification and properties of the soluble midgut trehalase from the gypsy moth, Lymantria dispar

The midgut trehalase (THA) from fifth instar Lymantria dispar (gypsy moth) larvae was purified to homogeneity by two separate methods: gel filtration followed by Rotofor preparative IEF, and affinity chromatography on trehalose coupled to Sepharose 6B followed by preparative polyacrylamide gel electrophoresis. Midgut THA from the last stadium L. dispar larvae existed mainly in soluble form and displayed a single band of activity in nondenaturing polyacrylamide gels when stained by a THA-specific staining procedure. Analytical IEF of purified midgut THA revealed a single protein band with an apparent pI of 4.6. SDS-PAGE and gel permeation studies indicated that the smallest active form of THA in the late fifth instar larval midgut was a monomeric protein with an approximate size of 60 kDa. A specific activity of 67 units/mg of protein at 30 degrees C and at pH 6.4 was determined for the enzyme purified by affinity chromatography and preparative gel electrophoresis. The midgut enzyme exhibited a very high substrate specificity with a Km of 0.4 mM for trehalose. The enzyme was maximally active at pH 5.4-6.0 and was thermally stable at temperatures up to 65 degrees C. The midgut THA was insensitive to inhibition by a high concentration of Tris, sucrose, p-nitrophenyl-beta-D-glucoside or phloridzin. Divalent cations metal ions, hypertrehalosaemic hormone and octopamine had no significant effect on the activity of the purified enzyme in vitro. The purified enzyme was inactivated by modification with DEP and was competitively inhibited by castanospermine with an apparent Ki of 0.8 x 10(-6)M at pH 6.4.

Immunological characterization of trichocyst proteins in the ciliate Pseudomicrothorax dubius

Ejectable trichocysts were isolated from the ciliate Pseudomicrothorax dubius. Polyclonal antibodies were raised against three groups of trichocyst proteins: G1 (30-31 kDa), G2 (26-27 kDa) and G3 (15-20 kDa). By indirect immunofluorescence, the three antisera strongly label the shafts of ejected trichocysts and the proximal ends of condensed trichocysts within the cells. By immunogold labeling for electron microscopy, the three sera specifically recognize the shafts of both extended and condensed trichocysts and shaft precursors in pretrichocysts as well. On one-dimensional immunoblots of isolated trichocysts, anti-G1 serum recognizes the G1 proteins, anti-G2 serum detects G2 proteins and some G1 proteins, and anti-G3 serum reacts with 15 bands, mainly the G3 and (30-41)-kDa proteins. In cells with and without trichocysts, the sera recognize non-ejectable trichocyst proteins at 41-42 kDa and 47 kDa. On two-dimensional immunoblots of isolated trichocysts, anti-G1 serum labels proteins with a pI of 4.75-5.7, anti-G2 serum labels proteins with a pI of 4.75-6.25 and anti-G3 serum labels proteins with a pI of 4.7-6.6. Analyses of cells with and without trichocysts allow identification of possible precursors between 41 and 47 kDa. Some are in the same pI range as their putative products, but others, labeled by anti-G3 serum, are less acidic than most of their mature products.

Detection of allergens in a cat pelt extract

Allergenic components of cat pelt extract fractionated by SDS-polyacrylamide gel electrophoresis (PAGE) and transferred to nitrocellulose membranes were identified using sera from 15 allergic patients who showed positive skin test and RAST to cat extract. Two components showed the highest IgE-binding frequency; 14 kD (being recognized by 86% of the sera examined) and 29 kD (73% of the sera tested). Both components were purified by electroelution and subjected to RAST inhibition assays. The 29 kD fraction was able to bind specific IgE to D. pteronyssinus and inhibited a RAST assay of 29 kD component (Der p I) purified from a D. pteronyssinus extract. These results could explain the finding of positive skin test with some commercial cat allergen solutions in patients with D. pteronyssinus allergy.

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.

Purification and characterization of a peanut-agglutinin-binding pancreatic-cancer-related serum mucus glycoprotein

A high-molecular-weight (approximately 3.5 x 10(3) kDa) peanut agglutinin (PNA)-binding glycoprotein was previously identified as a tumour marker in pancreatic cancer sera. In the present study the density of this glycoprotein has been estimated and further analysis performed using sequential lectin blotting combined with serial mild acid hydrolysis followed by repeated Smith degradation. This has allowed partial in-situ characterization of the carbohydrate side-chains. The PNA-binding glycoprotein variably expresses the blood group H and sialylated Lewis a antigens. H and sialyl Lea expression disappeared after mild acid hydrolysis and T (PNA acceptor) disappeared after the first Smith degradation step. T (beta gal(1-3)alpha galNAc) expression reappeared after a second Smith degradation, suggesting that the backbone regions of the mucin side-chains with this core sequence are built up by the further addition of at least 2 monosaccharides. A model has been constructed showing the minimum variations in side chain structure that would explain the results of the serial degradation and lectin blotting. Purification and caesium chloride density gradient centrifugation show that the intact PNA-binding glycoprotein has a density of greater than 1.48 g/ml, characteristic of a mucin. The development of assays using a panel of monoclonal antibodies (MAbs) or lectins directed against the different carbohydrate epitopes expressed on this mucin may provide better diagnostic accuracy for pancreatic cancer than current marker assays which rely on detection of a single epitope.

A mutant poliovirus containing a novel proteolytic cleavage site in VP3 is altered in viral maturation

A six-amino-acid insertion containing a Q-G amino acid pair was introduced into the carboxy terminus of the capsid protein VP3 (between residues 236 and 237). Transfection of monkey cells with full-length poliovirus cDNA containing the insertion described above yields a mutant virus (Sel-1C-02) in which cleavage occurs almost entirely at the inserted Q-G amino acid pair instead of at the wild-type VP3-VP1 cleavage site. Mutant Sel-1C-02 is delayed in the kinetics of virus production at 39 degrees C and exhibits a defect in VP0 cleavage into VP2 and VP4 at 39 degrees C. Sucrose gradient analysis of HeLa cell extracts prepared from cells infected by Sel-1C-02 at 39 degrees C shows an accumulation of fast-sedimenting replication-packaging complexes and a significant amount of uncleaved VP0 present in fractions containing mature virions. Our data provide in vivo evidence for the importance of determinants other than the conserved amino acid pair (Q-G) for recognition and cleavage of the P1 precursor by proteinase 3CD and show that an alteration in the carboxy terminus of VP3 or the amino terminus of VP1 affects the process of viral maturation.

Fatty acid acylation of vaccinia virus proteins

Labeling of vaccinia virus-infected cells with [3H]myristic acid resulted in the incorporation of label into two viral proteins with apparent molecular weights of 35,000 and 25,000 (designated M35 and M25, respectively). M35 and M25 were expressed in infected cells after the onset of viral DNA replication, and both proteins were present in purified intracellular virus particles. Virion localization experiments determined M25 to be a constituent of the virion envelope, while M35 appeared to be peripherally associated with the virion core. M35 and M25 labeled by [3H]myristic acid were stable to treatment with neutral hydroxylamine, suggesting an amide-linked acylation of the proteins. Chromatographic identification of the protein-bound fatty acid moieties liberated after acid methanolysis of M25, isolated from infected cells labeled during a 4-h pulse, resulted in the recovery of 25% of the protein-bound fatty acid as myristate-associated label and 75% as palmitate, indicating that interconversion of myristate to palmitate had occurred during the labeling period. Similar analyses of M25 and M35, isolated from infected cells labeled during a 0.5-h pulse, determined that 46 and 43%, respectively, of the protein-bound label had been elongated to palmitate even during this brief labeling period. In contrast, M25 and M35 isolated from purified intracellular virions labeled continuously during 24 h of growth contained 75 and 70%, respectively, myristate-associated label, suggesting greater stability of these proteins or a favored interaction of the proteins containing myristate with the maturing or intracellular virion.

Direct N-terminal sequence analysis of rat liver plasma membrane glycoproteins separated by two-dimensional polyacrylamide gel electrophoresis

Nine previously uncharacterized membrane glycoproteins from normal rat liver have been analyzed by amino acid sequencing from two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) after transblotting to Immobilon-P membranes. Three of these components show altered levels of expression in liver tumors. A single electroblotted polyacrylamide gel yielded sufficient quantities of these glycoproteins for amino acid sequencing and the N-terminal structure could be determined for four of them. The remaining five glycoproteins of interest were not sequenceable in this manner, presumably because they had blocked N-termini. Prior to electrophoresis, two enrichment methods were applied to the crude liver membrane preparations: affinity chromatography with concanavalin A to isolate the plasma membrane glycoproteins and then fast protein liquid chromatography on Superose 12 to obtain components having a specific range of molecular weights. These materials were next subjected to 2-D PAGE using pH 4-6 carrier ampholytes in the first dimension and 7.5% sodium dodecyl sulfate gels in the second. The proteins were then electroblotted to Immobilon-P membranes and located by staining with Coomassie Brilliant Blue R-250. Our results demonstrate that N-terminal sequencing (gas-phase) can be achieved on polypeptides obtained from approximately 250 micrograms of total glycoproteins applied to a single 2-D gel.

Isolation of aldehyde oxidase (EC 1.2.3.1) from potato extracts by preparative page

A method is proposed for the isolation (and purification) of enzymes, with retention of their activity, from solutions or gels of preparative PAGE runs. It is based on the inclusion of Sephadex G-25 as a supporting medium for a collector buffer in otherwise normal disc-PAGE gels. The collector buffer has a lower pH and higher concentration than the stacking gel buffer. This makes the proteins concentrate in a very narrow, slowly moving band in the Sephadex on electrophoresis, and makes their recovery easy. The method is illustrated by the isolation of aldehyde oxidase from potato extracts (which was unsuccessful by classical methods), and of one isoenzyme from commercial lipoxygenase after preparative PAGE. Recovery of chicken egg albumin after PAGE was over 90%.

Conversion of the beckman liquid phase sequencer to a gas-liquid phase sequencer

As an effective aid to extend the microsequencing capabilities the Beckman protein/peptide sequenator Series 890C has been successfully converted to a gas-liquid system, in which coupling buffer 25% trimethylamine was employed as a gas, and heptafluorobutyric acid as a liquid. The system has been found to be efficient for microsequencing (less than 100 pmol). The details of mechanical, plumbing, and other minor changes are described in this paper along with the results of sequencing proteins and peptides, directly and from blots.

Identification of an endothelial cell product as an inhibitor of tissue factor activity

An endothelial cell glycoprotein that inhibits the initiation of the coagulation process promoted by tissue factor has been isolated by heparin-sepharose, hydroxyapatite and gel filtration chromatography. As is the case for several other species synthesized by this cell type, the N-linked carbohydrate moiety is sulfated. The identification of this inhibitor hints at the possible existence of a functional balance, between the activator of the coagulation cascade and its inhibitor, which may become perturbed in various pathophysiological conditions.

Mapping and sequence of the gene encoding protein p37, a major structural protein of African swine fever virus

The gene encoding protein p37, one of the major structural proteins of African swine fever (ASF) virus has been mapped and sequenced. Protein p37 was obtained from purified virions and the first 27 amino acids from its NH2-terminal end were identified by automatic Edman degradation. To map the gene encoding protein p37, a mixture of 20-mer deoxyoligonucleotides based upon a part of this amino acid sequence was hybridized to cloned ASF virus restriction fragments. This allowed localization of the gene in fragment KpnI F/HindIII G1 of the African swine fever virus genome. An analysis of the DNA sequence from this region revealed an open reading frame encoding 418 amino acids. In this sequence, the 27 NH2-terminal amino acids determined by sequence analysis of protein p37 are preceded by a stretch of 132 amino acids residues, indicating that protein p37 is synthesized as a polypeptide of higher molecular weight and then post-translationally processed by cleavage of a Gly-Ala bond. This processing event accounts for the antigenic relationship of protein p37 to a virus-induced, nonstructural protein with a relative molecular weight of 60 kD.

Purification of proteins from polyacrylamide gels, free of detergent or dye

A two step procedure recovers proteins from sodium dodecyl sulfate polyacrylamide gels. The proteins are eluted by electrophoretic dialysis. The eluent is then passed through an Amberlite CG-400 anion-exchange resin. The recovery of protein is nearly total. The recovered proteins have no detectable sodium dodecyl sulfate contamination. With gels that have been stained with Coomassie Brilliant Blue R, the procedure recovers the proteins free of the dye. We have used this procedure successfully during the purification of epidermal glycoproteins.

A hydroxyproline-rich protein in the soybean cell wall

A cDNA clone that hybridizes to an mRNA (1A10) that accumulates to a substantial level in the axis of the germinating soybean seed was sequenced. The amino acid sequence of the clone indicates an almost perfect repeat of Pro-Pro-Val-Tyr-Lys resulting in a protein containing 40% proline and lacking serine and histidine. On the likelihood that such a protein might be a hydroxyproline-rich cell-wall glycoprotein (HRGP), cell walls of a soybean cell culture were extracted by procedures used to obtain soluble basic cell-wall glycoproteins, and the proteins were fractionated and purified. A 33-kDa protein (and possibly a 28-kDa protein) was obtained that has an amino acid distribution similar to that of the cDNA clone. The protein lacks histidine and serine and contains 20% hydroxyproline and 20% proline. The HRGP is thus distinct both in its amino acid content and in its pentameric repeat of Pro-Pro-Val-Tyr-Lys, with half of the prolines being hydroxylated.

Preparative elution of proteins blotted to Immobilon membranes

Conditions for the preparative elution of proteins from Immobilon membranes after transfer of proteins to this matrix from sodium dodecyl sulfate-polyacrylamide gels have been established. Proteins were completely eluted from the membrane at room temperature by short incubation in 50 mM Tris-HCl, pH 9.0, containing 2% SDS and 1% Triton X-100. Good protein recoveries were also obtained in the same buffer containing 1% Triton X-100 only. The efficiency of elution was practically independent of the molecular weight of proteins, the method allowed for the precise excision of protein bands, and the proteins eluted from the matrix were not degraded. In some cases it was possible to recover enzymatic activity of the eluted proteins.

Recovery of polypeptides from polyacrylamide gels by electrophoretic elution in a centrifugation concentrator

A method for recovery of polypeptides from polyacrylamide gels by electrophoretic elution in a commercially available concentrator, the Amicon-Centricon sample reservoir, has been devised. The recoveries were greater than 90% with four different polypeptides tested (12.5 to 80 kDa). After elution, sample concentration or salt exchange can be carried out without sample transfer. There were no loss of sample during the postelution procedures when the elution buffer was replaced by 0.01 or 0.05% sodium dodecyl sulfate.

Biosynthesis and phosphorylation of vaccinia virus structural protein VP11

One of the major DNA binding proteins contained in vaccinia virus is an 11-kDA species denoted VP11. The biosynthesis of VP11, a late polypeptide, occurs subsequent to the initiation of viral DNA replication. In particular, VP11 synthesis is blocked by cytosine arabinoside, a specific inhibitor of DNA synthesis. We show here that VP11 is specifically phosphorylated subsequent to translation. Phosphorylated VP11 is present both in viral core particles and in the cytoplasm of virus-infected cells. Kinetic analysis reveals that the total amount of phosphorylated VP11 species increases rapidly and remains approximately constant for as long as 17 hr postinfection. Phosphorylation occurs at two different serine residues, progressing from either site singly to the diphosphorylated product. Under steady-state conditions, the phosphorylated derivative constitutes approximately 85% of total VP11 in extracts of vaccinia virus-infected cells. Even though 15% of the VP11 remains unphosphorylated in cell extracts, only phosphorylated VP11 is found in mature viral cores.

Biochemical characterization of a T-lymphoma-specific 90,000 molecular weight disulfide linked dimeric glycoprotein

The biochemical features of a membrane antigen detected by a mouse monoclonal antibody (A1) raised against the murine thymoma cell line EL4 are described. This reagent detected a novel disulfide-linked 90,000 mol. wt dimeric membrane glycoprotein composed of two chains of approx 45,000 mol. wt. Endo-beta-N-acetylglucosaminidase F digestion generated a single 28,000 polypeptide, thus suggesting that the A1 molecule is a homodimer. No structural homology between the A1 molecule and the human T 90/44 protein (9.3 antigen) could be revealed by peptide mapping analysis. In view of the fact that three polypeptides of mol. wts 28,000-30,000, 21,000 and 15,000 respectively co-precipitated with the A1 antigen, the possible relationship of the A1 molecular complex to other known T-cell surface antigens including the antigen receptor is discussed.

Purification and Some Properties of a Membrane-Bound Aminopeptidase A from Streptococcus cremoris

A membrane-bound l -α-glutamyl (aspartyl)-peptide hydrolase (aminopeptidase A) (EC 3.4.11.7) from Streptococcus cremoris HP has been purified to homogeneity. The free γ-carboxyl group rather than the amino group of the N-terminal l -α-glutamyl (aspartyl) residue appeared to be essential for catalysis. No endopeptidase activity could be established with this enzyme. The native enzyme is a polymeric, most probably trimeric, metalloenzyme (relative molecular weight, approximately 130,000) which shows on sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels apparent high relative molecular weight values due to (lipid?) material dissociable with butanol. The subunit (relative molecular weight, approximately 43,000) is catalytically inactive. The enzyme is inactivated completely by dithiothreitol, chelating agents, and the bivalent metal ions Cu 2+ and Hg 2+ . Of the sulfhydryl-blocking reagents tested, only p -hydroxymercuribenzoate appeared to inhibit the enzyme. Activity lost by treatment with a chelating agent could be restored by Co 2+ and Zn 2+ . The importance of the occurrence of an aminopeptidase A in S. cremoris with respect to growth in milk is discussed.

Intracellular growth factors in polycythemia vera and other myeloproliferative disorders

In polycythemia vera, idiopathic myelofibrosis, and essential thrombocytosis, hematopoietic cell proliferation is increased in the absence of a recognizable stimulus, suggesting the autonomous production of growth factors in these disorders. Sonicates of peripheral blood mononuclear cells (PBMNC) from patients with polycythemia vera, idiopathic myelofibrosis, and essential thrombocytosis contained soluble factors that stimulated the proliferation of quiescent-confluent 3T3 cells. PBMNC sonicates from normal individuals; from patients with secondary erythrocytosis, chronic myelogenous leukemia, B-cell chronic lymphocytic leukemia, and acute myelogenous leukemia; and from K-562 and HL-60 cells did not stimulate proliferation. Polycythemia vera PBMNC sonicates also induced anchorage-independent colony formation in soft agar by normal rat kidney fibroblasts. Both the mitogenic and transforming activities of the polycythemia vera PBMNC sonicates resided in the T-lymphocyte-depleted mononuclear fraction of the PBMNC and were not secreted. By gel filtration, reversed-phase HPLC and NaDodSO4/PAGE, the mitogenic and transforming activities in the polycythemia vera PBMNC were localized to three proteins with molecular masses of 13-, 17-, and 65-kDa. The 13-kDa protein was only mitogenic, and the 17-kDa protein was only transforming, whereas the 65-kDa protein had both mitogenic and transforming activity. These proteins may be involved in the autonomous hematopoiesis that characterizes polycythemia vera, idiopathic myelofibrosis, and essential thrombocytosis.

Amino-terminal deletion mutants of the Rous sarcoma virus glycoprotein do not block signal peptide cleavage but can block intracellular transport

Protein sequence requirements for cleavage of the signal peptide from the Rous sarcoma virus glycoprotein have been investigated through the use of deletion mutagenesis. The phenotypes of these mutants have been characterized by expression of the cloned, mutated env genes in CV-1 cells using a late replacement SV40 vector. The deletion mutations were generated by Ba131 digestion at the XhoI site located near the 5' end of the coding sequence for the structural protein gp85, which is found at the amino terminus of the precursor glycoprotein, Pr95. The results of experiments with three mutants (X1, X2, and X3) are presented. Mutant X1 has a 14 amino acid deletion encompassing amino acids 4-17 of gp85, which results in the loss of one potential glycosylation site. In mutants X2 and X3 the amino terminal nine and six amino acids, respectively, of gp85 are deleted. During the biosynthesis of all three mutant polypeptides, the signal peptide is efficiently and accurately cleaved from the nascent protein, even though in mutants X2 and X3 the cleavage site itself has been altered. In these mutants the alanine/aspartic acid cleavage site has been mutated to alanine/asparagine and alanine/glutamine, respectively. These results are consistent with the concept that sequences C-terminal to the signal peptidase site are unimportant in defining the site of cleavage in eucaryotes. Mutants X2 and X3 behave like wild-type with respect to protein glycosylation, palmitic acid addition, cleavage to gp85 and gp37, and expression on the cell surface. Mutant X1, on the other hand, is defective in intracellular transport. Although it is translocated across the rough endoplasmic reticulum and core-glycosylated, its transport appears to be blocked at an early Golgi compartment. No terminal glycosylation of the protein, cleavage of the precursor protein to the mature products, or expression on the cell surface is observed. The deletion in X1 thus appears to destroy signals required for export to the cell surface.

Purification of phospholipid methyltransferase from rat liver microsomal fraction

Phospholipid methyltransferase, the enzyme that converts phosphatidylethanolamine into phosphatidylcholine with S-adenosyl-L-methionine as the methyl donor, was purified to apparent homogeneity from rat liver microsomal fraction. When analysed by SDS/polyacrylamide-gel electrophoresis only one protein, with molecular mass about 50 kDa, is detected. This protein could be phosphorylated at a single site by incubation with [alpha-32P]ATP and the catalytic subunit of cyclic AMP-dependent protein kinase. A less-purified preparation of the enzyme is mainly composed of two proteins, with molecular masses about 50 kDa and 25 kDa, the 50 kDa form being phosphorylated at the same site as the homogeneous enzyme. After purification of both proteins by electro-elution, the 25 kDa protein forms a dimer and migrates on SDS/polyacrylamide-gel electrophoresis with molecular mass about 50 kDa. Peptide maps of purified 25 kDa and 50 kDa proteins are identical, indicating that both proteins are formed by the same polypeptide chain(s). It is concluded that rat liver phospholipid methyltransferase can exist in two forms, as a monomer of 25 kDa and as a dimer of 50 kDa. The dimer can be phosphorylated by cyclic AMP-dependent protein kinase.

Determination of the Proteolytic Processing Sites in the Polyprotein Encoded by the Bottom-Component RNA of Cowpea Mosaic Virus

The bottom-component RNA (B-RNA) of cowpea mosaic virus is expressed by the production of a ∼200,000-dalton polyprotein (200K polyprotein), from which the functional proteins are formed by specific proteolytic cleavages. Partial amino-terminal sequences of the various B-RNA-encoded proteins have now been determined. Comparison of the information obtained with the B-RNA sequence allowed the localization of the coding regions for these proteins on B-RNA, the calculation of their precise molecular weights, and the determination of the cleavage sites at which they are released from the polyprotein precursor. Sequence analysis of the 32K protein, which is derived from the amino-terminal end of the 200K polyprotein, indicated that the AUG codon at nucleotide position 207 of the RNA sequence is the translation initiation codon. Sequence analysis of the 170K, 110K, 87K, 84K, 60K, and 58K proteins revealed the existence of three types of cleavage site in the 200K polyprotein: glutamine-serine (two sites), glutamine-methionine (one site), and glutamine-glycine (one site) amino acid pairs. The nature of these cleavage sites suggested that two different viral proteases are involved in the processing of the B-RNA-encoded polyprotein.

Determination of attachment sites for N-linked carbohydrate groups of class II histocompatibility alpha-chain and analysis of possible O-linked glycosylation of alpha- and gamma-chains

Two glycopeptide fractions were isolated from a tryptic digest of the human class II antigen alpha-subunit, by chromatography on Lens culinaris and Ricinus communis lectin columns, respectively. Partial NH2-terminal sequence analysis of radiochemically labelled glycopeptide fractions allowed alignment with two stretches of the deduced DR alpha sequence, each encompassing a signal for N-linked glycosylation, i.e. Asn-X-Thr(Ser). The fraction displaying affinity for L. culinaris lectin was susceptible to the action of endo-beta-N-acetylglucosaminidase H whereas the fraction adsorbed to R. communis was not. Since DR alpha is known to carry only one N-linked carbohydrate chain in the high-mannose form, this glycan could thereby be mapped to Asn 78. Accordingly, the complex N-linked carbohydrate is attached to Asn 118. Moreover, analysis of material released from class II antigens and gamma-chains upon mild alkaline hydrolysis, indicates the presence of O-linked sugars on the alpha- and gamma- but not the beta-subunits.

Cellular and subcellular colocalization of nerve growth factor and epidermal growth factor in mouse submandibular glands

Immunocytochemical methods have been used to compare the cellular and subcellular distribution of nerve growth factor (NGF) and epidermal growth factor (EGF) in mouse submandibular glands. Rabbit antisera raised against purified proteins were characterized by immunoblot methods and were used to stain sections of salivary glands embedded in plastic. For light microscopy, antibodies were visualized by indirect immunofluorescence. For electron microscopy, thin sections were treated simultaneously with IgG against NGF and EGF coupled to colloidal gold particles of different size. Data indicate that NGF and EGF are present in all granular convoluted tubule cells and in no other cell type within the salivary gland. Ultrastructural analyses indicate that NGF and EGF are evenly distributed together within mature secretory granules, although a population of small granules was identified that is not immunoreactive for either protein. Taken together, the data suggest that granular convoluted tubule cells are homogeneous in the production and storage of NGF and EGF.

Larval salivary gland secretion proteins in Drosophila. Identification and characterization of the Sgs-5 structural gene

The 90BC locus on the polytene chromosomal map of Drosophila melanogaster contains the structural gene for a third-instar, salivary gland-specific, polyadenylated RNA (the group V RNA). This also belongs to the intermolt puff set whose dispersed and co-ordinately regulated members are (1) transcriptionally active in the salivary gland during the third-instar developmental stage and (2) comprise (at least in part) the structural genes for a set of salivary gland secretion proteins. Previous developmental studies of the group V intermolt gene (located cytogenetically within the 90B3-8 interval) suggest that it controls the expression of a salivary gland secretion protein. By analyzing different D. melanogaster laboratory stocks for variation in group V gene expression, we have been able to correlate the presence of the group V RNA with the salivary gland secretion protein P4. In vitro translation experiments show that the salivary gland messenger RNA population derived from a stock that fails to synthesize the group V RNA does not direct the synthesis of a polypeptide similar in molecular weight to protein P4. In addition, cloned genomic DNA segments complementary to the group V RNA are capable of arresting the in vitro translation of this protein. Comparative two-dimensional fractionation of cysteine-labeled, protease-generated peptides shows that (1) the in vitro translation product arrested by group V gene DNA is biochemically very similar to or identical with the salivary gland secretion protein P4, and (2) protein P4 is equivalent to the salivary gland secretion protein previously designated SGS-5. Since designations of the latter type have been employed in naming the genetic loci that represent the structural genes for the salivary gland secretion protein gene set, the group V gene (previous designation) represents the SGS-5 structural gene and its appropriate genetic designation should now be Sgs-5.