Isolation and partial characterization of endothelial cell extracellular complexes

Human endothelial cells release components into the growth medium that stimulate cell-substratum adhesion. Several macromolecular components were isolated by ultracentrifugation of the endothelial cell conditioned medium. The components were heterogeneous, consisting of several sizes when examined by sedimentation velocity and gel filtration. When the extracellular components were evaluated by electron microscopy, structurally discrete particles were observed. The extracellular components and the complexes mediated cell-substratum adhesion to both human umbilical and arterial endothelial cells. The majority of the extracellular components that promote endothelial cell adhesion were pelleted by ultracentrifugation. Although the complexes contained fibronectin, antibodies to fibronectin did not inhibit cell adhesion to the complexes. Significant inhibition of endothelial cell adhesion was observed in the presence of heparin and heparan sulfate. The supernatant fraction following ultracentrifugation of the growth medium contained a component that suppressed endothelial cell adhesion to culture dishes coated with fibronectin, type I collagen, and endothelial cell complexes. SDS-polyacrylamide gel electrophoresis indicated that the complexes contained several components, and the majority of the large-molecular-weight components were pelleted by ultracentrifugation. The conditioned medium from human endothelial cells contains specific complexes that promote cell-substratum adhesion and components that suppress cell-substratum adhesion.     

Isolation and characterization of a tumor-specific T suppressor factor from a T cell hybridoma

In our laboratory we have described a monoclonal antibody, B16G, which has been shown to bind to suppressive T cell factors (TsF) in DBA/2 mice. Therefore, B16G was used as a probe to identify T cell hybridomas secreting putative TsF. Hybridomas were obtained by the fusion of DBA/2 thymocytes stimulated in vivo by P815 tumor membrane extracts with the thymoma BW5147. One such hybridoma, A10, was selected and used for additional studies. From both the supernatants and ascites fluid of this hybrid a factor could be obtained that could specifically bind to both B16G and P815 antigen immunoadsorbent columns, and that scored positively with B16G in an ELISA after elution. Such reactivity could not be obtained from A10 supernatants or ascites absorbed over irrelevant columns, nor was it obtained from supernatants or ascites from other T cell hybrids that had scored B16G nonreactive in the original screening. In vivo studies indicated that affinity-purified A10 material injected into DBA/2J mice enhanced significantly the growth of P815 tumor cells, but not the growth of other DBA/2 syngeneic tumor lines such as L1210 or M-I. Additionally, this material did not inhibit the in vitro mixed leukocyte reaction (MLR) between DBA/2 splenocytes and allogeneic B10.BR target cells (unlike B16G purified material from whole DBA/2 spleens, which has been demonstrated to be suppressive in this type of MLR). Biochemical analysis of this tumor-specific TsF from A10 was undertaken; the native m.w. was found to be in the region of 80,000 and 90,000. Under reducing conditions, affinity-purified A10 TsF was found to resolve in SDS-PAGE as what appeared to be a heterodimer of 45,000 and 43,000. In most preparations, an associated molecule resolving at about 25,000 was observed. The implications of these observations are discussed.     

Isolation and characterization of polyadenylation complexes assembled in vitro

We developed a two-step purification of mammalian polyadenylation complexes assembled in vitro. Biotinylated pre-mRNAs containing viral or immunoglobulin poly(A) sites were incubated with nuclear extracts prepared from mouse myeloma cells under conditions permissive for in vitro cleavage and polyadenylation and the mixture was fractionated by gel filtration; complexes containing biotinylated pre-mRNA and bound proteins were affinity purified on avidin-agarose resin. Western analysis of known components of the polyadenylation complex demonstrated copurification of polyadenylation factors with poly(A) site-containing RNA but not with control RNA substrates containing either no polyadenylation signals or a point mutation of the AAUAAA polyadenylation signal. Polyadenylation complexes that were assembled on exogenous RNA eluted from the Sephacryl column in fractions consistent with their size range extending from 2 to 4 x 10(6) Mr. Complexes endogenous to the extract were of approximately the same apparent size, but more heterogeneous in distribution. This method can be used to study polyadenylation/cleavage complexes that may form upon a number of different RNA sequences, an important step towards defining which factors might differentially associate with specific RNAs.     

Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes

Background

T cell receptors (TCRs) can recognize diverse lipid and metabolite antigens presented by MHC-like molecules CD1 and MR1, and the molecular basis of many of these interactions has not been determined. Here we applied our protein docking algorithm TCRFlexDock, previously developed to perform docking of TCRs to peptide-MHC (pMHC) molecules, to predict the binding of αβ and γδ TCRs to CD1 and MR1, starting with the structures of the unbound molecules.

Results

Evaluating against TCR-CD1d complexes with crystal structures, we achieved near-native structures in the top 20 models for two out of four cases, and an acceptable-rated prediction for a third case. We also predicted the structure of an interaction between a MAIT TCR and MR1-antigen that has not been structurally characterized, yielding a top-ranked model that agreed remarkably with a characterized TCR-MR1-antigen structure that has a nearly identical TCR α chain but a different β chain, highlighting the likely dominance of the conserved α chain in MR1-antigen recognition. Docking performance was improved by re-training our scoring function with a set of TCR-pMHC complexes, and for a case with an outlier binding mode, we found that alternative docking start positions improved predictive accuracy. We then performed unbound docking with two mycolyl-lipid specific TCRs that recognize lipid-bound CD1b, which represent a class of interactions that is not structurally characterized. Highly-ranked models of these complexes showed remarkable agreement between their binding topologies, as expected based on their shared germline sequences, while differences in residue-level interactions with their respective antigens point to possible mechanisms underlying their distinct specificities.

Conclusions

Together these results indicate that flexible docking simulations can provide accurate models and atomic-level insights into TCR recognition of MHC-like molecules presenting lipid and other small molecule antigens.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-319) contains supplementary material, which is available to authorized users.     

Isolation and biochemical characterization of cell wall tight protein complex involved in self-flocculation of Kluyveromyces bulgaricus

Flocculation of yeasts is a cell–cell aggregation phenomenon which is driven by interactions between cell wall lectins and cell wall heteropolysaccharides. In Sabouraud medium, Kluyveromyces bulgaricus was highly flocculent. Incubation of flocculent K. bulgaricus cells with EDTA or Hecameg® led to extracts showing hemagglutinating and flocculating properties. Purification of the extracts by native PAGE gave two bands which allowed flocculation of deflocculated K. bulgaricus. Both bands with specific reflocculating activity were composed of five subunits, of which only three possessed weak reflocculating activity upon deflocculated yeast. The mixture of these three proteins allow the recovery of initial specific reflocculating activity of the complex. These three proteins, denoted p28, p36 and p48, presented, in their first 15 amino acids, homologies with glycolysis enzymes, i.e., 3-phosphoglycerate mutase, glyceraldehyde-3-phosphate dehydrogenase and enolase, respectively. However, no such enzymatic activity could be detected in the crude extract issued from treatment with EDTA and Hecameg® of flocculent yeast cells. When yeasts had grown in glucose poor medium, flocculation was drastically affected. The EDTA and Hecameg® crude extracts showed weak reflocculating activity. After PAGE, the protein complexes did not appear in the EDTA extract, but they did appear in the Hecameg® crude extract. These results suggest that: (i) self-flocculation of K. bulgaricus depends on the expression of different floc-forming protein complex, (ii) these proteins are galactose specific lectins showing homologies in their primary structure with glycolysis enzymes.     

Isolation and characterization of the enzymes involved in disintegration of the cell wall of Chlorella fusca

Using different chromatographical methods we have isolated an enzyme from the sporangia of Chlorella fusca Shihira et Krauss var. vacuolata , strain SAG 211–8b, which is responsible for the partial disintegration of the sporangium wall. We refer to it as carbohydrate-releasing activity (CRA). It is an endoenzyme and splits oligosaccharides from the inner layer of the cell wall. In appropriate tests it shows β- d -fucosidase activity (EC 3.2.1.,38): The protein has a molecular weight around 45 kDa and an isoelectric point of pH 4.3; maximum activity is found at pH 5.4 and 60°C, although this temperature inactivates the enzyme quickly. β- d -Mannosidase (EC 3.2.1.25) and β- d -glucosidase (EC 3.2.1.21) were also found in the presence of CRA. These glycosidases were identified as exoenzymes. They are involved in the further degradation of the liberated obligosaccharides.     

Isolation and characterization of Ni-specific T cell clones from patients with Ni-contact dermatitis

Ni-specific T lymphocyte clones (TLC) were isolated from two patients with Ni-contact dermatitis. All of the isolated TLC required both histocompatible antigen-presenting cells (APC) and Ni for induction of proliferation. By using a panel of HLA-typed Epstein Barr virus-transformed B cells (EBV-B cells) as APC and monoclonal anti-DR antibody, the clones were shown to recognize Ni in the context of HLA class II determinants. All of the clones that were isolated are OKT3+, OKT4+, OKT8-. In the presence of Ni, they polyclonally activate autologous B cells, and in the presence of Ni and autologous EBV-B cells, they produce IL 2 and very high levels of IFN-gamma. The Ni-specific clones should be helpful in the identification of the Ni-induced antigen which is recognized by T cells.     

Isolation and characterization of novel suppressor T cell clones from murine fetal thymus

Murine fetal thymus from C57BL/6J (B6) and DBA/2J contains a cell population that suppresses CTL responses to alloantigens. This suppressor cell population was found to exist in high frequency in murine fetal thymus at the 14th day of gestation. The activity of this cell in the thymus declined rapidly with increasing time of gestation, and suppressor activity in the thymus was undetectable by the time of birth. On the other hand, suppressor activity could be detected in organ cultures of 14-day fetal thymus even after the organs were cultured for 14 or 21 days. Fetal thymocytes from B6 or DBA/2J mice were grown as long-term lines in interleukin 2 (IL 2)-containing medium. Clones of suppressor cells were derived from long-term cultures by micromanipulation. The clones had an average doubling time of 13 to 16 hr and were dependent on IL 2 for growth. The clones were 10- to 100-fold more efficient in suppressing CTL responses to alloantigens than day 15 fetal thymocytes. Analyses of cell surface molecules with the use of monoclonal antibodies and conventional anti-H-2 sera by radioactive binding assays showed that cloned suppressor cells from B6 fetal thymus were Thy-1 and Lyt-2+, and expressed little or no L3T4, Lyt-1, H-2K, H-2D, and class II molecules. The suppressor clones lacked the cytolytic activity of conventional CTL and also served as very poor target cells in CTL-mediated cytolysis. The suppressor function of the cloned cells was radiation-resistant, and this suppression could not be reversed by the addition of excess exogenous IL 2. The cloned cells suppressed CTL responses only when they were added within the first 48 hr of a 5-day culture period. Analyses of the antigen specificity of the suppressor cells showed that they suppressed CTL responses in a nonantigen-specific manner.     

Isolation and characterization of cell membranes

The steps outlined above should provide a framework for developing and evaluating a scheme for isolating a particular membrane system of interest. Further characterization often focuses on the specific research interests of an investigator. Most subsequent techniques will probably involve biochemical analyses of protein and lipid components and biophysical analyses of membrane properties. The techniques to be used, such as SDS gel electrophoresis, enzyme kinetics, receptor binding, protein purification, etc. are not unique to membrane systems and will not be described in detail. However, it is likely that the functional relevance and success of subsequent analyses will be aided if the starting membranes are as homogeneous and well-characterized as possible. Even if some of the fractionation steps are bypassed, such as might occur if a specific membrane protein is detergent-extracted, purified, and reconstituted directly from a crude homogenate, a full understanding of membrane protein function will probably require complementary studies on intact cells and isolated membranes.     

Isolation and partial characterization of nickel complexes in higher plants

The essential trace element, nickel, is readily taken up by plants. The biochemical properties of the nickel complex in intrinsically labeled potato and alfalfa were compared and contrasted to ionic nickel. Potato and alfalfa exhibit a similar in vivo nickel complex. The approximate mol wt is 2200–2400 daltons. The complex has a lower polarity than thoes ionic nickel. The majority of the complex is a cationic species with a minor anionic species. This is confirmed with electrophoresis, ion exchange chromatography and the two nickel conplexes' affinity for cationic and anionic resins. Protein does not appear to be associated with either complex.     

Isolation and characterization of hamster brain polyribosome-cytomatrix complexes.

We have developed a method for the isolation of a brain subcellular fraction enriched in both highly aggregated polyribosomes and cytoskeletal proteins. This method is based on gentle dispersion of brain tissue and low speed centrifugation. This fraction is enriched in typical cytoskeletal proteins as glial fibrillary protein, neurofilament proteins and actin. Messenger RNA did not seem to be involved in the polyribosome association to the cytomatrix as shown by the effect of exposure to micrococcal nuclease. On the other hand, in vivo disruption of protein synthesis by acute experimental phenylketonuria, hypothermia or heat-shock did not cause the release of ribosomes from the cytomatrix.     

T cell recognition of Mlsc. I. Influence of MHC gene products in Mlsc-specific T cell recognition

Monospecific T cell clones have been proven to be powerful tools for the characterization of T cell recognition in many Ag-specific as well as allo-specific T cell responses. In this report, in order to elucidate the mechanism of T cell recognition of minor stimulating locus Ag (Mlsc) determinants, Mlsc-specific cloned T cells were employed together with primary T cell responses to clarify the role of MHC-gene products in Mlsc-specific T cell recognition. The results indicated that T cells recognize Mlsc determinants in conjunction with I-region MHC gene products. Moreover, certain MHC haplotypes (e.g., H-2a and H-2k) appear to function efficiently in the "presentation" of Mlsc, whereas other haplotypes (e.g., H-2b and H-2q) function poorly if at all in presenting Mlsc. Experiments with the use of stimulators derived from F1 hybrids between the low stimulatory H-2b, Mlsc strain, C3H.SW, and a panel of Mlsb, H-2-different or intra-H-2 recombinant strains strongly suggested that expression of E alpha E beta molecules on stimulators plays a critical role for Mlsc stimulation. The functional importance of the E alpha E beta product in Mlsc recognition was further demonstrated by the ability of anti-E alpha monoclonal antibody to inhibit the response of cloned Mlsc-specific T cells. Inhibition of the same Mlsc-specific response by anti-A beta k antibody suggests that the A beta product may also play a role in T cell responses to Mlsc.     

Isolation of a plant glycoprotein involved with control of intercellular recognition

A recognition molecule was isolated from stigmas of S-allele genotype S₂S₂ of Brassica oleracea var. capitata L. After Sephadex chromatography, it eluted as a single symmetrical peak during diethylaminoethane-cellulose chromatography. A high degree of purity was affirmed by: sedimentation as a single peak during ultracentrifugation through 5 to 20% sucrose gradients; elution as a single peak from Sephadex G-100; visualization as a single band which stains with Coomassie blue and periodic acid Schiff reagent after electrophoresis on polyacrylamide gels. Other criteria supporting the conclusion that it is a glycoprotein are: (a) the highly purified preparation is anthrone-positive and has a Lowry protein to anthrone-positive carbohydrate ratio of 1.3; (b) the preparation contains arabinose, galactose, glucose, and mannose, although it is not precipitated by concanavalin A; (c) the immunological properties of the molecule are lost following protease treatment, and it has a molecular weight of 90,000 by Sephadex gel-filtration analysis and 54,500 by velocity sedimentation analysis.     

Isolation and characterization of lipid-protein complexes present in commercial albumin preparations

Most commercially available albumin preparations examined by us contain phospholipids, cholesterol and apolipoprotein impurities. As these albumin preparations are frequently used in large amounts in systems involving lipoprotein metabolism these impurities may reach remarkable levels to introduce exogenous effects in these studies. We have studied in detail tow bovine albumin preparations differing in their content of these contaminants. Using preparative ultracentrifugation, we have isolated from both albumins a lipid protein complex at a buoyant density of d = 1.063-1.21 g/ml with a chemical composition resembling plasma high density lipoproteins. This complex when further characterized proved also to have a similar apoprotein composition to bovine plasma high density lipoproteins. Electron microscopic study of this complex revealed discoidal particles closely resembling nascent high density lipoproteins recovered from rat liver or lymph. The similarity of these lipid-protein complexes to high density lipoproteins, accounts for some reported effects caused by commercially available albumin preparations on cholesterol excretion from cells in tissue culture and their ability to act as acceptors for surface remnants released upon VLDL catabolism in vitro.     

Isolation and preliminary characterization of corticosterone-receptor complexes in mouse placental tissue

The $\text{in vitro}$ binding of several radioactive steroids was examined in mouse placental tissue, using Sephadex chromatography to separate the labelled steroid complex from free steroids. Binding was exhibited by cortisol, corticosterone and progesterone, but not cortisone. Cortexolone, an antiglucocorticoid, was tested in the system and found to reduce the binding of the active steroids. The displacement of labelled corticosterone by addition of unlabelled steroids was also examined. Preliminary characterization of the corticosterone receptor using hydrolytic enzymes suggested a protein nature on the basis of degradation by pronase but not by nucleases.     

Isolation and characterization of the fragrant cyclamen O-methyltransferase involved in flower coloration

Anthocyanin O-methyltransferase (OMT) is one of the key enzymes for anthocyanin modification and flower pigmentation. We previously bred a novel red-purple-flowered fragrant cyclamen (KMrp) from the purple-flowered fragrant cyclamen 'Kaori-no-mai' (KM) by ion-beam irradiation. Since the major anthocyanins in KMrp and KM petals were delphinidin 3,5-diglucoside and malvidin 3,5-diglucoside, respectively, inactivation of a methylation step in the anthocyanin biosynthetic pathway was indicated in KMrp. We isolated and compared OMT genes expressed in KM and KMrp petals. RT-PCR analysis revealed that CkmOMT2 was expressed in the petals of KM but not in KMrp. Three additional CkmOMTs with identical sequences were expressed in petals of both KM and KMrp. Genomic PCR analysis revealed that CkmOMT2 was not amplified from the KMrp genome, indicating that ion-beam irradiation caused a loss of the entire CkmOMT2 region in KMrp. In vitro enzyme assay demonstrated that CkmOMT2 catalyzes the 3' or 3',5' O-methylation of the B-ring of anthocyanin substrates. These results suggest that CkmOMT2 is functional for anthocyanin methylation, and defective expression of CkmOMT2 is responsible for changes in anthocyanin composition and flower coloration in KMrp.     

Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis

The plant Golgi plays a pivotal role in the biosynthesis of cell wall matrix polysaccharides, protein glycosylation, and vesicle trafficking. Golgi-localized proteins have become prospective targets for reengineering cell wall biosynthetic pathways for the efficient production of biofuels from plant cell walls. However, proteomic characterization of the Golgi has so far been limited, owing to the technical challenges inherent in Golgi purification. In this study, a combination of density centrifugation and surface charge separation techniques have allowed the reproducible isolation of Golgi membranes from Arabidopsis (Arabidopsis thaliana) at sufficiently high purity levels for in-depth proteomic analysis. Quantitative proteomic analysis, immunoblotting, enzyme activity assays, and electron microscopy all confirm high purity levels. A composition analysis indicated that approximately 19% of proteins were likely derived from contaminating compartments and ribosomes. The localization of 13 newly assigned proteins to the Golgi using transient fluorescent markers further validated the proteome. A collection of 371 proteins consistently identified in all replicates has been proposed to represent the Golgi proteome, marking an appreciable advancement in numbers of Golgi-localized proteins. A significant proportion of proteins likely involved in matrix polysaccharide biosynthesis were identified. The potential within this proteome for advances in understanding Golgi processes has been demonstrated by the identification and functional characterization of the first plant Golgi-resident nucleoside diphosphatase, using a yeast complementation assay. Overall, these data show key proteins involved in primary cell wall synthesis and include a mixture of well-characterized and unknown proteins whose biological roles and importance as targets for future research can now be realized.