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PubMed1988

The human intermediate-affinity interleukin 2 receptor consists of two distinct, partially homologous glycoproteins.

In this report we demonstrate that the human intermediate-affinity-type interleukin (IL) 2 receptor (IL 2R) consists of two distinct glycoproteins designated H1 and H2, whereas the high-affinity IL 2R consists of three chains, H1, H2 and the light chain (L), the Tac antigen. They are neither linked by disulfide bridges to each other nor to the L chain. Similar to the L chain, H1 and H2 apparently carry intramolecular disulfide bonds. From affinity-labeled IL 2 intermediate-affinity receptor complexes, we deduced an apparent mol. mass of 70 kDa for H1 and of 75 kDa for H2 in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and of 55 kDa for H1 and of 85 kDa for H2 in SDS-PAGE/urea. As demonstrated by limiting proteolysis, both glycoproteins display high homologies or even identity proximal to the IL 2-binding sites. The areas which are responsible for the striking differences between H1 and H2 in SDS-PAGE/urea are located distally to the IL2-binding site and, in contrast to the L chain, are protected from the action of exogenous proteases by the plasma membrane.

Cross-Linking Reagents↗
PubMed1992

Human U937 cell surface peptidase activities: characterization and degradative effect on tumor necrosis factor-alpha.

Surface peptidase activities on the human monocytic lineage cell line U937 were characterized. Two diisopropyl phosphofluoridate (DFP)-inhibitable serine peptidases were identified by differences in their hydrolytic activities on chromogenic peptides: one removed tripeptides from the free NH2-terminal end of the synthetic peptide Ala-Ala-Phe-p-nitroanilide (pNA) and was not inhibited by inhibitors of metallo-, cysteic-, and aspartic-proteinases, or by those of elastase-, trypsin- and chymotrypsin-like enzymes, suggesting the presence of a hitherto unidentified serine tripeptidyl endopeptidase; the other peptidase catalyzed the release of Gly-Pro from Gly-Pro-pNA and was inhibited by DFP, phenylmethyl sulfonyl fluoride and diprotin A, thus resembling dipeptidyl peptidase IV (DPP IV) with respect to its substrate specificity and inhibitor profile. A group of N-exo-aminopeptidase activities specifically inhibited by bestatin, was also detected when Ala-, Leu-, Arg- and Lys-pNA were used a substrates. The activities were surface associated and not secreted as determined by extracellular location of product and enzymatic recovery in highly purified U937 cell membranes. Peripheral monocytes and macrophages were found to virtually exhibit identical levels of these two classes of peptidase activities when compared to those detected on U937 cells. The relative contributions of these hydrolytic enzymes to the cleavage of bioactive and radioiodinated cytokines including tumor necrosis factor-alpha (TNF-alpha), interleukin-1 alpha and interferon-gamma was next examined. The results indicated that N-aminopeptidases do not appear to participate in the catabolism of any tested cytokine. In contrast, the most interesting finding was that both serine peptidases participate in TNF-alpha degradation. Analysis of the final proteolytic digestion products demonstrated the disappearance of the native 17-kDa molecule TNF-alpha, and the concomitant release of biologically inactive fragments of less than or equal to 2 kDa. Together, these observations indicate new roles for both the DPP IV-like enzyme and the tripeptidyl endopeptidase located at the surface of human monocytic cells, including the regulation of the extracellular TNF-alpha concentration. Thus, the identification of functional ectopeptidases provides insight into their potential role in both normal and malignant monocytic function.

Amino Acid Sequence↗
PubMed1988

Peptide mapping of polypeptides separated by two-dimensional electrophoresis: protease digestion directly on the two-dimensional gel followed by electrophoresis in reverse direction.

A method is described which allows to reveal simultaneously the proteolytic patterns of numerous polypeptides separated by two-dimensional electrophoresis. After two-dimensional electrophoresis, the gels were dipped successively in buffers for preequilibration, protease digestion, and reequilibration. They were then returned to the electrophoresis tank, and electrophoresis was continued for a short time. After silver staining, digestion products appeared, lined up behind the original polypeptide spots. The method allows proteolytic patterns of numerous polypeptides to be visualized simply and quickly. Among proteins of wheat leaves, 31 groups of related polypeptides were found according to the similarity of their proteolytic patterns.

Electrophoresis, Gel, Two-Dimensional↗
PubMed1988

Extraction of plant proteins for two-dimensional electrophoresis.

Three different extraction procedures for two-dimensional electrophoresis of plant proteins are compared: (i) extraction of soluble proteins with a nondenaturing Tris-buffer, (ii) denaturing extraction in presence of sodium dodecyl sulfate at elevated temperature allowing the solubilization of membrane proteins in addition to a recovery of soluble proteins, and (iii) a trichloroacetic acid-acetone procedure allowing the direct precipitation of total proteins.

Electrophoresis, Gel, Two-Dimensional↗
PubMed1998

Routine identification of proteins from sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gels or polyvinyl difluoride membranes using matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS).

As the resource laboratory for Rockefeller University our emphasis continues to be on methodology development for the routine analysis of low abundance proteins isolated from native sources. In the past ten years, gel electrophoresis of proteins has become the method of choice for the preparation of microgram and submicrogram quantities of protein for primary structural characterization, and over 95% of the samples submitted for protein identification are either in a gel or bound to polyvinyl difluoride membranes (PVDF). As such, we employ multiple microanalytical approaches encompassing Edman sequence degradation, amino acid and matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometric analysis to provide an integrated protein characterization of such samples. Here we describe the two major services we employ when providing protein identification from in-gel or PVDF-bound proteins.

Amino Acid Sequence↗
PubMed1998

An algorithm for the identification of proteins using peptides with ragged N- or C-termini generated by sequential endo- and exopeptidase digestions.

We have developed an algorithm (MassDynSearch) for identifying proteins using a combination of peptide masses with small associated sequences (tags). Unlike the approach developed by Matthias Mann, 'Tag searching', in which the sequence tags are generated by gas phase fragmentation of peptides in a mass spectrometer, 'Rag Tag' searching uses peptide tags which are generated enzymatically or chemically. The protein is digested either chemically or with an endopeptidase and the resultant mixture is then subjected to partial exopeptidase degradation. The mixture is analyzed by matrix assisted laser desorption and ionization time of flight mass spectrometry and a list of intact peptide masses is generated, each associated with a set of degradation product masses which serve as unique tags. These 'tagged masses' are used as the input to an algorithm we have written, MassDynSearch, which searches protein and DNA databases for proteins which contain similar tagged motifs. The method is simple, rapid and can be fully automated. The main advantage of this approach is that the specificity of the initial digestion is unimportant since multiple peptides with tags are used to search the database. This is especially useful for proteins like membrane, cytoskeletal, and other proteins where specific endopeptidases are less efficient and lower specificity proteases such as chymotrypsin, pepsin, and elastase must be used.

Algorithms↗
PubMed2006

Less common applications of monoliths: I. Microscale protein mapping with proteolytic enzymes immobilized on monolithic supports.

This review summarizes the recent contributions to the rapidly growing area of immobilized enzymes employing both silica and synthetic polymer-based monoliths as supports. Focus is mainly on immobilized proteolytic enzyme reactors designed for studies in proteomics. Porous monoliths emerged first as a new class of stationary phases for HPLC in the early 1990s. Soon thereafter, they were also used as supports for immobilization of proteins and preparation of both stationary phases for bioaffinity chromatography and enzymatic reactors. Organic polymer-based monoliths are typically prepared using a simple molding process carried out within the confines of a "mold" such as chromatographic column or capillary. Polymerization of a mixture comprising monomers, initiator, and porogenic solvent affords macroporous materials. In contrast, silica-based monoliths are first formed as a rigid rod from tetraalkoxysilane in the presence of PEG and subsequently encased with a plastic tube. Both types of monolith feature large through-pores that enable a rapid flow-through. Since all the solutions must flow through the monolith, the convection considerably accelerates mass transfer within the monolith. As a result, reactors including enzyme immobilized on monolithic support exhibit much higher activity compared to the reactions in solution.

Acrylamide↗
PubMed1987

Kinetic description of proteolysis. Part 3. Total kinetics of peptide bonds hydrolysis in peptide mixtures.

A theoretical analysis of the general kinetics of peptide bond hydrolysis in peptide mixtures has been carried out. It is shown that the equation for the hydrolysis rate must include ensemble-averaged values which change as functions during hydrolysis. Thus the problem of describing the hydrolysis is reduced to finding these functions. As an example of theoretical prediction for the behavior of the averaged functions the procedure of calculating the averaged constant of chymotrypsin substrate specificity as a function of the degree of hydrolysis is presented. The analysis performed enables to find factors responsible for the decrease of hydrolysis rate, in particular, the role of the substrate specificity range and the S/E ratio. The design of specific experiments making it possible to measure the averaged values in the course of hydrolysis has been considered.

Chymotrypsin↗
PubMed1991

Involvement of 3p deletions in sporadic and hereditary forms of renal cell carcinoma.

Deletions of the short arm of chromosome 3 and associated allele losses have been reported in the majority of sporadic renal cell carcinomas (RCC). On the basis of the combined cytogenetic and molecular data, it is reasonable to assume that a putative RCC locus, which contributes to tumor development by its loss, is located telomerically of the D3F15S2 site. Using H3E4, a D3F15S2-specific probe, we have isolated a cDNA clone (cl.4-2), and a sequence comparison revealed that the cDNA clone corresponds to the human acyl-peptide hydrolase gene. The gene is fairly universally expressed, but in RCC biopsies its expression is severely reduced, compared to the normal kidney. Cl.4-2 was used for in situ hybridization on metaphase chromosomes prepared from an Epstein-Barr virus (EBV) transformed lymphoblastoid cell line, derived from a t(3;8) (p14.2;q24.1) carrying member of the RCC family described by Cohen et al. in 1979 (N Engl J Med: 301:592-595). Carriers of this translocation regularly develop RCC by middle age. We now report that D3F15S2 is localized on the telomeric side of the constitutional breakpoint, in 3p21. The region of 3p affected by this familial translocation is thus not identical with the region of 3p most frequently deleted in sporadic RCC.

Alleles↗
PubMed1988

Topology of the 32-kd liver gap junction protein determined by site-directed antibody localizations.

Synthetic peptides corresponding to sequences in the human liver gap junction protein were chemically synthesized and used for generation of peptide antisera to defined sequences in the protein. The antibodies were affinity purified and characterized by demonstrating that they specifically recognized both their corresponding synthetic peptide (as indicated by dot blot analysis) and the native 32-kd gap junction protein (by immunoblotting). The specificity of a subset of the different site-specific antibodies was subsequently confirmed by demonstration of their binding to specific gap junction fragments produced by treatment with a lysine-specific endoproteinase. Immunoelectron microscopy was used to localize the specific peptide antibody epitopes to either the cytoplasmic or extracellular surfaces of the gap junction. Results indicate a transmembrane orientation for the protein with the amino and carboxyl termini located on the cytoplasmic side of the membrane. Based on these data, a model is proposed for the transmembrane folding of the gap junction protein.

Amino Acid Sequence↗
PubMed1981

Biodegradation of a poly-(alpha-amino acid) hydrogel. II. In vitro.

Proteolytic enzymes have been employed in an in vitro model to simulate the in vivo degradation of a synthetic poly(amino acid) hydrogel. Trypsin and collagenase had no effect on crosslinked poly(2-hydroxyethyl-L-glutamine) but pronase and papain dissolved the hydrogel. The initial effect of papain was to decrease the effective crosslink density without producing soluble material. This effect was similar to that observed previously in vivo. Analysis of the papain digestion products showed that oligomers of degree of polymerization 4-9 were the chief products. The rate at which oligomers were formed increased with increasing crosslink density. This phenomenon was attributed to hydrophobic effects.

Biocompatible Materials↗
PubMed1985

Cross-phyletic bioactivity of arthropod neurohormones and molluscan ganglion extracts: evidence of an extended peptide family.

Two structurally related arthropod neuropeptides, red pigment concentrating hormone (RPCH) and adipokinetic hormone (AKH), are potent excitors of the heart of the clam Mercenaria mercenaria. The response is bimodal: whereas the threshold for affected hearts is 1-3 X 10(-9) M, about 40% of the preparations are virtually unresponsive. Aqueous extracts of Mercenaria ganglia contain a substance which concentrates the red pigment in the erythrophores of intact destalked Uca pugilator and even of its isolated legs. This substance is retained on Sephadex G-15 and co-elutes with synthetic shrimp RPCH. The active fractions also concentrate the erythrophores and the leucophores of destalked shrimp (Penaeus). Neither dopamine nor the molluscan neuropeptide FMRFamide had any chromatophorotropic effect in these assays. The activity of the ganglion extracts was abolished by digestion with chymotrypsin. In conclusion, molluscan ganglion extracts contain a peptide factor, possibly an analog of RPCH, that concentrates the pigments of crustacean chromatophores by a direct action on the cells.

Animals↗
PubMed1983

Lytic enzyme activity in autolysing mycelium of Aspergillus niger.

We have studied changes in the activity of some lytic enzymes contained in mycelium of Aspergillus niger in cultures relative to the autolytic phase of growth. Acid phosphatase, polygalacturonidase and alpha-amylase activity reached its highest level (40.7, and 8 U/sample, respectively) at the initiation of the autolytic phase of growth. 1.3-beta-Glucanase and beta-N-acetylglucosaminidase reached its highest level (3.5 and 2 U/sample, respectively) during the first days of autolysis. Alkaline phosphatase, cellulase, invertase, esterase, chitinase and proteolytic activity is also present in autolysing mycelium of A. niger, though comparatively low. Their maximum activity coincided with the beginning of the autolytic phase of growth. In all enzymes studied here, as autolyis proceeded, enzyme activity decreased by about 90%. Only esterase activity remained nearly constant throughout the whole period of autolysis described here.

Acetylglucosaminidase↗