Datasets:

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bionlp_st_2011_epi

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[ { "id": "PMID-2505674__text", "type": "abstract", "text": [ "Asparagine-linked glycosylation of the scrapie and cellular prion proteins. \nPost-translational modification of the scrapie prion protein (PrP) is thought to account for the unusual features of this protein. Molecular cloning of a PrP cDNA identified two potential Asn-linked glycosylation sites. Both the scrapie (PrPSc) and cellular (PrPC) isoforms were susceptible to digestion by peptide N-glycosidase F (PNGase F) but resistant to endoglycosidase H as measured by migration in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. PNGase F digestion of PrPC yielded two proteins of Mr26K and 28K; however, the 26-k species was only a minor component. In contrast, PNGase F digestion of PrPSc yielded equimolar amounts of two proteins of Mr26K and 28K. The significance of this altered stoichiometry between the 26- and 28-kDa deglycosylated forms of PrP during scrapie infection remains to be established. Both isoforms as well as PrP 27-30, which is produced by limited proteolysis of PrPSc, exhibited a reduced number of charge isomers after PNGase F digestion. The molecular weight of PrP 27-30 was reduced from 27K-30K by PNGase F digestion to 20K-22K while anhydrous hydrogen fluoride or trifluoromethanesulfonic acid treatment reduced the molecular weight to 19K-21K and 20K-22K, respectively. Denatured PrP 27-30 was radioiodinated and then assessed for its binding to lectin columns. PrP 27-30 was bound to wheat germ agglutinin (WGA) or lentil lectins and eluted with N-acetylglucosamine or alpha-methyl-mannoside, respectively. Digestion of PrP 27-30 with sialidase prevented its binding to WGA but enhanced its binding to Ricinus communis lectin. These findings argue that PrP 27-30 probably possesses Asn-linked, complex oligosaccharides with terminal sialic acids, penultimate galactoses, and fucose residues attached to the innermost N-acetyl-glucosamine. Whether differences in Asn-linked oligosaccharide structure between PrPC and PrPSc exist and are responsible for the distinct properties displayed by these two isoforms remain to be established.\n" ], "offsets": [ [ 0, 2075 ] ] } ]

[ { "id": "PMID-2505674_T1", "type": "Protein", "text": [ "prion proteins" ], "offsets": [ [ 60, 74 ] ], "normalized": [] }, { "id": "PMID-2505674_T2", "type": "Protein", "text": [ "prion protein" ], "offsets": [ [ 124, 137 ] ], "normalized": [] }, { "id": "PMID-2505674_T3", "type": "Protein", "text": [ "PrP" ], "offsets": [ [ 139, 142 ] ], "normalized": [] }, { "id": "PMID-2505674_T4", "type": "Protein", "text": [ "PrP" ], "offsets": [ [ 231, 234 ] ], "normalized": [] }, { "id": "PMID-2505674_T5", "type": "Protein", "text": [ "PrPSc" ], "offsets": [ [ 315, 320 ] ], "normalized": [] }, { "id": "PMID-2505674_T6", "type": "Protein", "text": [ "PrPC" ], "offsets": [ [ 336, 340 ] ], "normalized": [] }, { "id": "PMID-2505674_T7", "type": "Protein", "text": [ "peptide N-glycosidase F" ], "offsets": [ [ 384, 407 ] ], "normalized": [] }, { "id": "PMID-2505674_T8", "type": "Protein", "text": [ "PNGase F" ], "offsets": [ [ 409, 417 ] ], "normalized": [] }, { "id": "PMID-2505674_T9", "type": "Protein", "text": [ "endoglycosidase H" ], "offsets": [ [ 436, 453 ] ], "normalized": [] }, { "id": "PMID-2505674_T10", "type": "Protein", "text": [ "PNGase F" ], "offsets": [ [ 541, 549 ] ], "normalized": [] }, { "id": "PMID-2505674_T11", "type": "Protein", "text": [ "PrPC" ], "offsets": [ [ 563, 567 ] ], "normalized": [] }, { "id": "PMID-2505674_T12", "type": "Protein", "text": [ "PNGase F" ], "offsets": [ [ 674, 682 ] ], "normalized": [] }, { "id": "PMID-2505674_T13", "type": "Protein", "text": [ "PrPSc" ], "offsets": [ [ 696, 701 ] ], "normalized": [] }, { "id": "PMID-2505674_T14", "type": "Protein", "text": [ "PrP" ], "offsets": [ [ 860, 863 ] ], "normalized": [] }, { "id": "PMID-2505674_T15", "type": "Protein", "text": [ "PrP 27-30" ], "offsets": [ [ 941, 950 ] ], "normalized": [] }, { "id": "PMID-2505674_T16", "type": "Protein", "text": [ "PrPSc" ], "offsets": [ [ 996, 1001 ] ], "normalized": [] }, { "id": "PMID-2505674_T17", "type": "Protein", "text": [ "PNGase F" ], "offsets": [ [ 1054, 1062 ] ], "normalized": [] }, { "id": "PMID-2505674_T18", "type": "Protein", "text": [ "PrP 27-30" ], "offsets": [ [ 1098, 1107 ] ], "normalized": [] }, { "id": "PMID-2505674_T19", "type": "Protein", "text": [ "PNGase F" ], "offsets": [ [ 1136, 1144 ] ], "normalized": [] }, { "id": "PMID-2505674_T20", "type": "Protein", "text": [ "PrP 27-30" ], "offsets": [ [ 1320, 1329 ] ], "normalized": [] }, { "id": "PMID-2505674_T21", "type": "Protein", "text": [ "PrP 27-30" ], "offsets": [ [ 1402, 1411 ] ], "normalized": [] }, { "id": "PMID-2505674_T22", "type": "Protein", "text": [ "lectins" ], "offsets": [ [ 1463, 1470 ] ], "normalized": [] }, { "id": "PMID-2505674_T23", "type": "Protein", "text": [ "PrP 27-30" ], "offsets": [ [ 1561, 1570 ] ], "normalized": [] }, { "id": "PMID-2505674_T24", "type": "Protein", "text": [ "sialidase" ], "offsets": [ [ 1576, 1585 ] ], "normalized": [] }, { "id": "PMID-2505674_T25", "type": "Protein", "text": [ "PrP 27-30" ], "offsets": [ [ 1694, 1703 ] ], "normalized": [] }, { "id": "PMID-2505674_T26", "type": "Protein", "text": [ "PrPC" ], "offsets": [ [ 1948, 1952 ] ], "normalized": [] }, { "id": "PMID-2505674_T27", "type": "Protein", "text": [ "PrPSc" ], "offsets": [ [ 1957, 1962 ] ], "normalized": [] }, { "id": "PMID-2505674_T28", "type": "Entity", "text": [ "Asparagine" ], "offsets": [ [ 0, 10 ] ], "normalized": [] }, { "id": "PMID-2505674_T32", "type": "Entity", "text": [ "Asn" ], "offsets": [ [ 1723, 1726 ] ], "normalized": [] }, { "id": "PMID-2505674_T33", "type": "Entity", "text": [ "complex oligosaccharides" ], "offsets": [ [ 1735, 1759 ] ], "normalized": [] }, { "id": "PMID-2505674_T35", "type": "Entity", "text": [ "Asn" ], "offsets": [ [ 1903, 1906 ] ], "normalized": [] }, { "id": "PMID-2505674_T36", "type": "Entity", "text": [ "oligosaccharide" ], "offsets": [ [ 1914, 1929 ] ], "normalized": [] } ]

[ { "id": "PMID-2505674_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 18, 31 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2505674_T1" }, { "role": "Site", "ref_id": "PMID-2505674_T28" } ] }, { "id": "PMID-2505674_E2", "type": "Deglycosylation", "trigger": { "text": [ "deglycosylated" ], "offsets": [ [ 836, 850 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2505674_T14" } ] }, { "id": "PMID-2505674_E3", "type": "Glycosylation", "trigger": { "text": [ "Asn-linked" ], "offsets": [ [ 1723, 1733 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2505674_T25" }, { "role": "Site", "ref_id": "PMID-2505674_T32" }, { "role": "Sidechain", "ref_id": "PMID-2505674_T33" } ] }, { "id": "PMID-2505674_E4", "type": "Glycosylation", "trigger": { "text": [ "Asn-linked" ], "offsets": [ [ 1903, 1913 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2505674_T26" }, { "role": "Site", "ref_id": "PMID-2505674_T35" }, { "role": "Sidechain", "ref_id": "PMID-2505674_T36" } ] }, { "id": "PMID-2505674_E5", "type": "Glycosylation", "trigger": { "text": [ "Asn-linked" ], "offsets": [ [ 1903, 1913 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2505674_T27" }, { "role": "Site", "ref_id": "PMID-2505674_T35" }, { "role": "Sidechain", "ref_id": "PMID-2505674_T36" } ] } ]

[ { "id": "PMID-2505674_1", "entity_ids": [ "PMID-2505674_T2", "PMID-2505674_T3" ] }, { "id": "PMID-2505674_2", "entity_ids": [ "PMID-2505674_T7", "PMID-2505674_T8" ] } ]

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[ { "id": "PMID-2557001__text", "type": "abstract", "text": [ "The catalytic mechanism of the hydroxylation reaction of peptidyl proline and lysine does not require protein disulphide-isomerase activity. \nProlyl 4-hydroxylase, an alpha 2 beta 2 tetramer, catalyses the formation of 4-hydroxyproline in collagens. The beta subunit is known to be identical with the enzyme protein disulphide-isomerase and to possess disulphide-isomerase activity even when present in the prolyl 4-hydroxylase tetramer. We here report that lysyl hydroxylase, a homodimer, and algal prolyl 4-hydroxylase, a monomer, do not contain detectable protein disulphide-isomerase activity. Since the hydroxylase reaction mechanisms are similar, the data suggest that the protein disulphide-isomerase activity of the vertebrate prolyl 4-hydroxylase beta subunit is unlikely to be involved in the catalytic mechanism of the hydroxylation reaction.\n" ], "offsets": [ [ 0, 854 ] ] } ]

[ { "id": "PMID-2557001_T1", "type": "Protein", "text": [ "protein disulphide-isomerase" ], "offsets": [ [ 308, 336 ] ], "normalized": [] }, { "id": "PMID-2557001_T2", "type": "Protein", "text": [ "prolyl 4-hydroxylase" ], "offsets": [ [ 500, 520 ] ], "normalized": [] }, { "id": "PMID-2557001_T3", "type": "Protein", "text": [ "prolyl 4-hydroxylase beta subunit" ], "offsets": [ [ 735, 768 ] ], "normalized": [] } ]

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[ { "id": "PMID-2648381__text", "type": "abstract", "text": [ "Purification and analysis of RNA polymerase II transcription factors by using wheat germ agglutinin affinity chromatography. \nWe recently found that many RNA polymerase II transcription factors are modified with N-acetylglucosamine residues. These sugar moieties confer upon transcription factors an ability to bind the lectin wheat germ agglutinin. We have taken advantage of this interaction to devise a purification procedure for the \"GC-box\" binding transcription factor Sp1. Crude nuclear extracts are first subjected to wheat germ agglutinin affinity chromatography and then subjected to sequence-specific DNA affinity chromatography. The Sp1 protein purified by this procedure is at least 95% pure, and the overall recovery is greater than 80%. In addition to yielding larger quantities of Sp1 than conventional schemes, the new purification procedure is also simpler and more rapid. We show that wheat germ agglutinin affinity chromatography can also be used to purify the glycosylated forms of the CCAAT-binding transcription factor. Thus, wheat germ agglutinin affinity chromatography may aid the purification of other transcription factors that bear N-acetylglucosamine residues. Furthermore, the ability to separate glycosylated forms of transcription factors from their unglycosylated counterparts by wheat germ agglutinin affinity chromatography should facilitate investigations into the role of N-acetylglucosamine residues in the functioning of transcription factor proteins.\n" ], "offsets": [ [ 0, 1492 ] ] } ]

[ { "id": "PMID-2648381_T1", "type": "Protein", "text": [ "Sp1" ], "offsets": [ [ 475, 478 ] ], "normalized": [] }, { "id": "PMID-2648381_T2", "type": "Protein", "text": [ "Sp1" ], "offsets": [ [ 645, 648 ] ], "normalized": [] }, { "id": "PMID-2648381_T3", "type": "Protein", "text": [ "Sp1" ], "offsets": [ [ 797, 800 ] ], "normalized": [] }, { "id": "PMID-2648381_T4", "type": "Protein", "text": [ "CCAAT-binding transcription factor" ], "offsets": [ [ 1007, 1041 ] ], "normalized": [] } ]

[ { "id": "PMID-2648381_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 981, 993 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2648381_T4" } ] } ]

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[ { "id": "PMID-2653852__text", "type": "abstract", "text": [ "Acetylation and deacetylation of histone H4 continue through metaphase with depletion of more-acetylated isoforms and altered site usage. \nAntibodies specific for acetylated isoforms of histone H4 have been used to compare acetylation of this histone in interphase and metaphase cells. Two rabbit antisera (R5 and R6) were used, each specific for H4 molecules acetylated at one of the four possible acetylation sites, namely Lys-5 (R6) and Lys-12 (R5). Both antisera bound preferentially to the more-acetylated H4 isoforms (H4Ac2-4). To test for continued H4 acetylation in metaphase chromosomes. Chinese hamster ovary cells were blocked in metaphase and treated for one hour with the deacetylase inhibitor sodium butyrate. Isolated chromosomes were assayed for H4 acetylation by antibody labeling and flow cytometry. H4 acetylation was increased several fold by this brief butyrate treatment. The increase was in direct proportion to DNA content, with no evidence for exceptionally high- or low-labeling chromosomes. The results demonstrate that a cycle of H4 acetylation and deacetylation continues within metaphase chromosomes. Immunofluorescence microscopy showed labeling to be distributed throughout the chromosome, but with variable intensity. Western blotting and immunostaining with R5 and R6 showed a net reduction in labeling of H4 from metaphase cells, with major reductions in the more-acetylated isoforms H4Ac3-4. In contrast, labeling of H4Ac1 was reduced to a lesser extent (R6) or increased (R5). This increase indicates more frequent use of the acetylation site at lysine 12 in H4Ac1 from metaphase cells.\n" ], "offsets": [ [ 0, 1624 ] ] } ]

[ { "id": "PMID-2653852_T1", "type": "Protein", "text": [ "histone H4" ], "offsets": [ [ 33, 43 ] ], "normalized": [] }, { "id": "PMID-2653852_T2", "type": "Protein", "text": [ "histone H4" ], "offsets": [ [ 186, 196 ] ], "normalized": [] }, { "id": "PMID-2653852_T3", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 243, 250 ] ], "normalized": [] }, { "id": "PMID-2653852_T4", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 347, 349 ] ], "normalized": [] }, { "id": "PMID-2653852_T5", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 511, 513 ] ], "normalized": [] }, { "id": "PMID-2653852_T6", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 524, 526 ] ], "normalized": [] }, { "id": "PMID-2653852_T7", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 556, 558 ] ], "normalized": [] }, { "id": "PMID-2653852_T8", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 762, 764 ] ], "normalized": [] }, { "id": "PMID-2653852_T9", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 818, 820 ] ], "normalized": [] }, { "id": "PMID-2653852_T10", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1058, 1060 ] ], "normalized": [] }, { "id": "PMID-2653852_T11", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1340, 1342 ] ], "normalized": [] }, { "id": "PMID-2653852_T12", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1419, 1421 ] ], "normalized": [] }, { "id": "PMID-2653852_T13", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1453, 1455 ] ], "normalized": [] }, { "id": "PMID-2653852_T14", "type": "Protein", "text": [ "H4" ], "offsets": [ [ 1596, 1598 ] ], "normalized": [] }, { "id": "PMID-2653852_T21", "type": "Entity", "text": [ "Lys-5" ], "offsets": [ [ 425, 430 ] ], "normalized": [] }, { "id": "PMID-2653852_T22", "type": "Entity", "text": [ "Lys-12" ], "offsets": [ [ 440, 446 ] ], "normalized": [] }, { "id": "PMID-2653852_T31", "type": "Entity", "text": [ "lysine 12" ], "offsets": [ [ 1583, 1592 ] ], "normalized": [] } ]

[ { "id": "PMID-2653852_E1", "type": "Acetylation", "trigger": { "text": [ "Acetylation" ], "offsets": [ [ 0, 11 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T1" } ] }, { "id": "PMID-2653852_E2", "type": "Deacetylation", "trigger": { "text": [ "deacetylation" ], "offsets": [ [ 16, 29 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T1" } ] }, { "id": "PMID-2653852_E3", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 94, 104 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T1" } ] }, { "id": "PMID-2653852_E4", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 163, 173 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T2" } ] }, { "id": "PMID-2653852_E5", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 223, 234 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T3" } ] }, { "id": "PMID-2653852_E6", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 360, 370 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T4" }, { "role": "Site", "ref_id": "PMID-2653852_T21" } ] }, { "id": "PMID-2653852_E7", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 360, 370 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T4" }, { "role": "Site", "ref_id": "PMID-2653852_T22" } ] }, { "id": "PMID-2653852_E8", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 500, 510 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T5" } ] }, { "id": "PMID-2653852_E9", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 559, 570 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T7" } ] }, { "id": "PMID-2653852_E10", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 765, 776 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T8" } ] }, { "id": "PMID-2653852_E11", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 821, 832 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T9" } ] }, { "id": "PMID-2653852_E12", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 1061, 1072 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T10" } ] }, { "id": "PMID-2653852_E13", "type": "Deacetylation", "trigger": { "text": [ "deacetylation" ], "offsets": [ [ 1077, 1090 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T10" } ] }, { "id": "PMID-2653852_E14", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 1399, 1409 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T12" } ] }, { "id": "PMID-2653852_E15", "type": "Acetylation", "trigger": { "text": [ "use" ], "offsets": [ [ 1552, 1555 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2653852_T14" }, { "role": "Site", "ref_id": "PMID-2653852_T31" } ] } ]

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[ { "id": "PMID-2702305__text", "type": "abstract", "text": [ "Hypomethylation of ras oncogenes in chemically induced and spontaneous B6C3F1 mouse liver tumors. \nThe male hybrid B6C3F1 mouse exhibits a 30% spontaneous hepatoma incidence, and both males and females of this strain are sensitive to chemical induction of liver tumors. The Ha-ras, Ki-ras, and myc oncogenes have been implicated in a variety of solid tumors. Specifically, Ha- and, less frequently Ki-ras have been reported to be activated in B6C3F1 mouse liver tumors, and such activated oncogenes frequently contain a particular point mutation. In light of indications that the transforming capacity of some oncogenes is directly related to the level of the gene product, we hypothesized that transcriptional control of Ha-ras, Ki-ras, and myc is compromised in B6C3F1 mouse liver tumors. A positive correlation has been established between gene expression and hypomethylation. Therefore, the methylation states of these genes were examined in spontaneous liver tumors and in tumors induced by two diverse hepatocarcinogens: phenobarbital and chloroform. Ha-ras was found to be hypomethylated in all tumors examined, whereas Ki-ras was sometimes hypomethylated; such hypomethylation might play a role in the promotion stage of carcinogenesis. The methylation state of myc was unaltered, although this gene appeared to be amplified in tumors. These results suggest that a component of the mechanism by which these oncogenes are activated in B6C3F1 mouse liver tumors involves loss of stringent control of expression, via hypomethylation of the ras oncogenes and, possibly, amplification of myc. These results support the assertion that tumors induced by different classes of carcinogens or arising spontaneously share common biochemical pathways of oncogene activation during tumorigenesis.\n" ], "offsets": [ [ 0, 1792 ] ] } ]

[ { "id": "PMID-2702305_T1", "type": "Protein", "text": [ "Ha-ras" ], "offsets": [ [ 274, 280 ] ], "normalized": [] }, { "id": "PMID-2702305_T2", "type": "Protein", "text": [ "Ki-ras" ], "offsets": [ [ 282, 288 ] ], "normalized": [] }, { "id": "PMID-2702305_T3", "type": "Protein", "text": [ "myc" ], "offsets": [ [ 294, 297 ] ], "normalized": [] }, { "id": "PMID-2702305_T4", "type": "Protein", "text": [ "Ha-" ], "offsets": [ [ 373, 376 ] ], "normalized": [] }, { "id": "PMID-2702305_T5", "type": "Protein", "text": [ "Ki-ras" ], "offsets": [ [ 398, 404 ] ], "normalized": [] }, { "id": "PMID-2702305_T6", "type": "Protein", "text": [ "Ha-ras" ], "offsets": [ [ 722, 728 ] ], "normalized": [] }, { "id": "PMID-2702305_T7", "type": "Protein", "text": [ "Ki-ras" ], "offsets": [ [ 730, 736 ] ], "normalized": [] }, { "id": "PMID-2702305_T8", "type": "Protein", "text": [ "myc" ], "offsets": [ [ 742, 745 ] ], "normalized": [] }, { "id": "PMID-2702305_T9", "type": "Protein", "text": [ "Ha-ras" ], "offsets": [ [ 1057, 1063 ] ], "normalized": [] }, { "id": "PMID-2702305_T10", "type": "Protein", "text": [ "Ki-ras" ], "offsets": [ [ 1127, 1133 ] ], "normalized": [] }, { "id": "PMID-2702305_T11", "type": "Protein", "text": [ "myc" ], "offsets": [ [ 1270, 1273 ] ], "normalized": [] }, { "id": "PMID-2702305_T12", "type": "Protein", "text": [ "myc" ], "offsets": [ [ 1591, 1594 ] ], "normalized": [] } ]

[ { "id": "PMID-2702305_E1", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 895, 906 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2702305_T6" } ] }, { "id": "PMID-2702305_E2", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 895, 906 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2702305_T7" } ] }, { "id": "PMID-2702305_E3", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 895, 906 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2702305_T8" } ] }, { "id": "PMID-2702305_E4", "type": "DNA_methylation", "trigger": { "text": [ "hypomethylated" ], "offsets": [ [ 1080, 1094 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2702305_T9" } ] }, { "id": "PMID-2702305_E5", "type": "DNA_methylation", "trigger": { "text": [ "hypomethylated" ], "offsets": [ [ 1148, 1162 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2702305_T10" } ] }, { "id": "PMID-2702305_E6", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1249, 1260 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2702305_T11" } ] } ]

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[ { "id": "PMID-2777__text", "type": "abstract", "text": [ "Synthesis of angiotensin II antagonists containing N- and O-methylated and other amino acid residues. \n[1-N-Methylisoasparagine,8-isoleucine]- (I), [1-sarcosine,4-N-methyltyrosine,8-isoleucine]- (II), [1-sarcosine,5-N-methylisoleucine,8-isoleucine]- (III), [1-sarcosine,8-N-methylisoleucine]- (IV), [1-sarcosine8k-N-methylisoleucine,8-N-methylisoleucine]- (V), [1-sarcosine,8-O-methylthreonine]- (VI), [1-sarcosine,8-methionine]- (VII), and [1-sarcosine,8-serine]angiotensin II (VIII), synthesized by Merrifield's solid-phase procedure, possess respectively 0.8, 0.3, 0.5, 1.0, 0.0, 0.5, 3.7, and 0.7% pressor activity of angiotensin II (vagotomized, ganglion-blocked rats). They caused an initial rise in blood pressure (30 min of infusion, 250 ng/kg/min in vagotomized, ganglion-blocked rats) of 16.57, 9.80, 22.80, 32.00, 7.00, 15.06, 32.50, and 11.42 mmHg and showed secretory activity (isolated cat adrenal medulla) of 1.0, 0.1, 0.01, 0.1, less than 0.01, 0.1, less than 0.01, and 0.05% of angiotensin II. On isolated organs pA2 values (rabbit aortic strips) of 8.74, 7.44, 7.64, 7.85, 7.89, 8.76, 8.63, and 8.08, and pA2 values (cat adrenal medulla of 8.16, 9.16, 9.31, 8.00, 8.00, 7.00, 9.16, and 9.33 were obtained. Dose ratios (ratio of ED20 of angiotensin II during infusion of the antagonist and before infusion of the antagonist) in vagotomized, ganglion-blocked rats, infused at 250 ng/kg/min, were 33.43, 2.14, 3.26, 2.99, 0.62, 62.52, incalculable, and 11.15, respectively. The results obtained suggest that (a) analogs I and VI are potent antagonists of the pressor response of angiotensin II in normal rat, VI being the most potent antagonist thus far synthesized; (b) replacement of position 4 (Tyr) with MeTyr or position 5 and/or 8 (Ile) with Melle in [1-sarcosine,8-isoleucine]angiotensin II reduced the antagonist activity of this peptide (rabbit aortic strips and rats), indicating that steric hindrance imposed due to N-methylation in positions 4, 5, or 8 was not favorable in eliminating the initial pressor activity or prolonging the duration of action of [Sar1, Ile8]angiotensin II without reducing its antagonistic properties; (c) except II, none of the analogs showed any enhanced duration of action, suggesting that N-methylation in positions 5 or 8 did not afford protection against proteolytic enzymes; and (d) perfusion studies in cat adrenals indicated that all of these analogs are only very weak secretagogues. With the exception of [Sar1,Thr(ObetaMe)8]angiotensin II, which gave lower antagonistic properties, all other analogs had either similar antagonistic properties or were better antagonists in adrenal medulla than in smooth muscle.\n" ], "offsets": [ [ 0, 2677 ] ] } ]

[ { "id": "PMID-2777_T1", "type": "Protein", "text": [ "angiotensin II" ], "offsets": [ [ 13, 27 ] ], "normalized": [] }, { "id": "PMID-2777_T2", "type": "Protein", "text": [ "angiotensin II" ], "offsets": [ [ 463, 477 ] ], "normalized": [] }, { "id": "PMID-2777_T3", "type": "Protein", "text": [ "angiotensin II" ], "offsets": [ [ 622, 636 ] ], "normalized": [] }, { "id": "PMID-2777_T4", "type": "Protein", "text": [ "angiotensin II" ], "offsets": [ [ 995, 1009 ] ], "normalized": [] }, { "id": "PMID-2777_T5", "type": "Protein", "text": [ "angiotensin II" ], "offsets": [ [ 1254, 1268 ] ], "normalized": [] }, { "id": "PMID-2777_T6", "type": "Protein", "text": [ "angiotensin II" ], "offsets": [ [ 1594, 1608 ] ], "normalized": [] }, { "id": "PMID-2777_T7", "type": "Protein", "text": [ "angiotensin II" ], "offsets": [ [ 1798, 1812 ] ], "normalized": [] }, { "id": "PMID-2777_T8", "type": "Protein", "text": [ "angiotensin II" ], "offsets": [ [ 2489, 2503 ] ], "normalized": [] } ]

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[ { "id": "PMID-2793841__text", "type": "abstract", "text": [ "Hydroxylation of CMP-NeuAc controls the expression of N-glycolylneuraminic acid in GM3 ganglioside of the small intestine of inbred rats. \nAn enzymatic activity responsible for the hydroxylation of CMP-NeuAc into CMP-N-glycolylneuraminic acid (CMP-NeuGc) was found in the cytosolic fraction after cellular fractionation of the mucosa of rat small intestine. It was maximum in the presence of NADPH or NADH, but it was reduced by 50% by addition of 1 mM EDTA. The Km value for CMP-NeuAc was 0.6 microM. The CMP-NeuAc hydroxylase activity paralleled the expression of the GM3 (NeuGc) phenotype in the epithelium of the small intestine and was not measurable in the mutant rats BN and SHR that only expressed GM3 (NeuAc). Furthermore, the only form of CMP-sialic acid present in the intestinal mucosa of the mutants was CMP-NeuAc, whereas in the other strains CMP-NeuGc accounted for 70-85% of the native CMP-sialic acids. Wild-type and CMP-NeuAc hydroxylase-deficient inbred rats were mated. Individuals of F1 and backcross generations were typed for the phenotypes GM3(NeuGc)/GM3(NeuAc) and the activity of CMP-NeuAc hydroxylase in the small intestine. It was found that the expression of NeuGc in GM3 depends on a single autosomal dominant gene and correlates with the activity of CMP-NeuAc hydroxylase. Two tissues other than small intestine, kidney and spleen, which expressed GM3(NeuGc) in BN and SHR, also expressed the CMP-NeuAc hydroxylase activity, as in the other strains. It was concluded that the key enzyme responsible for the presence of NeuGc in GM3 is a CMP-NeuAc hydroxylase and that mutant rats carry a defect that is specific to intestine. The comparative analysis of the respective contribution of NeuGc and NeuAc to the glycoprotein sialic acids of the small intestine showed that CMP-NeuAc hydroxylase is also responsible for part of the NeuGc present in the glycoproteins. However, the occurrence of 20-30% of NeuGc in the intestinal glycoproteins of the CMP-NeuAc hydroxylase-deficient rats indicated that there is another enzyme providing intestinal glycoproteins with NeuGc and operating under a different genetic control.\n" ], "offsets": [ [ 0, 2147 ] ] } ]

[ { "id": "PMID-2793841_T1", "type": "Protein", "text": [ "CMP-NeuAc hydroxylase" ], "offsets": [ [ 506, 527 ] ], "normalized": [] }, { "id": "PMID-2793841_T2", "type": "Protein", "text": [ "CMP-NeuAc hydroxylase" ], "offsets": [ [ 934, 955 ] ], "normalized": [] }, { "id": "PMID-2793841_T3", "type": "Protein", "text": [ "CMP-NeuAc hydroxylase" ], "offsets": [ [ 1106, 1127 ] ], "normalized": [] }, { "id": "PMID-2793841_T4", "type": "Protein", "text": [ "CMP-NeuAc hydroxylase" ], "offsets": [ [ 1281, 1302 ] ], "normalized": [] }, { "id": "PMID-2793841_T5", "type": "Protein", "text": [ "CMP-NeuAc hydroxylase" ], "offsets": [ [ 1424, 1445 ] ], "normalized": [] }, { "id": "PMID-2793841_T6", "type": "Protein", "text": [ "CMP-NeuAc hydroxylase" ], "offsets": [ [ 1568, 1589 ] ], "normalized": [] }, { "id": "PMID-2793841_T7", "type": "Protein", "text": [ "CMP-NeuAc hydroxylase" ], "offsets": [ [ 1800, 1821 ] ], "normalized": [] }, { "id": "PMID-2793841_T8", "type": "Protein", "text": [ "CMP-NeuAc hydroxylase" ], "offsets": [ [ 1976, 1997 ] ], "normalized": [] } ]

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[ { "id": "PMID-282603__text", "type": "abstract", "text": [ "Displacement and aberrant methylation in vitro of H-1 histone in rat liver nuclei after half-saturation of chromatin with polycations. \nRadiomethyl incorporation in vitro into Nepsilon-methyllysine of histones from rat liver nuclei incubated in the presence of S-adenosyl[methyl-3H]methionine is stimulated if the polycations polylysines, protamines, or histones are added to the incubation mixture. Maximal stimulation occurs at a cation/nucleotide ratio of 0.5. Past this point stimulation drops, except in the case of very lysine-rich histone H-1, for which the maximal level of incorporation remains constant upon further addition of this histone. Bio-Gel P-10 chromatography, differential precipitation, and gel electrophoresis of radiomethylated histones indicate that although the usual incorporation of radiomethyl into histone H-3 is not affected, active methylation of H-1 occurs in the presence of polycations. Column chromatographic amino acid analysis reveals that the methylation of H-1 will specifically generate Nepsilon-monomethyllysine. Except for this condition, H-1 is never methylated in vivo or in incubated cell nuclei. Because H-1 is the weakest bound histone in chromatin, the above phenomena may be explained by assuming that, within the chromatin, polycations displace the lysine-rich histone towards the nucleosome, which results in its abberant methylation, assuming that the native nucleosome is the seat of the histone lysine methyltransferase.\n" ], "offsets": [ [ 0, 1476 ] ] } ]

[ { "id": "PMID-282603_T1", "type": "Protein", "text": [ "H-1 histone" ], "offsets": [ [ 50, 61 ] ], "normalized": [] }, { "id": "PMID-282603_T2", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 201, 209 ] ], "normalized": [] }, { "id": "PMID-282603_T3", "type": "Protein", "text": [ "histone H-1" ], "offsets": [ [ 538, 549 ] ], "normalized": [] }, { "id": "PMID-282603_T4", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 643, 650 ] ], "normalized": [] }, { "id": "PMID-282603_T5", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 752, 760 ] ], "normalized": [] }, { "id": "PMID-282603_T6", "type": "Protein", "text": [ "histone H-3" ], "offsets": [ [ 828, 839 ] ], "normalized": [] }, { "id": "PMID-282603_T7", "type": "Protein", "text": [ "H-1" ], "offsets": [ [ 879, 882 ] ], "normalized": [] }, { "id": "PMID-282603_T8", "type": "Protein", "text": [ "H-1" ], "offsets": [ [ 997, 1000 ] ], "normalized": [] }, { "id": "PMID-282603_T9", "type": "Protein", "text": [ "H-1" ], "offsets": [ [ 1082, 1085 ] ], "normalized": [] }, { "id": "PMID-282603_T10", "type": "Protein", "text": [ "H-1" ], "offsets": [ [ 1151, 1154 ] ], "normalized": [] }, { "id": "PMID-282603_T11", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 1176, 1183 ] ], "normalized": [] }, { "id": "PMID-282603_T12", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 1312, 1319 ] ], "normalized": [] }, { "id": "PMID-282603_T13", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 1442, 1449 ] ], "normalized": [] } ]

[ { "id": "PMID-282603_E1", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 26, 37 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-282603_T1" } ] }, { "id": "PMID-282603_E2", "type": "Methylation", "trigger": { "text": [ "radiomethylated" ], "offsets": [ [ 736, 751 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-282603_T5" } ] }, { "id": "PMID-282603_E3", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 864, 875 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-282603_T7" } ] }, { "id": "PMID-282603_E4", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 982, 993 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-282603_T8" } ] }, { "id": "PMID-282603_E5", "type": "Methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 1095, 1105 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-282603_T9" } ] } ]

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[ { "id": "PMID-2908442__text", "type": "abstract", "text": [ "Cortical cytoskeleton of giant moth eggs. \nUnfertilized eggs of several species of giant moths contain a substantial cortical cytoskeleton. This structure is assembled during oogenesis, and contains actin as a major fibrillar component. The presence of actin was confirmed by gel electrophoresis and binding to phalloidin, DNase I, and a monoclonal antibody against cytoskeletal actin. Several lines of evidence suggest that the fat body is a source of the actin in the oocyte and that the transport and acquisition of actin by the ovary are similar to the mechanism of vitellogenin acquisition. A possible role for the cortical cytoskeleton in directing early embryogenesis is discussed.\n" ], "offsets": [ [ 0, 689 ] ] } ]

[ { "id": "PMID-2908442_T1", "type": "Protein", "text": [ "phalloidin" ], "offsets": [ [ 311, 321 ] ], "normalized": [] }, { "id": "PMID-2908442_T2", "type": "Protein", "text": [ "DNase I" ], "offsets": [ [ 323, 330 ] ], "normalized": [] } ]

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[ { "id": "PMID-2912379__text", "type": "abstract", "text": [ "Deamidation of calmodulin at neutral and alkaline pH: quantitative relationships between ammonia loss and the susceptibility of calmodulin to modification by protein carboxyl methyltransferase. \nMeasurements of ammonia release provide the first direct evidence that calmodulin becomes extensively deamidated during incubations at 37 degrees C, pH 7.4 or pH 11. A stoichiometry of 0.5 mol of NH3 released/mol of calmodulin is observed after 2 h at pH 11 or after 8-9 days at pH 7.4. These treatments also increase the ability of calmodulin to serve as a substrate for the isoaspartate-specific protein carboxyl methyltransferase from bovine brain. The stoichiometries of methylation are highly correlated with the stoichiometries of ammonia release. Deamidation and increased methyl-accepting capacity also occur in parallel for seven other proteins (aldolase, bovine serum albumin, cytochrome c, lysozyme, ovalbumin, ribonuclease A, and triosephosphate isomerase) upon incubation at pH 11. However, in comparison to calmodulin, these other proteins show very little deamidation and increased methylation capacity following incubation at pH 7.4. Deamidation of calmodulin at pH 7.4 is unaffected by the addition of 10(-7) M Ca2+; however, at 4 X 10(-6) M Ca2+, the rate of deamidation is inhibited by approximately 70%. The Ca2+-protection effect is consistent with the suggestion (B. A. Johnson, N. E. Freitag, and D. W. Aswad, (1985) J. Biol. Chem. 260, 10913-10916) that deamidation occurs preferentially at Asn-60 and/or Asn-97, each of which resides in a distinct Ca2+-binding domain.\n" ], "offsets": [ [ 0, 1589 ] ] } ]

[ { "id": "PMID-2912379_T1", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 15, 25 ] ], "normalized": [] }, { "id": "PMID-2912379_T2", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 128, 138 ] ], "normalized": [] }, { "id": "PMID-2912379_T3", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 266, 276 ] ], "normalized": [] }, { "id": "PMID-2912379_T4", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 411, 421 ] ], "normalized": [] }, { "id": "PMID-2912379_T5", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 528, 538 ] ], "normalized": [] }, { "id": "PMID-2912379_T6", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 867, 880 ] ], "normalized": [] }, { "id": "PMID-2912379_T7", "type": "Protein", "text": [ "cytochrome c" ], "offsets": [ [ 882, 894 ] ], "normalized": [] }, { "id": "PMID-2912379_T8", "type": "Protein", "text": [ "ribonuclease A" ], "offsets": [ [ 917, 931 ] ], "normalized": [] }, { "id": "PMID-2912379_T9", "type": "Protein", "text": [ "triosephosphate isomerase" ], "offsets": [ [ 937, 962 ] ], "normalized": [] }, { "id": "PMID-2912379_T10", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 1016, 1026 ] ], "normalized": [] }, { "id": "PMID-2912379_T11", "type": "Protein", "text": [ "calmodulin" ], "offsets": [ [ 1160, 1170 ] ], "normalized": [] } ]

[ { "id": "PMID-2912379_E1", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 670, 681 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2912379_T5" } ] } ]

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[ { "id": "PMID-2912499__text", "type": "abstract", "text": [ "Nonenzymatically glycated serum albumin: interaction with galactose-specific liver lectins. \nThe possible interaction of galactose/glucose-specific liver lectins with nonenzymatically glycated human serum albumin was analyzed. The binding activity of the asialoglycoprotein receptor on hepatocytes and of the corresponding lectin on Kupffer cells was determined using freshly isolated liver cells from Wistar rats. Nonenzymatically glucosylated or galactosylated human serum albumin (HSA) did not inhibit lectin binding in a competitive adhesion assay (less than 15% inhibition). In contrast, lactosylated HSA strongly interacted with the two liver lectins (more than 80% inhibition). Lectin binding increased with lactosylation reaching a maximum at 44-49 mol D-galactose bound per mol HSA. In conclusion, at least in certain cases, nonenzymatically glycated proteins may interact with endogenous lectins.\n" ], "offsets": [ [ 0, 907 ] ] } ]

[ { "id": "PMID-2912499_T1", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 26, 39 ] ], "normalized": [] }, { "id": "PMID-2912499_T2", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 199, 212 ] ], "normalized": [] }, { "id": "PMID-2912499_T3", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 469, 482 ] ], "normalized": [] }, { "id": "PMID-2912499_T4", "type": "Protein", "text": [ "HSA" ], "offsets": [ [ 484, 487 ] ], "normalized": [] }, { "id": "PMID-2912499_T5", "type": "Protein", "text": [ "HSA" ], "offsets": [ [ 606, 609 ] ], "normalized": [] }, { "id": "PMID-2912499_T6", "type": "Protein", "text": [ "HSA" ], "offsets": [ [ 787, 790 ] ], "normalized": [] } ]

[ { "id": "PMID-2912499_E1", "type": "Glycosylation", "trigger": { "text": [ "glucosylated" ], "offsets": [ [ 432, 444 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-2912499_T3" } ] } ]

[ { "id": "PMID-2912499_1", "entity_ids": [ "PMID-2912499_T3", "PMID-2912499_T4" ] } ]

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[ { "id": "PMID-3028206__text", "type": "abstract", "text": [ "Accurate, quantitative assays for the hydrolysis of soluble type I, II, and III 3H-acetylated collagens by bacterial and tissue collagenases. \nAccurate and quantitative assays for the hydrolysis of soluble 3H-acetylated rat tendon type I, bovine cartilage type II, and human amnion type III collagens by both bacterial and tissue collagenases have been developed. The assays are carried out at any temperature in the 1-30 degrees C range in a single reaction tube and the progress of the reaction is monitored by withdrawing aliquots as a function of time, quenching with 1,10-phenanthroline, and quantitation of the concentration of hydrolysis fragments. The latter is achieved by selective denaturation of these fragments by incubation under conditions described in the previous paper of this issue. The assays give percentages of hydrolysis of all three collagen types by neutrophil collagenase that agree well with the results of gel electrophoresis experiments. The initial rates of hydrolysis of all three collagens are proportional to the concentration of both neutrophil or Clostridial collagenases over a 10-fold range of enzyme concentrations. All three assays can be carried out at collagen concentrations. that range from 0.06 to 2 mg/ml and give linear double reciprocal plots for both tissue and bacterial collagenases that can be used to evaluate the kinetic parameters Km and kcat or Vmax. The assay developed for the hydrolysis of rat type I collagen by neutrophil collagenase is shown to be more sensitive by at least one order of magnitude than comparable assays that use rat type I collagen fibrils or gels as substrate.\n" ], "offsets": [ [ 0, 1641 ] ] } ]

[ { "id": "PMID-3028206_T1", "type": "Protein", "text": [ "II" ], "offsets": [ [ 68, 70 ] ], "normalized": [] }, { "id": "PMID-3028206_T2", "type": "Protein", "text": [ "type II" ], "offsets": [ [ 256, 263 ] ], "normalized": [] }, { "id": "PMID-3028206_T3", "type": "Protein", "text": [ "neutrophil collagenase" ], "offsets": [ [ 875, 897 ] ], "normalized": [] }, { "id": "PMID-3028206_T4", "type": "Protein", "text": [ "neutrophil collagenase" ], "offsets": [ [ 1471, 1493 ] ], "normalized": [] } ]

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[ { "id": "PMID-3036097__text", "type": "abstract", "text": [ "The role of insulin in the modulation of glucagon-dependent control of phenylalanine hydroxylation in isolated liver cells. \nThe stimulation of phenylalanine hydroxylation in isolated liver cells by sub-maximally effective concentrations of glucagon (less than 0.1 microM) is antagonized by insulin (0.1 nM-0.1 microM). This phenomenon is a consequence of a decrease in the glucagon-stimulated phosphorylation of phenylalanine hydroxylase from liver cells incubated in the presence of insulin. The impact of insulin on the phosphorylation state and activity of the hydroxylase is mimicked by incubation of liver cells in the presence of orthovanadate (10 microM). A series of cyclic AMP and cyclic GMP analogues enhanced phenylalanine hydroxylation: in each case insulin diminished the stimulation of flux. These results are discussed in the light of the characteristics of insulin action on other metabolic processes.\n" ], "offsets": [ [ 0, 919 ] ] } ]

[ { "id": "PMID-3036097_T1", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 12, 19 ] ], "normalized": [] }, { "id": "PMID-3036097_T2", "type": "Protein", "text": [ "glucagon" ], "offsets": [ [ 41, 49 ] ], "normalized": [] }, { "id": "PMID-3036097_T3", "type": "Protein", "text": [ "glucagon" ], "offsets": [ [ 241, 249 ] ], "normalized": [] }, { "id": "PMID-3036097_T4", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 291, 298 ] ], "normalized": [] }, { "id": "PMID-3036097_T5", "type": "Protein", "text": [ "glucagon" ], "offsets": [ [ 374, 382 ] ], "normalized": [] }, { "id": "PMID-3036097_T6", "type": "Protein", "text": [ "phenylalanine hydroxylase" ], "offsets": [ [ 413, 438 ] ], "normalized": [] }, { "id": "PMID-3036097_T7", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 485, 492 ] ], "normalized": [] }, { "id": "PMID-3036097_T8", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 508, 515 ] ], "normalized": [] }, { "id": "PMID-3036097_T9", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 763, 770 ] ], "normalized": [] }, { "id": "PMID-3036097_T10", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 874, 881 ] ], "normalized": [] } ]

[ { "id": "PMID-3036097_E1", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 394, 409 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3036097_T6" } ] }, { "id": "PMID-3036097_E2", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 523, 538 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3036097_T6" } ] } ]

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[ { "id": "PMID-3075618__text", "type": "abstract", "text": [ "Tubulin post-translational modifications and the construction of microtubular organelles in Trypanosoma brucei. \nWe have used specific monoclonal antibodies to facilitate a study of acetylated and tyrosinated alpha-tubulin in the microtubule (MT) arrays in the Trypanosoma brucei cell. Acetylated alpha-tubulin is not solely located in the stable microtubular arrays but is present even in the ephemeral microtubules of the mitotic spindle. Moreover, there is a uniform distribution of this isoform in all arrays. Studies of flagella complexes show that acetylation is concomitant with assembly of MTs. There is no subsequent major modulation in the content of acetylated alpha-tubulin in MTs. Conversely, polymerizing flagellar MTs have a high tyrosinated alpha-tubulin content, which is subsequently reduced to a basal level at a discrete point in the cell cycle. The MTs of the intranuclear mitotic spindle appear never to contain tyrosinated alpha-tubulin, suggesting that they are actually constructed of detyrosinated alpha-tubulin or that detyrosination is extremely rapid at this time in the cell cycle. T. brucei therefore, represents a cell type with extremely active mechanisms for the post-translational modification of alpha-tubulin. Our analyses of the timing of acquisition and modulation in relation to MT construction in T. brucei, suggest that acetylation and detyrosination of alpha-tubulin are two independently regulated post-translational modifications, that are not uniquely associated with particular subsets of MTs of defined lability, position or function. Post-assembly detyrosination of alpha-tubulin may provide a mechanism whereby the cell could discriminate between new and old MTs, during construction of the cytoskeleton through the cell cycle. However, we also suggest that continuation of detyrosination, allows the cell, at cell division, to partition into daughter cells two equivalent sets of cytoskeletal MTs.\n" ], "offsets": [ [ 0, 1949 ] ] } ]

[ { "id": "PMID-3075618_T1", "type": "Protein", "text": [ "alpha-tubulin" ], "offsets": [ [ 209, 222 ] ], "normalized": [] }, { "id": "PMID-3075618_T2", "type": "Protein", "text": [ "alpha-tubulin" ], "offsets": [ [ 297, 310 ] ], "normalized": [] }, { "id": "PMID-3075618_T3", "type": "Protein", "text": [ "alpha-tubulin" ], "offsets": [ [ 672, 685 ] ], "normalized": [] }, { "id": "PMID-3075618_T4", "type": "Protein", "text": [ "alpha-tubulin" ], "offsets": [ [ 757, 770 ] ], "normalized": [] }, { "id": "PMID-3075618_T5", "type": "Protein", "text": [ "alpha-tubulin" ], "offsets": [ [ 946, 959 ] ], "normalized": [] }, { "id": "PMID-3075618_T6", "type": "Protein", "text": [ "alpha-tubulin" ], "offsets": [ [ 1024, 1037 ] ], "normalized": [] }, { "id": "PMID-3075618_T7", "type": "Protein", "text": [ "alpha-tubulin" ], "offsets": [ [ 1232, 1245 ] ], "normalized": [] }, { "id": "PMID-3075618_T8", "type": "Protein", "text": [ "alpha-tubulin" ], "offsets": [ [ 1396, 1409 ] ], "normalized": [] }, { "id": "PMID-3075618_T9", "type": "Protein", "text": [ "alpha-tubulin" ], "offsets": [ [ 1615, 1628 ] ], "normalized": [] } ]

[ { "id": "PMID-3075618_E1", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 182, 192 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3075618_T1" } ] }, { "id": "PMID-3075618_E2", "type": "Acetylation", "trigger": { "text": [ "Acetylated" ], "offsets": [ [ 286, 296 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3075618_T2" } ] }, { "id": "PMID-3075618_E3", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 554, 565 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3075618_T2" } ] }, { "id": "PMID-3075618_E4", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 661, 671 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3075618_T3" } ] }, { "id": "PMID-3075618_E5", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 1362, 1373 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3075618_T8" } ] } ]

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[ { "id": "PMID-3108247__text", "type": "abstract", "text": [ "Lethal perinatal osteogenesis imperfecta due to the substitution of arginine for glycine at residue 391 of the alpha 1(I) chain of type I collagen. \nA baby with the lethal perinatal form of osteogenesis imperfecta was shown to have a structural defect in the alpha 1(I) chain of type I procollagen. Normal and mutant alpha 1(I) CB8 cyanogen bromide peptides, from the helical part of the alpha 1(I) chains, were purified from bone. Amino acid sequencing of tryptic peptides derived from the mutant alpha 1(I) CB8 peptide showed that the glycine residue at position 391 of the alpha 1(I) chain had been replaced by an arginine residue. This substitution accounted for the more basic charged form of this peptide that was observed on two-dimensional electrophoresis of the collagen peptides obtained from the tissues. The substitution was associated with increased enzymatic hydroxylation of lysine residues in the alpha 1(I) CB8 and the adjoining CB3 peptides but not in the carboxyl-terminal CB6 and CB7 peptides. This finding suggested that the sequence abnormality had interfered with the propagation of the triple helix across the mutant region. The abnormal collagen was not incorporated into the more insoluble fraction of bone collagen. The baby appeared to be heterozygous for the sequence abnormality and as the parents did not show any evidence of the defect it is likely that the baby had a new mutation of one allele of the pro-alpha 1(I) gene. The amino acid substitution could result from a single nucleotide mutation in the codon GGC (glycine) to produce the codon CGC (arginine).\n" ], "offsets": [ [ 0, 1595 ] ] } ]

[ { "id": "PMID-3108247_T1", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 111, 121 ] ], "normalized": [] }, { "id": "PMID-3108247_T2", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 259, 269 ] ], "normalized": [] }, { "id": "PMID-3108247_T3", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 317, 327 ] ], "normalized": [] }, { "id": "PMID-3108247_T4", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 388, 398 ] ], "normalized": [] }, { "id": "PMID-3108247_T5", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 498, 508 ] ], "normalized": [] }, { "id": "PMID-3108247_T6", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 576, 586 ] ], "normalized": [] }, { "id": "PMID-3108247_T7", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 913, 923 ] ], "normalized": [] }, { "id": "PMID-3108247_T8", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 1439, 1449 ] ], "normalized": [] }, { "id": "PMID-3108247_T10", "type": "Entity", "text": [ "lysine residues" ], "offsets": [ [ 890, 905 ] ], "normalized": [] } ]

[ { "id": "PMID-3108247_E1", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 873, 886 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3108247_T7" }, { "role": "Site", "ref_id": "PMID-3108247_T10" } ] } ]

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[ { "id": "PMID-3264725__text", "type": "abstract", "text": [ "Amino acid sequence and posttranslational modifications of human factor VIIa from plasma and transfected baby hamster kidney cells. \nBlood coagulation factor VII is a vitamin K dependent glycoprotein which in its activated form, factor VIIa, participates in the coagulation process by activating factor X and/or factor IX in the presence of Ca2+ and tissue factor. Three types of potential posttranslational modifications exist in the human factor VIIa molecule, namely, 10 gamma-carboxylated, N-terminally located glutamic acid residues, 1 beta-hydroxylated aspartic acid residue, and 2 N-glycosylated asparagine residues. In the present study, the amino acid sequence and posttranslational modifications of recombinant factor VIIa as purified from the culture medium of a transfected baby hamster kidney cell line have been compared to human plasma factor VIIa. By use of HPLC, amino acid analysis, peptide mapping, and automated Edman degradations, the protein backbone of recombinant factor VIIa was found to be identical with human factor VIIa. Neither recombinant factor VIIa nor human plasma factor VIIa was found to contain beta-hydroxyaspartic acid. In human plasma factor VIIa, the 10 N-terminally located glutamic acid residues were found to be fully gamma-carboxylated whereas 9 full and 1 partial gamma-carboxylated residues were found in the corresponding positions of the recombinant factor VIIa molecule. Asparagine residues 145 and 322 were found to be fully N-glycosylated in human plasma factor VIIa. In the recombinant factor VIIa, asparagine residue 322 was fully glycosylated whereas asparagine residue 145 was only partially (approximately 66%) glycosylated. Besides minor differences in the sialic acid and fucose contents, the overall carbohydrate compositions were nearly identical in recombinant factor VIIa and human plasma factor VIIa.(ABSTRACT TRUNCATED AT 250 WORDS)\n" ], "offsets": [ [ 0, 1898 ] ] } ]

[ { "id": "PMID-3264725_T1", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 65, 76 ] ], "normalized": [] }, { "id": "PMID-3264725_T2", "type": "Protein", "text": [ "coagulation factor VII" ], "offsets": [ [ 139, 161 ] ], "normalized": [] }, { "id": "PMID-3264725_T3", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 229, 240 ] ], "normalized": [] }, { "id": "PMID-3264725_T4", "type": "Protein", "text": [ "factor X" ], "offsets": [ [ 296, 304 ] ], "normalized": [] }, { "id": "PMID-3264725_T5", "type": "Protein", "text": [ "factor IX" ], "offsets": [ [ 312, 321 ] ], "normalized": [] }, { "id": "PMID-3264725_T6", "type": "Protein", "text": [ "tissue factor" ], "offsets": [ [ 350, 363 ] ], "normalized": [] }, { "id": "PMID-3264725_T7", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 441, 452 ] ], "normalized": [] }, { "id": "PMID-3264725_T8", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 721, 732 ] ], "normalized": [] }, { "id": "PMID-3264725_T9", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 851, 862 ] ], "normalized": [] }, { "id": "PMID-3264725_T10", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 988, 999 ] ], "normalized": [] }, { "id": "PMID-3264725_T11", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1037, 1048 ] ], "normalized": [] }, { "id": "PMID-3264725_T12", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1070, 1081 ] ], "normalized": [] }, { "id": "PMID-3264725_T13", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1099, 1110 ] ], "normalized": [] }, { "id": "PMID-3264725_T14", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1175, 1186 ] ], "normalized": [] }, { "id": "PMID-3264725_T15", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1399, 1410 ] ], "normalized": [] }, { "id": "PMID-3264725_T16", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1507, 1518 ] ], "normalized": [] }, { "id": "PMID-3264725_T17", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1539, 1550 ] ], "normalized": [] }, { "id": "PMID-3264725_T18", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1823, 1834 ] ], "normalized": [] }, { "id": "PMID-3264725_T19", "type": "Protein", "text": [ "factor VIIa" ], "offsets": [ [ 1852, 1863 ] ], "normalized": [] }, { "id": "PMID-3264725_T21", "type": "Entity", "text": [ "aspartic acid residue" ], "offsets": [ [ 559, 580 ] ], "normalized": [] }, { "id": "PMID-3264725_T23", "type": "Entity", "text": [ "asparagine residues" ], "offsets": [ [ 603, 622 ] ], "normalized": [] }, { "id": "PMID-3264725_T24", "type": "Entity", "text": [ "Asparagine residues 145" ], "offsets": [ [ 1421, 1444 ] ], "normalized": [] }, { "id": "PMID-3264725_T25", "type": "Entity", "text": [ "322" ], "offsets": [ [ 1449, 1452 ] ], "normalized": [] }, { "id": "PMID-3264725_T27", "type": "Entity", "text": [ "asparagine residue 322" ], "offsets": [ [ 1552, 1574 ] ], "normalized": [] }, { "id": "PMID-3264725_T29", "type": "Entity", "text": [ "asparagine residue 145" ], "offsets": [ [ 1606, 1628 ] ], "normalized": [] } ]

[ { "id": "PMID-3264725_E1", "type": "Hydroxylation", "trigger": { "text": [ "beta-hydroxylated" ], "offsets": [ [ 541, 558 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3264725_T7" }, { "role": "Site", "ref_id": "PMID-3264725_T21" } ] }, { "id": "PMID-3264725_E2", "type": "Glycosylation", "trigger": { "text": [ "N-glycosylated" ], "offsets": [ [ 588, 602 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3264725_T7" }, { "role": "Site", "ref_id": "PMID-3264725_T23" } ] }, { "id": "PMID-3264725_E3", "type": "Glycosylation", "trigger": { "text": [ "N-glycosylated" ], "offsets": [ [ 1476, 1490 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3264725_T16" }, { "role": "Site", "ref_id": "PMID-3264725_T24" } ] }, { "id": "PMID-3264725_E4", "type": "Glycosylation", "trigger": { "text": [ "N-glycosylated" ], "offsets": [ [ 1476, 1490 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3264725_T16" }, { "role": "Site", "ref_id": "PMID-3264725_T25" } ] }, { "id": "PMID-3264725_E5", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 1585, 1597 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3264725_T17" }, { "role": "Site", "ref_id": "PMID-3264725_T27" } ] }, { "id": "PMID-3264725_E6", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 1668, 1680 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3264725_T17" }, { "role": "Site", "ref_id": "PMID-3264725_T29" } ] } ]

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[ { "id": "PMID-3373428__text", "type": "abstract", "text": [ "Binding of gossypol derivatives to human serum albumin. \nIn light of our previous finding that gossypol competes effectively with bilirubin for the high affinity bilirubin binding site on human serum albumin, a study of the binding to albumin of four gossypol derivatives was undertaken. The derivatives are compounds in which the aldehyde groups of gossypol are converted to nitriles and the periphenolic groups are acylated with acetyl, propionyl, butyryl, or valeryl groups. These periacylated gossylic nitriles bind to the high affinity bilirubin binding site on human serum albumin, but with dissociation constants approximately 30 times greater than that of gossypol. The gossypol derivatives also bind to another site on albumin, but with dissociation constants approximately 6 times greater than those for the bilirubin site. This second site has been identified as the major drug binding site in domain III.\n" ], "offsets": [ [ 0, 917 ] ] } ]

[ { "id": "PMID-3373428_T1", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 41, 54 ] ], "normalized": [] }, { "id": "PMID-3373428_T2", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 194, 207 ] ], "normalized": [] }, { "id": "PMID-3373428_T3", "type": "Protein", "text": [ "albumin" ], "offsets": [ [ 235, 242 ] ], "normalized": [] }, { "id": "PMID-3373428_T4", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 573, 586 ] ], "normalized": [] }, { "id": "PMID-3373428_T5", "type": "Protein", "text": [ "albumin" ], "offsets": [ [ 728, 735 ] ], "normalized": [] } ]

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[ { "id": "PMID-3427073__text", "type": "abstract", "text": [ "Thermodynamic analysis of inducer binding to the lactose repressor protein: contributions of galactosyl hydroxyl groups and beta substituents. \nKinetic and equilibrium studies of the binding of modified beta-D-galactoside sugars to the lac repressor were carried out to generate thermodynamic data for protein-inducer interactions. The energetic contributions of the galactosyl hydroxyl groups to binding were assessed by using a series of methyl deoxyfluoro-beta-D-galactosides. The C-3 and C-6 hydroxyls contributed less than or equal to -2.3 and -1.7 +/- 0.3 kcal/mol to the binding free energy change, respectively, whereas the C-4 hydroxyl provided only a nominal contribution (-0.1 +/- 0.2 kcal/mol). Favorable contributions to the total binding free energy change were observed for replacement of O-methyl by S-methyl at the beta-anomeric position and for S-methyl by S-isopropyl. Negative delta H degrees values characteristic of protein-sugar complexes [Quiocho, F. A. (1986) Annu. Rev. Biochem. 55, 287-315] were observed for a series of beta-D-galactosides differing at the beta-glycosidic position. A decrease in delta H degrees of approximately 6 kcal/mol upon replacement of the O-methyl substituent by S-methyl indicates a substantial increase in van der Waals' interactions and/or hydrogen bonding in this region of the ligand binding site. The more favorable free energy change for the binding of the S-isopropyl vs S-methyl compound is due mainly to more positive entropic contributions, consistent with an increase in apolar interactions.(ABSTRACT TRUNCATED AT 250 WORDS)\n" ], "offsets": [ [ 0, 1591 ] ] } ]

[ { "id": "PMID-3427073_T1", "type": "Protein", "text": [ "lactose repressor" ], "offsets": [ [ 49, 66 ] ], "normalized": [] }, { "id": "PMID-3427073_T2", "type": "Protein", "text": [ "lac repressor" ], "offsets": [ [ 236, 249 ] ], "normalized": [] } ]

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[ { "id": "PMID-3497198__text", "type": "abstract", "text": [ "Site specific glycosylation patterns of H-2K: effects of allelic polymorphism and mitogenic stimulation. \nThe site-specific glycosylation patterns of two H-2K alleles, k and b, were determined on splenic T cells metabolically labeled with [3H]mannose. Cells from B10, B10.A, (B10 X B10.A)F1, and C3H mice were examined, along with the effect of short- (8 hr) and long-term (36 hr) mitogenic stimulation. For both glycosylation sites (Asn86 and Asn176) of both antigens, 80% of the structures consisted of mono- and bisialylated biantennary N-linked complex oligosaccharides, with the remaining consisting of smaller (probably high mannose) structures. Asn176 of both H-2Kk and H-2Kb contained the same ratio (2.8 to 1) of bi- to monosialylated chains. However, Asn86 of H-2Kb contained a higher ratio (5 to 1), while Asn86 of H-2Kk a lower ratio (1.5 to 1). This difference was seen on antigens isolated from cells of the parental strains as well as from the F1 cross. The glycosylation of H-2Kk did not vary between B10.A and C3H mice. Mitogenic stimulation increased markedly both total [3H]mannose incorporation and the spectrum of N-linked oligosaccharides labeled. For H-2Kk, it had no effect on sialylation, but resulted in a slight under galactosylation of the monosialylated structures at both sites. A comparison of the patterns seen here, determined on nontransformed T cells, with those previously determined on H-2Kk from a B lymphoma line, revealed marked differences in sialylation and branching patterns at both sites. These data indicate that glycosylation differences may be found between highly homologous (91%) alleles of an H-2 gene, even when co-dominantly expressed by F1 cells; however, the patterns do change with mitogenic stimulation, and between normal and transformed cells.\n" ], "offsets": [ [ 0, 1803 ] ] } ]

[ { "id": "PMID-3497198_T1", "type": "Protein", "text": [ "H-2K" ], "offsets": [ [ 40, 44 ] ], "normalized": [] }, { "id": "PMID-3497198_T2", "type": "Protein", "text": [ "H-2K alleles, k" ], "offsets": [ [ 154, 169 ] ], "normalized": [] }, { "id": "PMID-3497198_T3", "type": "Protein", "text": [ "b" ], "offsets": [ [ 174, 175 ] ], "normalized": [] }, { "id": "PMID-3497198_T4", "type": "Protein", "text": [ "H-2Kk" ], "offsets": [ [ 667, 672 ] ], "normalized": [] }, { "id": "PMID-3497198_T5", "type": "Protein", "text": [ "H-2Kb" ], "offsets": [ [ 677, 682 ] ], "normalized": [] }, { "id": "PMID-3497198_T6", "type": "Protein", "text": [ "H-2Kb" ], "offsets": [ [ 770, 775 ] ], "normalized": [] }, { "id": "PMID-3497198_T7", "type": "Protein", "text": [ "H-2Kk" ], "offsets": [ [ 826, 831 ] ], "normalized": [] }, { "id": "PMID-3497198_T8", "type": "Protein", "text": [ "H-2Kk" ], "offsets": [ [ 990, 995 ] ], "normalized": [] }, { "id": "PMID-3497198_T9", "type": "Protein", "text": [ "H-2Kk" ], "offsets": [ [ 1174, 1179 ] ], "normalized": [] }, { "id": "PMID-3497198_T10", "type": "Protein", "text": [ "H-2Kk" ], "offsets": [ [ 1423, 1428 ] ], "normalized": [] }, { "id": "PMID-3497198_T13", "type": "Entity", "text": [ "Asn86" ], "offsets": [ [ 434, 439 ] ], "normalized": [] }, { "id": "PMID-3497198_T14", "type": "Entity", "text": [ "Asn176" ], "offsets": [ [ 444, 450 ] ], "normalized": [] }, { "id": "PMID-3497198_T16", "type": "Entity", "text": [ "complex oligosaccharides" ], "offsets": [ [ 549, 573 ] ], "normalized": [] }, { "id": "PMID-3497198_T17", "type": "Entity", "text": [ "smaller (probably high mannose) structures" ], "offsets": [ [ 608, 650 ] ], "normalized": [] } ]

[ { "id": "PMID-3497198_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 14, 27 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T1" } ] }, { "id": "PMID-3497198_E2", "type": "Glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 124, 137 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T2" } ] }, { "id": "PMID-3497198_E3", "type": "Glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 124, 137 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T3" } ] }, { "id": "PMID-3497198_E4", "type": "Glycosylation", "trigger": { "text": [ "N-linked" ], "offsets": [ [ 540, 548 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T3" }, { "role": "Site", "ref_id": "PMID-3497198_T13" }, { "role": "Sidechain", "ref_id": "PMID-3497198_T16" } ] }, { "id": "PMID-3497198_E5", "type": "Glycosylation", "trigger": { "text": [ "N-linked" ], "offsets": [ [ 540, 548 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T3" }, { "role": "Site", "ref_id": "PMID-3497198_T13" }, { "role": "Sidechain", "ref_id": "PMID-3497198_T17" } ] }, { "id": "PMID-3497198_E6", "type": "Glycosylation", "trigger": { "text": [ "N-linked" ], "offsets": [ [ 540, 548 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T3" }, { "role": "Site", "ref_id": "PMID-3497198_T14" }, { "role": "Sidechain", "ref_id": "PMID-3497198_T16" } ] }, { "id": "PMID-3497198_E7", "type": "Glycosylation", "trigger": { "text": [ "N-linked" ], "offsets": [ [ 540, 548 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T3" }, { "role": "Site", "ref_id": "PMID-3497198_T14" }, { "role": "Sidechain", "ref_id": "PMID-3497198_T17" } ] }, { "id": "PMID-3497198_E8", "type": "Glycosylation", "trigger": { "text": [ "N-linked" ], "offsets": [ [ 540, 548 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T2" }, { "role": "Site", "ref_id": "PMID-3497198_T13" }, { "role": "Sidechain", "ref_id": "PMID-3497198_T16" } ] }, { "id": "PMID-3497198_E9", "type": "Glycosylation", "trigger": { "text": [ "N-linked" ], "offsets": [ [ 540, 548 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T2" }, { "role": "Site", "ref_id": "PMID-3497198_T13" }, { "role": "Sidechain", "ref_id": "PMID-3497198_T17" } ] }, { "id": "PMID-3497198_E10", "type": "Glycosylation", "trigger": { "text": [ "N-linked" ], "offsets": [ [ 540, 548 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T2" }, { "role": "Site", "ref_id": "PMID-3497198_T14" }, { "role": "Sidechain", "ref_id": "PMID-3497198_T16" } ] }, { "id": "PMID-3497198_E11", "type": "Glycosylation", "trigger": { "text": [ "N-linked" ], "offsets": [ [ 540, 548 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T2" }, { "role": "Site", "ref_id": "PMID-3497198_T14" }, { "role": "Sidechain", "ref_id": "PMID-3497198_T17" } ] }, { "id": "PMID-3497198_E12", "type": "Glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 973, 986 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3497198_T8" } ] } ]

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[ { "id": "PMID-3584101__text", "type": "abstract", "text": [ "Altered nucleosomes of active nucleolar chromatin contain accessible histone H3 in its hyperacetylated forms. \nChromatin of the organism Physarum polycephalum contains a class of conformationally altered nucleosomes previously localized to the transcribing regions of ribosomal genes in nucleoli. When nuclei are treated with 2-iodo[2-tritium]acetate, the histone H3 sulfhydryl group of the altered nucleosomes is derivatized while that of folded nucleosomes is not, and the labeled histones can then be identified by autoradiography of gels that separate H3 isoforms. The H3 derivatized is predominantly of tri- and tetraacetylated forms. In contrast, total free histone reacted with iodoacetate shows no preferential labeling of isoforms. Selective reaction of acetylated H3 is prevalent in both nucleolar and non-nucleolar chromatin. The results link specific patterns of H3 acetylation to changes in nucleosome conformation that occur during transcription.\n" ], "offsets": [ [ 0, 961 ] ] } ]

[ { "id": "PMID-3584101_T1", "type": "Protein", "text": [ "histone H3" ], "offsets": [ [ 69, 79 ] ], "normalized": [] }, { "id": "PMID-3584101_T2", "type": "Protein", "text": [ "histone H3" ], "offsets": [ [ 356, 366 ] ], "normalized": [] }, { "id": "PMID-3584101_T3", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 483, 491 ] ], "normalized": [] }, { "id": "PMID-3584101_T4", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 556, 558 ] ], "normalized": [] }, { "id": "PMID-3584101_T5", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 573, 575 ] ], "normalized": [] }, { "id": "PMID-3584101_T6", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 664, 671 ] ], "normalized": [] }, { "id": "PMID-3584101_T7", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 774, 776 ] ], "normalized": [] }, { "id": "PMID-3584101_T8", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 875, 877 ] ], "normalized": [] } ]

[ { "id": "PMID-3584101_E1", "type": "Acetylation", "trigger": { "text": [ "hyperacetylated" ], "offsets": [ [ 87, 102 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3584101_T1" } ] }, { "id": "PMID-3584101_E2", "type": "Acetylation", "trigger": { "text": [ "tri-" ], "offsets": [ [ 608, 612 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3584101_T5" } ] }, { "id": "PMID-3584101_E3", "type": "Acetylation", "trigger": { "text": [ "tetraacetylated" ], "offsets": [ [ 617, 632 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3584101_T5" } ] }, { "id": "PMID-3584101_E4", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 763, 773 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3584101_T7" } ] }, { "id": "PMID-3584101_E5", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 878, 889 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3584101_T8" } ] } ]

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[ { "id": "PMID-3663601__text", "type": "abstract", "text": [ "Distinguishing among protein kinases by substrate specificities. \nIn the previous paper, N-methylated peptides were shown to be sensitive probes of substrate conformation within the adenosine cyclic 3',5'-phosphate dependent protein kinase (A-kinase) active site. While it has been shown that other protein kinases will catalyze the phosphorylation of the same peptide sequences as A-kinase, there is as yet little information as to whether the protein kinases differentiate between substrates on the basis of conformation. For this reason, the conformationally restricted N-methylated peptides were used to probe the active site of guanosine cyclic 3',5'-phosphate dependent protein kinase (G-kinase), which is homologous in sequence to [Takio, K., Wade, R. D., Smith, S. B., Krebs, E. G., Walsh, K. A., & Titani, K. (1984) Biochemistry 23, 4207-4218] and which has substrate specificities similar to [Lincoln, T. M., & Corbin, J. D. (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 3239-3243] those of A-kinase. Although this enzyme appears to bind the peptides in a conformation resembling that of conformation A, it is more able to accommodate backbone methylation than is A-kinase. A peptide substrate at least 700-fold selective for G-kinase over A-kinase was found. Backbone methylation may, therefore, represent a way of making peptide substrates and inhibitors selective for a particular kinase.\n" ], "offsets": [ [ 0, 1397 ] ] } ]

[ { "id": "PMID-3663601_T1", "type": "Protein", "text": [ "guanosine cyclic 3',5'-phosphate dependent protein kinase" ], "offsets": [ [ 633, 690 ] ], "normalized": [] }, { "id": "PMID-3663601_T2", "type": "Protein", "text": [ "G-kinase" ], "offsets": [ [ 692, 700 ] ], "normalized": [] }, { "id": "PMID-3663601_T3", "type": "Protein", "text": [ "G-kinase" ], "offsets": [ [ 1231, 1239 ] ], "normalized": [] } ]

[]

[ { "id": "PMID-3663601_1", "entity_ids": [ "PMID-3663601_T1", "PMID-3663601_T2" ] } ]

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[ { "id": "PMID-3667584__text", "type": "abstract", "text": [ "Biosynthesis of chick type VI collagen. II. Processing and secretion in fibroblasts and smooth muscle cells. \nThe biosynthesis of type VI collagen was studied in \"matrix-free\" chick embryo smooth muscle cells and fibroblasts. Omission of ascorbate from the culture affected to a great extent the secretion in fibroblasts but had a very minor effect on smooth muscle cells. Quantitative analysis of the secretion process in continuous time course and in pulse-chase experiments confirmed that fibroblasts and smooth muscle cells secreted type VI collagen with the same chain composition but with different kinetics: after 4 h of chase more than 60% of the labeled type VI collagen was present in the culture medium of fibroblasts, whereas at the same time interval less than 25% was secreted by smooth muscle cells. The different kinetics depends on intrinsic properties of the cells, since it was detected also in adherent cells. However, even in fibroblasts, secretion of type VI collagen was much slower than secretion of fibronectin, of which more than 50% was already in the cell medium after 1 h of chase. Treatment of the cells with inhibitors of hydroxylation and glycosylation caused a shift in mobility that revealed a size heterogeneity in the Mr = 260,000 subunit. No evidence of processing was observed in chick cells for any of the subunits that were synthesized and secreted uncleaved. In addition, after several days of chase the Mr of the subunits of type VI collagen isolated from the matrix remained unchanged, thus excluding that in the chick even a partial or incomplete processing takes place.\n" ], "offsets": [ [ 0, 1617 ] ] } ]

[ { "id": "PMID-3667584_T1", "type": "Protein", "text": [ "fibronectin" ], "offsets": [ [ 1026, 1037 ] ], "normalized": [] } ]

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[ { "id": "PMID-3757037__text", "type": "abstract", "text": [ "Histones and histone acetylation during the embryonic development of Drosophila hydei. \nHistones and histone acetylation have been investigated during three stages of Drosophila hydei embryogenesis--early gastrula, late gastrula and organogenesis. No essential changes in the electrophoretic pattern of the histones have been revealed during the stages examined. However, we established an enhanced level of [14C]acetate incorporation at the time of extensive gene activation during gastrulation as well as some quantitative differences in the pattern of acetylation during gastrula and organogenesis. We consider most of them to be related to chromatin assembly during the stage of gastrulation and suggest that the correlation between histone acetylation and gene activity during Drosophila embryogenesis concerns histone H3 acetylation. The involvement of both acetylation and deacetylation in the steady-state acetylation level has been examined as well. We have found that the higher acetyltransferase activity is responsible for the enhanced level of acetate incorporation during gastrulation.\n" ], "offsets": [ [ 0, 1100 ] ] } ]

[ { "id": "PMID-3757037_T1", "type": "Protein", "text": [ "Histones" ], "offsets": [ [ 0, 8 ] ], "normalized": [] }, { "id": "PMID-3757037_T2", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 13, 20 ] ], "normalized": [] }, { "id": "PMID-3757037_T3", "type": "Protein", "text": [ "Histones" ], "offsets": [ [ 88, 96 ] ], "normalized": [] }, { "id": "PMID-3757037_T4", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 101, 108 ] ], "normalized": [] }, { "id": "PMID-3757037_T5", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 307, 315 ] ], "normalized": [] }, { "id": "PMID-3757037_T6", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 737, 744 ] ], "normalized": [] }, { "id": "PMID-3757037_T7", "type": "Protein", "text": [ "histone H3" ], "offsets": [ [ 816, 826 ] ], "normalized": [] } ]

[ { "id": "PMID-3757037_E1", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 21, 32 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3757037_T2" } ] }, { "id": "PMID-3757037_E2", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 109, 120 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3757037_T4" } ] }, { "id": "PMID-3757037_E3", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 555, 566 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3757037_T5" } ] }, { "id": "PMID-3757037_E4", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 745, 756 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3757037_T6" } ] }, { "id": "PMID-3757037_E5", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 827, 838 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3757037_T7" } ] } ]

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[ { "id": "PMID-3768165__text", "type": "abstract", "text": [ "Further characterization of the posttranslational modifications of core histones in response to heat and arsenite stress in Drosophila. \nThe effects of a heat shock or arsenite treatment on the methylation and acetylation of core histones have been investigated in Drosophila cultured cells. The decrease in H3 methylation, which is observed during a heat shock, is not a demethylation process, but results from methylation arrest. Two-dimensional gel electrophoresis leaves no ambiguity concerning the identity of H2B as a methylated protein, since H2B and D2, a nuclear nonhistone protein, which comigrate on one-dimensional gels, are well separated on these gels. Two-dimensional gel electrophoresis in the presence of Triton X-100 resolves each of the core histones into multiple forms resulting from posttranslational modifications. There are apparently, however, no histone variants in cultured Drosophila cells. At 23 degrees C, the various forms of the core histones resolved on two-dimensional gels are methylated. Under heat-shock or arsenite treatment, the methylation of all forms of H3 is decreased, while that of the various forms of H2B increase. These stress conditions also induce a generalized diminution in the acetylation of all forms of core histones. In the course of a heat shock, the synthesis of H2B is increased and this newly synthesized histone remains unacetylated during the shock. These changes in the patterns of core histone methylation and acetylation may be correlated with the reorganization of gene activity brought about by the heat shock.\n" ], "offsets": [ [ 0, 1578 ] ] } ]

[ { "id": "PMID-3768165_T1", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 72, 80 ] ], "normalized": [] }, { "id": "PMID-3768165_T2", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 230, 238 ] ], "normalized": [] }, { "id": "PMID-3768165_T3", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 308, 310 ] ], "normalized": [] }, { "id": "PMID-3768165_T4", "type": "Protein", "text": [ "H2B" ], "offsets": [ [ 515, 518 ] ], "normalized": [] }, { "id": "PMID-3768165_T5", "type": "Protein", "text": [ "H2B" ], "offsets": [ [ 550, 553 ] ], "normalized": [] }, { "id": "PMID-3768165_T6", "type": "Protein", "text": [ "D2" ], "offsets": [ [ 558, 560 ] ], "normalized": [] }, { "id": "PMID-3768165_T7", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 761, 769 ] ], "normalized": [] }, { "id": "PMID-3768165_T8", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 872, 879 ] ], "normalized": [] }, { "id": "PMID-3768165_T9", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 966, 974 ] ], "normalized": [] }, { "id": "PMID-3768165_T10", "type": "Protein", "text": [ "H3" ], "offsets": [ [ 1096, 1098 ] ], "normalized": [] }, { "id": "PMID-3768165_T11", "type": "Protein", "text": [ "H2B" ], "offsets": [ [ 1148, 1151 ] ], "normalized": [] }, { "id": "PMID-3768165_T12", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 1263, 1271 ] ], "normalized": [] }, { "id": "PMID-3768165_T13", "type": "Protein", "text": [ "H2B" ], "offsets": [ [ 1321, 1324 ] ], "normalized": [] }, { "id": "PMID-3768165_T14", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 1365, 1372 ] ], "normalized": [] }, { "id": "PMID-3768165_T15", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 1450, 1457 ] ], "normalized": [] } ]

[ { "id": "PMID-3768165_E1", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 194, 205 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T2" } ] }, { "id": "PMID-3768165_E2", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 210, 221 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T2" } ] }, { "id": "PMID-3768165_E3", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 311, 322 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T3" } ] }, { "id": "PMID-3768165_E4", "type": "Methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 524, 534 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T4" } ] }, { "id": "PMID-3768165_E5", "type": "Methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 1012, 1022 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T9" } ] }, { "id": "PMID-3768165_E6", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1068, 1079 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T10" } ] }, { "id": "PMID-3768165_E7", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1068, 1079 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T11" } ] }, { "id": "PMID-3768165_E8", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 1230, 1241 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T12" } ] }, { "id": "PMID-3768165_E9", "type": "Acetylation", "trigger": { "text": [ "unacetylated" ], "offsets": [ [ 1381, 1393 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T14" } ] }, { "id": "PMID-3768165_E10", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1458, 1469 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T15" } ] }, { "id": "PMID-3768165_E11", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 1474, 1485 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3768165_T15" } ] } ]

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[ { "id": "PMID-3917995__text", "type": "abstract", "text": [ "Aberrant regulation of methylesterase activity in cheD chemotaxis mutants of Escherichia coli. \nThe adaptation process in several cheD chemotaxis mutants, which carry defects in tsr, the serine transducer gene, was examined. cheD mutants are smooth swimming and generally nonchemotactic; the defect is dominant to the wild-type tsr gene (J. S. Parkinson, J. Bacteriol. 142:953-961, 1980). All classes of methyl-accepting chemotaxis proteins synthesized in unstimulated cheD strains are overmethylated relative to the wild type. We found that the steady-state rate of demethylation in cheD mutants was low; this may explain their overmethylated phenotype. In addition, all cheD mutants showed diminished responsiveness of methylesterase activity to attractant and repellent stimuli transduced by either the Tsr or Tar protein, and they did not adapt. These results suggest that the dominant nature of the cheD mutations is manifested as a general defect in the regulation of demethylation. Some of these altered properties of methylesterase activity in cheD mutants were exhibited in wild-type cells that were treated with saturating concentrations of serine. The mutant Tsr protein thus seems to be locked into a signaling mode that suppresses tumbling and inhibits methylesterase activity in a global fashion. We found that the Tar and mutant Tsr proteins synthesized in cheD strains were methylated and deamidated at the correct sites and that the mutations were not located in the methylated peptides. Thus, the signaling properties of the transducers may be controlled at sites distinct from the methyl-accepting sites.\n" ], "offsets": [ [ 0, 1624 ] ] } ]

[ { "id": "PMID-3917995_T1", "type": "Protein", "text": [ "cheD" ], "offsets": [ [ 50, 54 ] ], "normalized": [] }, { "id": "PMID-3917995_T2", "type": "Protein", "text": [ "cheD" ], "offsets": [ [ 130, 134 ] ], "normalized": [] }, { "id": "PMID-3917995_T3", "type": "Protein", "text": [ "tsr" ], "offsets": [ [ 178, 181 ] ], "normalized": [] }, { "id": "PMID-3917995_T4", "type": "Protein", "text": [ "cheD" ], "offsets": [ [ 225, 229 ] ], "normalized": [] }, { "id": "PMID-3917995_T5", "type": "Protein", "text": [ "tsr" ], "offsets": [ [ 328, 331 ] ], "normalized": [] }, { "id": "PMID-3917995_T6", "type": "Protein", "text": [ "cheD" ], "offsets": [ [ 469, 473 ] ], "normalized": [] }, { "id": "PMID-3917995_T7", "type": "Protein", "text": [ "cheD" ], "offsets": [ [ 584, 588 ] ], "normalized": [] }, { "id": "PMID-3917995_T8", "type": "Protein", "text": [ "cheD" ], "offsets": [ [ 672, 676 ] ], "normalized": [] }, { "id": "PMID-3917995_T9", "type": "Protein", "text": [ "Tsr" ], "offsets": [ [ 806, 809 ] ], "normalized": [] }, { "id": "PMID-3917995_T10", "type": "Protein", "text": [ "Tar" ], "offsets": [ [ 813, 816 ] ], "normalized": [] }, { "id": "PMID-3917995_T11", "type": "Protein", "text": [ "cheD" ], "offsets": [ [ 904, 908 ] ], "normalized": [] }, { "id": "PMID-3917995_T12", "type": "Protein", "text": [ "cheD" ], "offsets": [ [ 1052, 1056 ] ], "normalized": [] }, { "id": "PMID-3917995_T13", "type": "Protein", "text": [ "Tsr" ], "offsets": [ [ 1170, 1173 ] ], "normalized": [] }, { "id": "PMID-3917995_T14", "type": "Protein", "text": [ "Tar" ], "offsets": [ [ 1329, 1332 ] ], "normalized": [] }, { "id": "PMID-3917995_T15", "type": "Protein", "text": [ "Tsr" ], "offsets": [ [ 1344, 1347 ] ], "normalized": [] }, { "id": "PMID-3917995_T16", "type": "Protein", "text": [ "cheD" ], "offsets": [ [ 1372, 1376 ] ], "normalized": [] } ]

[ { "id": "PMID-3917995_E1", "type": "Methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 1390, 1400 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3917995_T14" } ] }, { "id": "PMID-3917995_E2", "type": "Methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 1390, 1400 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-3917995_T15" } ] } ]

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[ { "id": "PMID-6173216__text", "type": "abstract", "text": [ "Cold-sensitive ribosome assembly in an Escherichia coli mutant lacking a single methyl group in ribosomal protein L3. \nRibosomal protein methylation has been well documented but its function remains unclear. We have examined this phenomenon using an Escherichia coli mutant (prmB2), which fails to methylate glutamine residue number 150 of ribosomal protein L3. This mutant exhibits a cold-sensitive phenotype: its growth rate at 22 degrees C is abnormally low in complete medium. In addition, strains with this mutation accumulate abnormal and unstable ribosomal particles; 50-S and 30-S subunits are formed, but at a lower rate. Once assembled, ribosomes with unmethylated L3 are fully active by several criteria. (a) Protein synthesis in vitro with purified 70-S prmB2 ribosomes is as active as wild-type using either a natural (R17) or an artificial [poly(U)] messenger. (b) The induction of beta-galactosidase in vivo exhibits normal kinetics and the enzyme has a normal rate of thermal denaturation. (c) These ribosomes are standard when exposed in vitro to a low magnesium concentration or increasing molarities of LiCl. Efficient methylation of L3 in vitro requires either unfolded ribosomes or a mixture of ribosomal protein and RNA. We suggest that the L3-specific methyltransferase may qualify as one of the postulated 'assembly factors' of the E. coli ribosome.\n" ], "offsets": [ [ 0, 1374 ] ] } ]

[ { "id": "PMID-6173216_T1", "type": "Protein", "text": [ "L3" ], "offsets": [ [ 114, 116 ] ], "normalized": [] }, { "id": "PMID-6173216_T2", "type": "Protein", "text": [ "L3" ], "offsets": [ [ 358, 360 ] ], "normalized": [] }, { "id": "PMID-6173216_T3", "type": "Protein", "text": [ "L3" ], "offsets": [ [ 675, 677 ] ], "normalized": [] }, { "id": "PMID-6173216_T4", "type": "Protein", "text": [ "beta-galactosidase" ], "offsets": [ [ 896, 914 ] ], "normalized": [] }, { "id": "PMID-6173216_T5", "type": "Protein", "text": [ "L3" ], "offsets": [ [ 1153, 1155 ] ], "normalized": [] }, { "id": "PMID-6173216_T6", "type": "Protein", "text": [ "L3" ], "offsets": [ [ 1263, 1265 ] ], "normalized": [] }, { "id": "PMID-6173216_T8", "type": "Entity", "text": [ "glutamine residue number 150" ], "offsets": [ [ 308, 336 ] ], "normalized": [] } ]

[ { "id": "PMID-6173216_E1", "type": "Methylation", "trigger": { "text": [ "methylate" ], "offsets": [ [ 298, 307 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-6173216_T2" }, { "role": "Site", "ref_id": "PMID-6173216_T8" } ] }, { "id": "PMID-6173216_E2", "type": "Methylation", "trigger": { "text": [ "unmethylated" ], "offsets": [ [ 662, 674 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-6173216_T3" } ] }, { "id": "PMID-6173216_E3", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1138, 1149 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-6173216_T5" } ] } ]

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[ { "id": "PMID-6274318__text", "type": "abstract", "text": [ "Regulation of collagen post-translational modification in transformed human and chick-embryo cells. \nChanges in the regulation of collagen post-translational modification in transformed cells were studied in three established human sarcoma cell lines and in chick-embryo fibroblasts freshly transformed by Rous sarcoma virus. The collagens synthesized by all but one of these and by all the control human and chick-embryo cell lines were almost exclusively of types I and/or III. The relative rate of collagen synthesis and the amounts of prolyl hydroxylase activity and immunoreactive protein were markedly low in all the transformed human cell lines. The other enzymes studied, lysyl hydroxylase, hydroxylysyl galactosyltransferase and galactosylhydroxylysyl glucosyltransferase, never showed as large a decrease in activity as did prolyl hydroxylase, suggesting a more efficient regulation of the last enzyme than of the three others. The chick-embryo fibroblasts freshly transformed by Rous sarcoma virus differed from the human sarcoma cells in that prolyl hydroxylase activity was distinctly increased, whereas the decreases in immunoreactive prolyl hydroxylase protein and the three other enzyme activities were very similar to those in the simian-virus-40-transformed human fibroblasts. It seems possible that this increased prolyl hydroxylase activity is only a temporary phenomenon occurring shortly after the transformation, and may be followed by a decrease in activity later. The newly synthesized collagens of all the transformed cells that produced almost exclusively collagen types I and/or III had high extents of lysyl hydroxylation, and there was also an increase in the ratio of glycosylated to non-glycosylated hydroxylysine. The data suggest that one critical factor affecting modification is the rate of collagen synthesis, which affects the ratio of enzyme to substrate in the cell.\n" ], "offsets": [ [ 0, 1907 ] ] } ]

[ { "id": "PMID-6274318_T1", "type": "Protein", "text": [ "III" ], "offsets": [ [ 475, 478 ] ], "normalized": [] }, { "id": "PMID-6274318_T2", "type": "Protein", "text": [ "III" ], "offsets": [ [ 1607, 1610 ] ], "normalized": [] }, { "id": "PMID-6274318_T3", "type": "Entity", "text": [ "lysyl" ], "offsets": [ [ 1631, 1636 ] ], "normalized": [] }, { "id": "PMID-6274318_T7", "type": "Entity", "text": [ "hydroxylysine" ], "offsets": [ [ 1732, 1745 ] ], "normalized": [] } ]

[ { "id": "PMID-6274318_E1", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1637, 1650 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-6274318_T2" }, { "role": "Site", "ref_id": "PMID-6274318_T3" } ] }, { "id": "PMID-6274318_E2", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 1699, 1711 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-6274318_T2" }, { "role": "Site", "ref_id": "PMID-6274318_T7" } ] }, { "id": "PMID-6274318_E3", "type": "Glycosylation", "trigger": { "text": [ "non-glycosylated" ], "offsets": [ [ 1715, 1731 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-6274318_T2" }, { "role": "Site", "ref_id": "PMID-6274318_T7" } ] } ]

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[ { "id": "PMID-6440121__text", "type": "abstract", "text": [ "Partial methylation of two adjacent adenosines in ribosomes from Euglena gracilis chloroplasts suggests evolutionary loss of an intermediate stage in the methyl-transfer reaction. \nBacterial, cytoplasmic and organellar ribosomes from a wide phylogenetic spectrum of organisms have a characteristic m6(2)Am6(2)A structure near the 3' end of the RNA of the small ribosomal subunit (SSU). We have studied one of the few exceptions to this extremely conserved post-transcriptionally modified sequence, i.e. dimethylation of only one of the two A's in chloroplasts from Euglena gracilis. It was established that only the A closest to the 5' end is dimethylated, the other one being unmodified. The methylation reaction was studied in vitro using ribosomes from a kasugamycin resistant mutant (ksgA) of Escherichia coli and purified methyl-transferase. Using limited amounts of the methyl donor S-adenosylmethionine (SAM) a partial level of methylation (50% of control) was attained. It is shown that in this case the 3' proximal A is dimethylated while the other is not. This suggests that dimethylation takes place in two successive stages. Apparently in E. gracilis chloroplasts the first stage of methylation does not occur.\n" ], "offsets": [ [ 0, 1223 ] ] } ]

[ { "id": "PMID-6440121_T1", "type": "Protein", "text": [ "ksgA" ], "offsets": [ [ 788, 792 ] ], "normalized": [] } ]

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[ { "id": "PMID-6783428__text", "type": "abstract", "text": [ "Disorder of collagen metabolism in a patient with osteogenesis imperfecta (lethal type): increased degree of hydroxylation of lysine in collagen types I and III. \nTypes I, II and III collagen were isolated from calvarium, skin and cartilage from a patient with recessive lethal osteogenesis imperfecta. the distribution of the various collagen types was normal in all three tissues. The alpha-chains were purified by molecular sieve and ion-exchange chromatography and were found to differ from the corresponding alpha-chains of age-matched controls only in that the alpha 1(I), alpha 2 and alpha 1(III) chains contained higher amounts of hydroxylysine with proportionally less lysine. alpha 1(II) was normal. The excess hydroxylysine residues were all glycosylated in the case of alpha 1(I) chains, but only partly so for the alpha 2 chains. Similar observations were made with collagen from fetuses at various stages of development. In these fetuses, however, the increase in the degree of hydroxylation of lysine in alpha 1(I), alpha 2 and alpha 1(III) varied with age, being highest in the youngest fetus. Seen in the context of embryonic development, the collagen of the patient would correspond to that of a fetus younger than 18 weeks, and one could speculate that the defect seen in this patient is the result of a disturbed process of maturation of connective tissue.\n" ], "offsets": [ [ 0, 1377 ] ] } ]

[ { "id": "PMID-6783428_T1", "type": "Protein", "text": [ "III" ], "offsets": [ [ 157, 160 ] ], "normalized": [] }, { "id": "PMID-6783428_T2", "type": "Protein", "text": [ "II" ], "offsets": [ [ 172, 174 ] ], "normalized": [] }, { "id": "PMID-6783428_T3", "type": "Protein", "text": [ "III collagen" ], "offsets": [ [ 179, 191 ] ], "normalized": [] }, { "id": "PMID-6783428_T4", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 567, 577 ] ], "normalized": [] }, { "id": "PMID-6783428_T5", "type": "Protein", "text": [ "alpha 1(III)" ], "offsets": [ [ 591, 603 ] ], "normalized": [] }, { "id": "PMID-6783428_T6", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 781, 791 ] ], "normalized": [] }, { "id": "PMID-6783428_T7", "type": "Protein", "text": [ "alpha 1(I)" ], "offsets": [ [ 1019, 1029 ] ], "normalized": [] }, { "id": "PMID-6783428_T8", "type": "Protein", "text": [ "alpha 1(III)" ], "offsets": [ [ 1043, 1055 ] ], "normalized": [] }, { "id": "PMID-6783428_T10", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 126, 132 ] ], "normalized": [] }, { "id": "PMID-6783428_T11", "type": "Entity", "text": [ "hydroxylysine residues" ], "offsets": [ [ 721, 743 ] ], "normalized": [] }, { "id": "PMID-6783428_T14", "type": "Entity", "text": [ "lysine" ], "offsets": [ [ 1009, 1015 ] ], "normalized": [] } ]

[ { "id": "PMID-6783428_E1", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 109, 122 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-6783428_T1" }, { "role": "Site", "ref_id": "PMID-6783428_T10" } ] }, { "id": "PMID-6783428_E2", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 753, 765 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-6783428_T6" }, { "role": "Site", "ref_id": "PMID-6783428_T11" } ] }, { "id": "PMID-6783428_E3", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 992, 1005 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-6783428_T7" }, { "role": "Site", "ref_id": "PMID-6783428_T14" } ] }, { "id": "PMID-6783428_E4", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 992, 1005 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-6783428_T8" }, { "role": "Site", "ref_id": "PMID-6783428_T14" } ] } ]

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[ { "id": "PMID-7094019__text", "type": "abstract", "text": [ "Temperature-sensitive changes in the structure of globin chromatin in lines of red cell precursors transformed by ts-AEV. \nChicken bone marrow cells infected in vitro with a temperature-sensitive avian erythroblastosis virus fall to produce hemoglobin at 36 degrees C. When the product or products of the transforming gene (erb) are inactivated by a temperature shift to 42 degrees C in culture, several different cloned lines of cells infected with the temperature-sensitive avian erythroblastosis virus begin to make hemoglobin. This shift in phenotype correlates with an increase in hemoglobin mRNA specific to both adult and embryonic alpha and beta globin. The switch is accompanied by the acquisition of DNAase I-hypersensitive sites in one cell line (clone 2); however, a hypothetically more mature line (clone 3) has already acquired globin DNAase-hypersensitive sites but does not express hemoglobin until the temperature shift. Several (but not all) specific restriction sites associated with both the alpha and beta domains become unmethylated after the switch from 36 degrees C to 42 degrees C. The magnitude of these methylation switches is small compared with changes that occur in these genes during normal avian erythropoiesis. The results suggest that changes in chromosomal structure precede transcription and are not a consequence of transcription. Since (presumptive) precursor cloned lines can be established with some, but not all, of the structural properties of active globin chromatin, it is likely that many of these properties can be independently established and are not obligatorily related.\n" ], "offsets": [ [ 0, 1621 ] ] } ]

[ { "id": "PMID-7094019_T1", "type": "Protein", "text": [ "erb" ], "offsets": [ [ 324, 327 ] ], "normalized": [] }, { "id": "PMID-7094019_T2", "type": "Protein", "text": [ "alpha" ], "offsets": [ [ 639, 644 ] ], "normalized": [] }, { "id": "PMID-7094019_T3", "type": "Protein", "text": [ "beta globin" ], "offsets": [ [ 649, 660 ] ], "normalized": [] } ]

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[ { "id": "PMID-7511176__text", "type": "abstract", "text": [ "Studies of the conformation-dependent neutralizing epitopes of simian immunodeficiency virus envelope protein. \nIt has been shown previously that the major neutralizing epitopes in simian immunodeficiency virus (SIV) are discontinuous and conformation dependent and that the V3 loop, in contrast to that of human immunodeficiency virus (HIV) type 1, does not by itself elicit neutralizing antibodies (K. Javaherian et al., Proc. Natl. Acad. Sci. USA 89:1418-1422, 1992). We now present data showing that on the basis of fractionation of infected macaque sera, protease digestion of the envelope, and binding properties of two neutralizing monoclonal antibodies to SIV and SIV-HIV chimeric envelope proteins, changes in V3 can disrupt the conformation-dependent neutralization region. The chimeric protein did not produce significant neutralizing antibodies against either SIV or HIV. We also report that neutralizing antibodies elicited by recombinant SIV envelope proteins of mac251 and B670 isolates cross-neutralize. Finally, we show that deglycosylation of the SIV envelope results in a molecule which binds neither soluble CD4 nor the neutralizing monoclonal antibodies being investigated here and does not elicit sera with a significant neutralizing titer.\n" ], "offsets": [ [ 0, 1263 ] ] } ]

[ { "id": "PMID-7511176_T1", "type": "Protein", "text": [ "envelope protein" ], "offsets": [ [ 93, 109 ] ], "normalized": [] }, { "id": "PMID-7511176_T2", "type": "Protein", "text": [ "envelope proteins" ], "offsets": [ [ 689, 706 ] ], "normalized": [] }, { "id": "PMID-7511176_T3", "type": "Protein", "text": [ "envelope proteins" ], "offsets": [ [ 956, 973 ] ], "normalized": [] }, { "id": "PMID-7511176_T4", "type": "Protein", "text": [ "CD4" ], "offsets": [ [ 1128, 1131 ] ], "normalized": [] } ]

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[ { "id": "PMID-7626109__text", "type": "abstract", "text": [ "Beta 1-6 branching of N-linked carbohydrate is associated with K-ras mutation in human colon carcinoma cell lines. \nHere the K-ras genotypes of nine colon carcinoma cell lines are compared to the protein glycosylation patterns found in these cells. By a variety of methodologies utilizing lectins to probe carbohydrate structure, we find evidence that five out of six cell lines having K-ras mutations have elevated amounts of beta 1-6 branching at the trimannosyl core of N-linked carbohydrate. None of the three K-ras wild type cell lines assayed have evidence of elevated beta 1-6 branching. In five out of five cell lines examined, the amount of beta 1-6 branching correlates with the extent of cellular ras-GTP elevation and supports the hypothesis that expression of beta 1-6 branching in colon carcinoma cell lines is quantitatively linked to K-ras activation. These results are discussed in the context of the ras-signalling pathway.\n" ], "offsets": [ [ 0, 942 ] ] } ]

[ { "id": "PMID-7626109_T1", "type": "Protein", "text": [ "K-ras" ], "offsets": [ [ 63, 68 ] ], "normalized": [] }, { "id": "PMID-7626109_T2", "type": "Protein", "text": [ "K-ras" ], "offsets": [ [ 125, 130 ] ], "normalized": [] }, { "id": "PMID-7626109_T3", "type": "Protein", "text": [ "K-ras" ], "offsets": [ [ 386, 391 ] ], "normalized": [] }, { "id": "PMID-7626109_T4", "type": "Protein", "text": [ "K-ras" ], "offsets": [ [ 514, 519 ] ], "normalized": [] }, { "id": "PMID-7626109_T5", "type": "Protein", "text": [ "K-ras" ], "offsets": [ [ 850, 855 ] ], "normalized": [] } ]

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[ { "id": "PMID-7691738__text", "type": "abstract", "text": [ "Abnormal glycosylation of alpha 2-macroglobulin, a non-acute-phase protein in patients with autoimmune diseases. \nPrevious studies from this and other laboratories have shown that abnormal glycosylation of several acute-phase proteins can be detected in various pathological conditions including autoimmune diseases. In the present study, we have investigated if abnormal glycosylation is limited to acute-phase proteins. We used the concanavalin A (Con A) blots in conjunction with the peptide mapping techniques to analyze serum samples and cerebrospinal fluids (CSF) obtained from patients with autoimmune diseases: systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), mixed connective tissue disease (MCTD), scleroderma (SCL), Sjogren's syndrome (SS), and polymyositis (PM); diseases of probable autoimmune origin: hepatopathies (HP); diseases of suspected autoimmune origin: schizophrenia and Alzheimer's disease (AZ); and conditions not related to autoimmunity: pregnancy (PG) and elevation of the carcinoembryonic antigen (CEA), in comparison to normal donors (NHS). We have micropurified two human proteins; alpha 2-macroglobulin, a non-acute-phase protein and beta-chain of haptoglobin, a known acute-phase protein, from serum samples of individual patients with SLE, RA, MCTD, SCL and SS, and from PG and NHS for analysis. The identity of the purified proteins was confirmed by immunoblots using either monospecific polyclonal or monoclonal antibodies, and by direct N-terminal amino acid sequencing. Peptide maps for each of these proteins were generated using Staphylococcus aureus protease V8, a Glu-C endopeptidase. When the peptide fragments of alpha 2-macroglobulin were resolved by SDS-PAGE and visualized using silver staining, no differences were noted between patient samples and controls. However, when they were examined by lectin blots using Con A, the Con A-reactive fragments increased specifically and significantly in samples derived from patients of SLE, SCL, MCTD, and RA. Similarly when the peptide fragments of the beta-chain of haptoglobin were visualized by silver staining, no differences were noted; however, the Con A reactivity of specific fragments increased in SLE, RA, SCL, and SS patients. Analysis of these results indicated that there has been a selective increase in Con A-reactive fragments in both acute-phase and non-acute-phase proteins in autoimmune conditions. Thus, the study of changes in glycosylation patterns in selected serum proteins may be a valuable diagnostic approach to define the pathophysiology of inflammatory and autoimmune disorders.\n" ], "offsets": [ [ 0, 2611 ] ] } ]

[ { "id": "PMID-7691738_T1", "type": "Protein", "text": [ "alpha 2-macroglobulin" ], "offsets": [ [ 26, 47 ] ], "normalized": [] }, { "id": "PMID-7691738_T2", "type": "Protein", "text": [ "concanavalin A" ], "offsets": [ [ 434, 448 ] ], "normalized": [] }, { "id": "PMID-7691738_T3", "type": "Protein", "text": [ "Con A" ], "offsets": [ [ 450, 455 ] ], "normalized": [] }, { "id": "PMID-7691738_T4", "type": "Protein", "text": [ "carcinoembryonic antigen" ], "offsets": [ [ 1014, 1038 ] ], "normalized": [] }, { "id": "PMID-7691738_T5", "type": "Protein", "text": [ "CEA" ], "offsets": [ [ 1040, 1043 ] ], "normalized": [] }, { "id": "PMID-7691738_T6", "type": "Protein", "text": [ "alpha 2-macroglobulin" ], "offsets": [ [ 1126, 1147 ] ], "normalized": [] }, { "id": "PMID-7691738_T7", "type": "Protein", "text": [ "haptoglobin" ], "offsets": [ [ 1193, 1204 ] ], "normalized": [] }, { "id": "PMID-7691738_T8", "type": "Protein", "text": [ "protease V8" ], "offsets": [ [ 1604, 1615 ] ], "normalized": [] }, { "id": "PMID-7691738_T9", "type": "Protein", "text": [ "alpha 2-macroglobulin" ], "offsets": [ [ 1670, 1691 ] ], "normalized": [] }, { "id": "PMID-7691738_T10", "type": "Protein", "text": [ "Con A" ], "offsets": [ [ 1875, 1880 ] ], "normalized": [] }, { "id": "PMID-7691738_T11", "type": "Protein", "text": [ "Con A" ], "offsets": [ [ 1886, 1891 ] ], "normalized": [] }, { "id": "PMID-7691738_T12", "type": "Protein", "text": [ "haptoglobin" ], "offsets": [ [ 2070, 2081 ] ], "normalized": [] }, { "id": "PMID-7691738_T13", "type": "Protein", "text": [ "Con A" ], "offsets": [ [ 2158, 2163 ] ], "normalized": [] }, { "id": "PMID-7691738_T14", "type": "Protein", "text": [ "Con A" ], "offsets": [ [ 2321, 2326 ] ], "normalized": [] } ]

[ { "id": "PMID-7691738_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 9, 22 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7691738_T1" } ] } ]

[ { "id": "PMID-7691738_1", "entity_ids": [ "PMID-7691738_T2", "PMID-7691738_T3" ] }, { "id": "PMID-7691738_2", "entity_ids": [ "PMID-7691738_T4", "PMID-7691738_T5" ] } ]

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[ { "id": "PMID-7750474__text", "type": "abstract", "text": [ "Evidence that Rap1 carboxylmethylation is involved in regulated insulin secretion. \nProtein carboxylmethylation is a reversible posttranslational modification that regulates protein function. We examined the carboxylmethylation of small GTP-binding proteins in a pancreatic beta-cell line (beta TC cells). In vitro assays showed that carboxylmethylation of a membrane 23-kDa protein was induced by guanine nucleotides, best demonstrated by the nonhydrolyzable GTP analog, guanosine 5'-(3-O-thio)triphosphate (GTP gamma S). GTP gamma S also induced translocation of this 23-kilodalton (kDa) protein from cytosol to particulate fractions. Immunoblotting with antiserum sc-65 raised against Rap1 identified the carboxyl-methylated 23-kDa protein as Rap1. 1) The 23-kDa carboxyl-methylated protein separated by two-dimensional electrophoresis overlapped with the 23-kDa protein detected by immunoblotting. 2) GTP gamma S, in the presence of cytosol, increased the amount of detectable membrane-associated Rap1. Studies in intact beta TC cells demonstrated the carboxylmethylation of the 23-kDa protein in response to glucose and depolarizing concentrations of potassium, an effect that was abolished by the calcium channel inhibitor, D600. Similarly, N-acetyl-S-trans,trans-farnesyl-L-cysteine, an inhibitor of in vivo carboxylmethylation at COOH-terminal S-farnesylcysteine by methyltransferase, inhibited carboxylmethylation of the 23-kDa protein in intact cells and reduced insulin secretion in response to glucose and potassium. These data establish a correlation between insulin secretion and carboxylmethylation of a 23-kDa protein that comigrates with Rap1.\n" ], "offsets": [ [ 0, 1661 ] ] } ]

[ { "id": "PMID-7750474_T1", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 64, 71 ] ], "normalized": [] }, { "id": "PMID-7750474_T2", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 1473, 1480 ] ], "normalized": [] }, { "id": "PMID-7750474_T3", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 1572, 1579 ] ], "normalized": [] } ]

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[ { "id": "PMID-7831351__text", "type": "abstract", "text": [ "The effects of O- and N-linked glycosylation on the secretion and bile salt-stimulation of pancreatic carboxyl ester lipase activity. \nPancreatic carboxyl ester lipase is a glycoprotein that requires millimolar concentrations of trihydroxy bile salts, such as cholate, for maximal catalytic activity against cholesteryl esters and triglycerides. Binding of cholate, with subsequent activation, has been proposed to occur in the carboxy-terminal region of carboxyl ester lipase, which contains multiple sites for O-linked glycosylation (1). To investigate the role of O- and N-linked glycosylation in the secretion of carboxyl ester lipase by cells and its activation by cholate, rat carboxyl ester lipase cDNA was transfected into the mutant chinese hamster ovary cell line, IdID, and the ability of the cells to modify the expressed carboxyl ester lipase by N- and O-linked glycosylation was modulated by using various incubation conditions and metabolic inhibitors. The results showed that, similar to other lipases, maximal secretion of carboxyl ester lipase activity required N-linked glycosylation. In contrast, O-linked glycosylation did not affect the secretion of carboxyl ester lipase activity. In addition, the cholate stimulation of hydrolysis was also independent of O-linked glycosylation.\n" ], "offsets": [ [ 0, 1303 ] ] } ]

[ { "id": "PMID-7831351_T1", "type": "Protein", "text": [ "carboxyl ester lipase" ], "offsets": [ [ 102, 123 ] ], "normalized": [] }, { "id": "PMID-7831351_T2", "type": "Protein", "text": [ "carboxyl ester lipase" ], "offsets": [ [ 146, 167 ] ], "normalized": [] }, { "id": "PMID-7831351_T3", "type": "Protein", "text": [ "carboxyl ester lipase" ], "offsets": [ [ 455, 476 ] ], "normalized": [] }, { "id": "PMID-7831351_T4", "type": "Protein", "text": [ "carboxyl ester lipase" ], "offsets": [ [ 617, 638 ] ], "normalized": [] }, { "id": "PMID-7831351_T5", "type": "Protein", "text": [ "carboxyl ester lipase" ], "offsets": [ [ 683, 704 ] ], "normalized": [] }, { "id": "PMID-7831351_T6", "type": "Protein", "text": [ "carboxyl ester lipase" ], "offsets": [ [ 834, 855 ] ], "normalized": [] }, { "id": "PMID-7831351_T7", "type": "Protein", "text": [ "carboxyl ester lipase" ], "offsets": [ [ 1040, 1061 ] ], "normalized": [] }, { "id": "PMID-7831351_T8", "type": "Protein", "text": [ "carboxyl ester lipase" ], "offsets": [ [ 1172, 1193 ] ], "normalized": [] }, { "id": "PMID-7831351_T11", "type": "Entity", "text": [ "carboxy-terminal region" ], "offsets": [ [ 428, 451 ] ], "normalized": [] } ]

[ { "id": "PMID-7831351_E1", "type": "Glycosylation", "trigger": { "text": [ "O-" ], "offsets": [ [ 15, 17 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7831351_T1" } ] }, { "id": "PMID-7831351_E2", "type": "Glycosylation", "trigger": { "text": [ "N-linked glycosylation" ], "offsets": [ [ 22, 44 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7831351_T1" } ] }, { "id": "PMID-7831351_E3", "type": "Glycosylation", "trigger": { "text": [ "O-linked glycosylation" ], "offsets": [ [ 512, 534 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7831351_T3" }, { "role": "Site", "ref_id": "PMID-7831351_T11" } ] }, { "id": "PMID-7831351_E4", "type": "Glycosylation", "trigger": { "text": [ "O-" ], "offsets": [ [ 567, 569 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7831351_T4" } ] }, { "id": "PMID-7831351_E5", "type": "Glycosylation", "trigger": { "text": [ "N-linked glycosylation" ], "offsets": [ [ 574, 596 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7831351_T4" } ] }, { "id": "PMID-7831351_E6", "type": "Glycosylation", "trigger": { "text": [ "N-" ], "offsets": [ [ 859, 861 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7831351_T6" } ] }, { "id": "PMID-7831351_E7", "type": "Glycosylation", "trigger": { "text": [ "O-linked glycosylation" ], "offsets": [ [ 866, 888 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7831351_T6" } ] }, { "id": "PMID-7831351_E8", "type": "Glycosylation", "trigger": { "text": [ "N-linked glycosylation" ], "offsets": [ [ 1080, 1102 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7831351_T7" } ] }, { "id": "PMID-7831351_E9", "type": "Glycosylation", "trigger": { "text": [ "O-linked glycosylation" ], "offsets": [ [ 1117, 1139 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7831351_T8" } ] }, { "id": "PMID-7831351_E10", "type": "Glycosylation", "trigger": { "text": [ "O-linked glycosylation" ], "offsets": [ [ 1279, 1301 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7831351_T8" } ] } ]

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[ { "id": "PMID-7835977__text", "type": "abstract", "text": [ "Altered glycosylation and selected mutation in recombinant human complement component C9: effects on haemolytic activity. \nRecombinant wild-type and mutated forms of human complement component C9 have been synthesized in baculovirus-infected insect cells. Wild-type recombinant C9 was indistinguishable from native C9, as judged by haemolytic activity, trypsin and alpha-thrombin digestion, reaction with antibodies to C9, enzymatic deglycosylation to the same core size and polymerization in the presence of Zn2+. Replacement of the native signal peptide with the honey-bee melittin signal peptide, and replacement of Spodoptera frugiperda (Sf9) cells with Trichoplusia ni cells produced yields of 5 micrograms C9/ml supernatant. Three C9 mutants were generated; one mutant, with four acidic residues changed to alanines in a putative calcium-binding site, had the same biological activity as recombinant C9. Another mutant, lacking 23 N-terminal amino acids, previously showing increased polymerization when produced in vitro, polymerized on secretion, rendering it inactive. It was not possible to demonstrate haemolytic activity of the third mutant, cysteines 33 and 36 mutated to alanine, as it was secreted a hundredfold less than the wild-type protein.\n" ], "offsets": [ [ 0, 1260 ] ] } ]

[ { "id": "PMID-7835977_T1", "type": "Protein", "text": [ "complement component C9" ], "offsets": [ [ 65, 88 ] ], "normalized": [] }, { "id": "PMID-7835977_T2", "type": "Protein", "text": [ "complement component C9" ], "offsets": [ [ 172, 195 ] ], "normalized": [] }, { "id": "PMID-7835977_T3", "type": "Protein", "text": [ "C9" ], "offsets": [ [ 278, 280 ] ], "normalized": [] }, { "id": "PMID-7835977_T4", "type": "Protein", "text": [ "C9" ], "offsets": [ [ 315, 317 ] ], "normalized": [] }, { "id": "PMID-7835977_T5", "type": "Protein", "text": [ "alpha-thrombin" ], "offsets": [ [ 365, 379 ] ], "normalized": [] }, { "id": "PMID-7835977_T6", "type": "Protein", "text": [ "C9" ], "offsets": [ [ 419, 421 ] ], "normalized": [] }, { "id": "PMID-7835977_T7", "type": "Protein", "text": [ "melittin" ], "offsets": [ [ 575, 583 ] ], "normalized": [] }, { "id": "PMID-7835977_T8", "type": "Protein", "text": [ "C9" ], "offsets": [ [ 712, 714 ] ], "normalized": [] }, { "id": "PMID-7835977_T9", "type": "Protein", "text": [ "C9" ], "offsets": [ [ 737, 739 ] ], "normalized": [] }, { "id": "PMID-7835977_T10", "type": "Protein", "text": [ "C9" ], "offsets": [ [ 906, 908 ] ], "normalized": [] } ]

[ { "id": "PMID-7835977_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 8, 21 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7835977_T1" } ] }, { "id": "PMID-7835977_E2", "type": "Deglycosylation", "trigger": { "text": [ "deglycosylation" ], "offsets": [ [ 433, 448 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7835977_T3" } ] } ]

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[ { "id": "PMID-7848530__text", "type": "abstract", "text": [ "Dual activity of human pituitary thyrotrophin isoforms on thyroid cell growth. \nAlkaline (pI 8.6-7.5) and neutral (pI 7.0-6.0) isoforms of human TSH have been isolated from a highly purified intrapituitary preparation by isoelectric focusing and compared for their respective actions on thyroid cell proliferation. Both TSH isoforms displayed the same ability to bind to porcine thyroid membranes as the original hormone preparation, indicating a similar recognition at the receptor sites. Alkaline forms showed a higher potency in inducing either cyclic AMP (cAMP) production or [3H]thymidine incorporation in FRTL-5 cells (half-maximal effective doses (ED50 values) = 0.25 and 0.29 nM respectively) compared with their neutral counterparts (ED50 values = 0.66 and 0.70 nM respectively). Increasing the concentration of alkaline forms in the presence of a half-maximal concentration of neutral TSH resulted in a profound inhibition of cell growth without a significant change in cAMP. Conversely, increasing the amount of neutral forms in the presence of a half-maximal dose of alkaline TSH resulted in an additive response for cAMP production but not in cell proliferation. To assess whether glycosylation might be responsible for the variation in hormone action, both alkaline and neutral TSH isoforms were tested for recognition of their carbohydrate chains by concanavalin A (Con A) and ricin. No major difference was found in binding to Con A, indicating that the contribution of carbohydrates to changes in hormone pI was not related to core branching. Very few galactose residues were accessible in either hormone fraction since little binding to ricin was observed. Isoelectric focusing of TSH forms before and after neuraminidase treatment revealed that neutral forms had a higher sialic acid content than alkaline TSH. In conclusion, the current findings show that TSH isoforms differentially affect cAMP production and cell growth. TSH fractions with a high sialic acid content and a low mitogenic activity behave as antagonists to the more active forms for cell proliferation. It is suggested that physiological control of TSH action at the thyroid gland may reside in the respective amounts of various TSH forms which, once bound to their receptor, can induce variable activation of post-receptor events while controlling cell proliferation.\n" ], "offsets": [ [ 0, 2356 ] ] } ]

[ { "id": "PMID-7848530_T1", "type": "Protein", "text": [ "concanavalin A" ], "offsets": [ [ 1365, 1379 ] ], "normalized": [] }, { "id": "PMID-7848530_T2", "type": "Protein", "text": [ "Con A" ], "offsets": [ [ 1381, 1386 ] ], "normalized": [] }, { "id": "PMID-7848530_T3", "type": "Protein", "text": [ "Con A" ], "offsets": [ [ 1443, 1448 ] ], "normalized": [] } ]

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[ { "id": "PMID-7848530_1", "entity_ids": [ "PMID-7848530_T1", "PMID-7848530_T2" ] } ]

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[ { "id": "PMID-7876251__text", "type": "abstract", "text": [ "Studies on the structure and function of glycosylated and nonglycosylated neu differentiation factors. Similarities and differences of the alpha and beta isoforms. \nComparative analyses of both glycosylated and nonglycosylated neu differentiation factor (NDF) isoforms revealed significant similarities and differences of their overall structures and functions. Biophysical analyses confirmed that all NDF isoforms are monomeric, but have an extended ellipsoidal shape in solution. All full-length NDFs are similar in secondary and tertiary structures and they contain no alpha-helix but are abundant in beta-strand structures. A small NDF fragment containing only the epidermal growth factor domain is also rich in beta-strand structures, but exhibits tertiary structure different from the long NDF forms. Monoclonal antibodies that selectively recognize epidermal growth factor domains of human NDF-alpha and -beta can specifically bind the respective NDF-alpha and -beta isoforms independent of NDF origins. Western blot analysis and quantitative binding assays further identify that an NDF preparation produced naturally from Rat1-EJ cells contains both alpha and beta isoforms in a 3 to 2 ratio. In receptor-binding competition experiments, human and rat NDF-beta isoforms have higher affinity than NDF-alpha isoforms. NDF-beta isoforms can dramatically enhance the stimulation of DNA synthesis for transfected NIH3T3 cells that overexpress HER-3 and HER-4 receptors, while NDF-alpha isoforms can only stimulate proliferation of HER-4-transfected cells with lower activity. Taken together, NDF-alpha and -beta isoforms share similar gross protein conformations but are biologically distinct.\n" ], "offsets": [ [ 0, 1698 ] ] } ]

[ { "id": "PMID-7876251_T1", "type": "Protein", "text": [ "neu differentiation factors" ], "offsets": [ [ 74, 101 ] ], "normalized": [] }, { "id": "PMID-7876251_T2", "type": "Protein", "text": [ "neu differentiation factor" ], "offsets": [ [ 228, 254 ] ], "normalized": [] }, { "id": "PMID-7876251_T3", "type": "Protein", "text": [ "NDF" ], "offsets": [ [ 256, 259 ] ], "normalized": [] }, { "id": "PMID-7876251_T4", "type": "Protein", "text": [ "NDF" ], "offsets": [ [ 403, 406 ] ], "normalized": [] }, { "id": "PMID-7876251_T5", "type": "Protein", "text": [ "NDFs" ], "offsets": [ [ 499, 503 ] ], "normalized": [] }, { "id": "PMID-7876251_T6", "type": "Protein", "text": [ "NDF" ], "offsets": [ [ 637, 640 ] ], "normalized": [] }, { "id": "PMID-7876251_T7", "type": "Protein", "text": [ "epidermal growth factor" ], "offsets": [ [ 670, 693 ] ], "normalized": [] }, { "id": "PMID-7876251_T8", "type": "Protein", "text": [ "NDF-alpha" ], "offsets": [ [ 898, 907 ] ], "normalized": [] }, { "id": "PMID-7876251_T9", "type": "Protein", "text": [ "-beta" ], "offsets": [ [ 912, 917 ] ], "normalized": [] }, { "id": "PMID-7876251_T10", "type": "Protein", "text": [ "NDF-alpha" ], "offsets": [ [ 955, 964 ] ], "normalized": [] }, { "id": "PMID-7876251_T11", "type": "Protein", "text": [ "-beta" ], "offsets": [ [ 969, 974 ] ], "normalized": [] }, { "id": "PMID-7876251_T12", "type": "Protein", "text": [ "NDF" ], "offsets": [ [ 999, 1002 ] ], "normalized": [] }, { "id": "PMID-7876251_T13", "type": "Protein", "text": [ "NDF" ], "offsets": [ [ 1091, 1094 ] ], "normalized": [] }, { "id": "PMID-7876251_T14", "type": "Protein", "text": [ "NDF-beta" ], "offsets": [ [ 1261, 1269 ] ], "normalized": [] }, { "id": "PMID-7876251_T15", "type": "Protein", "text": [ "NDF-alpha" ], "offsets": [ [ 1305, 1314 ] ], "normalized": [] }, { "id": "PMID-7876251_T16", "type": "Protein", "text": [ "NDF-beta" ], "offsets": [ [ 1325, 1333 ] ], "normalized": [] }, { "id": "PMID-7876251_T17", "type": "Protein", "text": [ "HER-3" ], "offsets": [ [ 1447, 1452 ] ], "normalized": [] }, { "id": "PMID-7876251_T18", "type": "Protein", "text": [ "HER-4" ], "offsets": [ [ 1457, 1462 ] ], "normalized": [] }, { "id": "PMID-7876251_T19", "type": "Protein", "text": [ "NDF-alpha" ], "offsets": [ [ 1480, 1489 ] ], "normalized": [] }, { "id": "PMID-7876251_T20", "type": "Protein", "text": [ "HER-4" ], "offsets": [ [ 1535, 1540 ] ], "normalized": [] }, { "id": "PMID-7876251_T21", "type": "Protein", "text": [ "NDF-alpha" ], "offsets": [ [ 1596, 1605 ] ], "normalized": [] }, { "id": "PMID-7876251_T22", "type": "Protein", "text": [ "-beta" ], "offsets": [ [ 1610, 1615 ] ], "normalized": [] } ]

[ { "id": "PMID-7876251_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 41, 53 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7876251_T1" } ] }, { "id": "PMID-7876251_E2", "type": "Glycosylation", "trigger": { "text": [ "nonglycosylated" ], "offsets": [ [ 58, 73 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7876251_T1" } ] }, { "id": "PMID-7876251_E3", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 195, 207 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7876251_T2" } ] }, { "id": "PMID-7876251_E4", "type": "Glycosylation", "trigger": { "text": [ "nonglycosylated" ], "offsets": [ [ 212, 227 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7876251_T2" } ] } ]

[ { "id": "PMID-7876251_1", "entity_ids": [ "PMID-7876251_T2", "PMID-7876251_T3" ] } ]

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[ { "id": "PMID-7892262__text", "type": "abstract", "text": [ "Activation-dependent carboxyl methylation of neutrophil G-protein gamma subunit. \nThe gamma subunits of heterotrimeric guanine nucleotide-binding regulatory (G) proteins (G gamma) are post-translationally processed at their C termini by prenylation, proteolysis, and carboxyl methylation. Whereas prenylation of G gamma is required for membrane association of G proteins, the role of carboxyl methylation is unknown. Here we show that human neutrophils express G gamma 2 but not G gamma 3 or G gamma 7 and that carboxyl methylation of G gamma 2 is associated with signal transduction. In a reconstituted cell-free system, neutrophil G gamma 2 was labeled by the methyl donor S-[methyl-3H]adenosyl-L-methionine. Carboxyl methylation was confirmed by alkaline hydrolysis and quantitation of volatile [3H]methanol. Neutrophil G gamma 2 methylation was stimulated by activation of G protein with guanosine 5'-[beta, gamma-thio]triphosphate. We estimate that after 1 hr of G-protein activation at least 6% of the total pool of G gamma 2 was carboxyl-methylated. The inflammatory agonist fMet-Leu-Phe stimulated guanosine 5'-[beta,gamma-thio]triphosphate-dependent carboxyl methylation. Methylation of G gamma 2 was inhibited by the carboxyl methyltransferase inhibitor N-acetyl-S-trans,trans-farnesylcysteine at concentrations that affected signal transduction in neutrophils. These results demonstrate that activation of neutrophil Gi is associated with alpha-carboxyl methyl esterification of G gamma 2 and suggest that carboxyl methylation of G gamma may play a role in signal transduction.\n" ], "offsets": [ [ 0, 1589 ] ] } ]

[ { "id": "PMID-7892262_T1", "type": "Protein", "text": [ "G gamma 2" ], "offsets": [ [ 461, 470 ] ], "normalized": [] }, { "id": "PMID-7892262_T2", "type": "Protein", "text": [ "G gamma 3" ], "offsets": [ [ 479, 488 ] ], "normalized": [] }, { "id": "PMID-7892262_T3", "type": "Protein", "text": [ "G gamma 7" ], "offsets": [ [ 492, 501 ] ], "normalized": [] }, { "id": "PMID-7892262_T4", "type": "Protein", "text": [ "G gamma 2" ], "offsets": [ [ 535, 544 ] ], "normalized": [] }, { "id": "PMID-7892262_T5", "type": "Protein", "text": [ "G gamma 2" ], "offsets": [ [ 633, 642 ] ], "normalized": [] }, { "id": "PMID-7892262_T6", "type": "Protein", "text": [ "G gamma 2" ], "offsets": [ [ 823, 832 ] ], "normalized": [] }, { "id": "PMID-7892262_T7", "type": "Protein", "text": [ "G gamma 2" ], "offsets": [ [ 1022, 1031 ] ], "normalized": [] }, { "id": "PMID-7892262_T8", "type": "Protein", "text": [ "G gamma 2" ], "offsets": [ [ 1196, 1205 ] ], "normalized": [] }, { "id": "PMID-7892262_T9", "type": "Protein", "text": [ "G gamma 2" ], "offsets": [ [ 1490, 1499 ] ], "normalized": [] } ]

[ { "id": "PMID-7892262_E1", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 520, 531 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7892262_T4" } ] }, { "id": "PMID-7892262_E2", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 720, 731 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7892262_T5" } ] }, { "id": "PMID-7892262_E3", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 833, 844 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7892262_T6" } ] }, { "id": "PMID-7892262_E4", "type": "Methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 1045, 1055 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7892262_T7" } ] }, { "id": "PMID-7892262_E5", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1168, 1179 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7892262_T7" } ] }, { "id": "PMID-7892262_E6", "type": "Methylation", "trigger": { "text": [ "Methylation" ], "offsets": [ [ 1181, 1192 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7892262_T8" } ] }, { "id": "PMID-7892262_E7", "type": "Methylation", "trigger": { "text": [ "methyl esterification" ], "offsets": [ [ 1465, 1486 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-7892262_T9" } ] } ]

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[ { "id": "PMID-7896835__text", "type": "abstract", "text": [ "Mouse mammary tumors express elevated levels of RNA encoding the murine homology of SKY, a putative receptor tyrosine kinase. \nTo gain insight into the signal transduction pathways utilized by the Wnt-1-responsive mammary epithelial cell line C57MG, we screened for non-src family member tyrosine kinases expressed in these cells using a polymerase chain reaction-based technique. We identified five cDNA clones encoding receptor tyrosine kinases for which the ligand is known (fibroblast growth factor receptor, platelet-derived growth factor receptor, epithelial growth factor receptor, insulin receptor, and insulin-like growth factor receptor), two putative receptor tyrosine kinases for which the ligand remains to be identified (the products of ryk and the mouse klg homolog), and a novel tyrosine kinase. We cloned cDNAs encoding both the murine and human homologs of this kinase, the sequences of which were subsequently published under the names sky (Ohashi, K., Mizuno, K., Kuma, K., Miyata, T., and Nakamura, T. (1994) Oncogene 9, 699-705) and rse (Mark, M. R., Scadden, D. T., Wang, Z., Gu, Q., Goddard, A., and Godowski, P. J. (1994) J. Biol. Chem. 269, 10720-10728). Mouse sky RNA levels are abundant in mammary tumors derived from transgenic mice that express wnt-1, fgf-3, or both oncogenes in their mammary glands. However, little or no expression of sky is detected in mammary glands from virgin animals or in preneoplastic mammary glands from wnt-1 transgenic mice. Moreover, we find that the human homolog of sky is expressed at elevated levels when normal human mammary epithelial cells are rendered tumorigenic by the introduction of two viral oncogenes. Transient transfection of the human SKY cDNA into the quail fibrosarcoma cell line QT6 reveals that SKY is an active tyrosine kinase that augments the level of cellular phosphotyrosine. Introduction of murine Sky into RatB1a fibroblasts by retrovirus-mediated gene transfer results in morphological transformation, growth in soft agar, and the formation of tumors in nude mice. These data raise the possibility that the Sky tyrosine kinase is involved in the development and/or progression of mammary tumors.\n" ], "offsets": [ [ 0, 2186 ] ] } ]

[ { "id": "PMID-7896835_T1", "type": "Protein", "text": [ "SKY" ], "offsets": [ [ 84, 87 ] ], "normalized": [] }, { "id": "PMID-7896835_T2", "type": "Protein", "text": [ "Wnt-1" ], "offsets": [ [ 197, 202 ] ], "normalized": [] }, { "id": "PMID-7896835_T3", "type": "Protein", "text": [ "epithelial growth factor receptor" ], "offsets": [ [ 554, 587 ] ], "normalized": [] }, { "id": "PMID-7896835_T4", "type": "Protein", "text": [ "insulin receptor" ], "offsets": [ [ 589, 605 ] ], "normalized": [] }, { "id": "PMID-7896835_T5", "type": "Protein", "text": [ "insulin-like growth factor receptor" ], "offsets": [ [ 611, 646 ] ], "normalized": [] }, { "id": "PMID-7896835_T6", "type": "Protein", "text": [ "ryk" ], "offsets": [ [ 751, 754 ] ], "normalized": [] }, { "id": "PMID-7896835_T7", "type": "Protein", "text": [ "klg" ], "offsets": [ [ 769, 772 ] ], "normalized": [] }, { "id": "PMID-7896835_T8", "type": "Protein", "text": [ "sky" ], "offsets": [ [ 955, 958 ] ], "normalized": [] }, { "id": "PMID-7896835_T9", "type": "Protein", "text": [ "sky" ], "offsets": [ [ 1187, 1190 ] ], "normalized": [] }, { "id": "PMID-7896835_T10", "type": "Protein", "text": [ "wnt-1" ], "offsets": [ [ 1275, 1280 ] ], "normalized": [] }, { "id": "PMID-7896835_T11", "type": "Protein", "text": [ "fgf-3" ], "offsets": [ [ 1282, 1287 ] ], "normalized": [] }, { "id": "PMID-7896835_T12", "type": "Protein", "text": [ "sky" ], "offsets": [ [ 1368, 1371 ] ], "normalized": [] }, { "id": "PMID-7896835_T13", "type": "Protein", "text": [ "wnt-1" ], "offsets": [ [ 1462, 1467 ] ], "normalized": [] }, { "id": "PMID-7896835_T14", "type": "Protein", "text": [ "sky" ], "offsets": [ [ 1529, 1532 ] ], "normalized": [] }, { "id": "PMID-7896835_T15", "type": "Protein", "text": [ "SKY" ], "offsets": [ [ 1713, 1716 ] ], "normalized": [] }, { "id": "PMID-7896835_T16", "type": "Protein", "text": [ "SKY" ], "offsets": [ [ 1777, 1780 ] ], "normalized": [] }, { "id": "PMID-7896835_T17", "type": "Protein", "text": [ "Sky" ], "offsets": [ [ 1886, 1889 ] ], "normalized": [] }, { "id": "PMID-7896835_T18", "type": "Protein", "text": [ "Sky" ], "offsets": [ [ 2097, 2100 ] ], "normalized": [] } ]

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[ { "id": "PMID-7907588__text", "type": "abstract", "text": [ "Glycosylation sites selectively interfere with alpha-toxin binding to the nicotinic acetylcholine receptor. \nSequence analysis reveals unique features in the alpha-subunit of nicotinic acetylcholine receptors from the alpha-toxin-resistant cobra and mongoose. Included are N-linked glycosylation signals just amino-terminal to the Tyr190, Cys192-Cys193 region of the ligand binding domain, substitution of Trp187 and Phe189 by non-aromatic residues and alteration of the proline sequence Pro194-X-X-Pro197. Glycosylation signals were inserted into the toxin-sensitive mouse alpha-subunit by the mutations F189N and W187N/F189T. The F189N alpha-subunit, when transfected with beta, gamma and delta, showed a 140-fold loss of alpha-bungarotoxin affinity, whereas the W187N/F189T double mutation exhibited a divergence in alpha-toxin affinities at the two sites, one class showing a 600-fold and the other showing an 11-fold reduction. The W187N mutant and the double mutant F189N/S191A lacking the requisite glycosylation signals exhibited little alteration in affinity, as did the P194L and P197H mutations. The glycosylation sites had little or no influence on binding of toxins of intermediate (alpha-conotoxin, 1500 Da) or small mass (lophotoxin, 500 Da) and of the agonist, carbamylcholine. The two sites for the binding of alpha-conotoxin M1 have widely divergent dissociation constants of 2.1 and 14,800 nM. Expression of alpha/gamma- and alpha/delta-subunit pairs indicated that the high and low affinity sites are formed by the alpha/delta and alpha/gamma contacts, respectively.\n" ], "offsets": [ [ 0, 1587 ] ] } ]

[ { "id": "PMID-7907588_T1", "type": "Protein", "text": [ "alpha-toxin" ], "offsets": [ [ 47, 58 ] ], "normalized": [] }, { "id": "PMID-7907588_T2", "type": "Protein", "text": [ "alpha-toxin" ], "offsets": [ [ 218, 229 ] ], "normalized": [] }, { "id": "PMID-7907588_T3", "type": "Protein", "text": [ "alpha-toxin" ], "offsets": [ [ 819, 830 ] ], "normalized": [] }, { "id": "PMID-7907588_T4", "type": "Protein", "text": [ "alpha-conotoxin M1" ], "offsets": [ [ 1327, 1345 ] ], "normalized": [] } ]

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[ { "id": "PMID-7945210__text", "type": "abstract", "text": [ "Gene dissection demonstrates that the Escherichia coli cysG gene encodes a multifunctional protein. \nThe C-terminus of the Escherichia coli CysG protein, consisting of amino acids 202-457, was expressed as a recombinant protein using gene dissection methodology. Analysis of the activity of this truncated protein, termed CysGA, revealed that it was able to methylate uroporphyrinogen III in the same S-adenosyl-L-methionine (SAM)-dependent manner as the complete CysG protein. However, this truncated protein was not able to complement E. coli cysG cells, thereby suggesting that the first 201 amino acids of the CysG protein had an enzymic activity associated with the conversion of dihydrosirohydrochlorin into sirohaem. Analysis of the N-terminus of the CysG protein revealed the presence of a putative pyridine dinucleotide binding site. When the purified CysG protein was incubated with NADP+, uroporphyrinogen III and SAM the enzyme was found to catalyse a coenzyme-mediated dehydrogenation to form sirohydrochlorin. The CysGA protein on the other hand showed no such coenzyme-dependent activity. Analysis of the porphyrinoid material isolated from strains harbouring plasmids containing the complete and truncated cysG genes suggested that the CysG protein was also involved in ferrochelation. The evidence presented in this paper suggests that the CysG protein is a multifunctional protein involved in SAM-dependent methylation, pyridine dinucleotide dependent dehydrogenation and ferrochelation.\n" ], "offsets": [ [ 0, 1506 ] ] } ]

[ { "id": "PMID-7945210_T1", "type": "Protein", "text": [ "cysG" ], "offsets": [ [ 55, 59 ] ], "normalized": [] }, { "id": "PMID-7945210_T2", "type": "Protein", "text": [ "CysG" ], "offsets": [ [ 140, 144 ] ], "normalized": [] }, { "id": "PMID-7945210_T3", "type": "Protein", "text": [ "CysG" ], "offsets": [ [ 322, 326 ] ], "normalized": [] }, { "id": "PMID-7945210_T4", "type": "Protein", "text": [ "CysG" ], "offsets": [ [ 464, 468 ] ], "normalized": [] }, { "id": "PMID-7945210_T5", "type": "Protein", "text": [ "cysG" ], "offsets": [ [ 545, 549 ] ], "normalized": [] }, { "id": "PMID-7945210_T6", "type": "Protein", "text": [ "CysG" ], "offsets": [ [ 614, 618 ] ], "normalized": [] }, { "id": "PMID-7945210_T7", "type": "Protein", "text": [ "CysG" ], "offsets": [ [ 758, 762 ] ], "normalized": [] }, { "id": "PMID-7945210_T8", "type": "Protein", "text": [ "CysG" ], "offsets": [ [ 861, 865 ] ], "normalized": [] }, { "id": "PMID-7945210_T9", "type": "Protein", "text": [ "CysG" ], "offsets": [ [ 1028, 1032 ] ], "normalized": [] }, { "id": "PMID-7945210_T10", "type": "Protein", "text": [ "cysG" ], "offsets": [ [ 1222, 1226 ] ], "normalized": [] }, { "id": "PMID-7945210_T11", "type": "Protein", "text": [ "CysG" ], "offsets": [ [ 1252, 1256 ] ], "normalized": [] }, { "id": "PMID-7945210_T12", "type": "Protein", "text": [ "CysG" ], "offsets": [ [ 1357, 1361 ] ], "normalized": [] } ]

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[ { "id": "PMID-7995344__text", "type": "abstract", "text": [ "The primate placenta and human chorionic gonadotropin. \nIn the primate placenta various peptide and proteohormones are synthesized which control growth and development of the fetus as well as the exchange of nutrients and metabolic products between the mother and the fetus. In humans, maintenance of pregnancy in the first trimester depends on the synthesis of the bioactive glycoprotein hormone human chorionic gonadotropin (hCG). It is expressed in placenta by the syncytiothrophoblast of early pregnancy. In cell culture, hCG production seems to mark a certain step in the process of differentiation of cytotrophoblasts and choriocarcinoma cells. It is neither understood how hCG synthesis is initiated and maintained at the beginning of gestation nor what control mechanisms are responsible for the down-regulation of the synthesis at the end of the first trimester. Besides a long list of various other substances which have been described to act as intrinsic placental stimulators of hCG biosynthesis, gonadoliberin and gamma-aminobutyric acid seem to play an important role. This establishes to some extent an analogy to the regulation of gonadotropin synthesis in the central nervous system. Recently, a full-length form of functional LH/hCG receptors of approximately 80 kD has been found in term placenta suggesting autoregulation as a regulatory principle of hCG biosynthesis. In the first trimester placenta as well as in choriocarcinoma cells a truncated form (50 kd) of LH/hCG receptors seems to exist. In these cases, exogenous hCG was unable to down-regulate its own synthesis. The carbohydrate moiety of hCG influences folding, subunit assembly, circulatory half-life, receptor interaction and biological response. A surplus of glycosylation may prevent subunit assembly. Experimental deglycosylation induces a different conformation of hCG, which partly acquires antagonistic properties. Recent results indicate that cAMP, which increases transcription and mRNA stability, also expands the N-glycosylation capacity and thus may accomplish an over-all coordination of hCG biosynthesis including post-translational events.\n" ], "offsets": [ [ 0, 2140 ] ] } ]

[ { "id": "PMID-7995344_T1", "type": "Protein", "text": [ "LH/hCG receptors" ], "offsets": [ [ 1244, 1260 ] ], "normalized": [] }, { "id": "PMID-7995344_T2", "type": "Protein", "text": [ "LH/hCG receptors" ], "offsets": [ [ 1485, 1501 ] ], "normalized": [] } ]

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[ { "id": "PMID-8054365__text", "type": "abstract", "text": [ "Characterization of the prenylated protein methyltransferase in human endometrial carcinoma. \nThe processing of ras and of other GTP-binding proteins includes a final reversible step in which the carboxy terminal prenylated cysteine is methylated by the enzyme prenylated protein methyltransferase (PPMTase). The significance of this modification and of the role of PPMTase in human tumors has yet to be fully elucidated. Here we characterize the PPMTase of human endometrial carcinomas (tumors in which the frequency of ras gene mutations is relatively high) and compare it to the PPMTase of the normal endometrium. Our results show that in both types of tissues the enzyme is bound to the membranes. It can utilize synthetic substrates such as N-acetyl-S-farnesyl-L-cysteine (Km = 18-20 microM) and is blocked by the PPMTase inhibitor S-farnesylthioacetic acid (Ki = 2 microM). In vitro methylation assays and [alpha-32P]GTP blot-overlay assays showed that the major endogenous PPMTase substrates are small GTP-binding proteins. Methylation of these proteins in vitro is blocked by farnesylthioacetic acid. The kinetic properties of PPMTase from the carcinomas and the normal tissues are very similar. However, levels of PPMTase activity (but not of its endogenous substrates) are higher in the carcinomatous endometrium than in the normal one. The elevated enzyme activity is restricted to the crude mitochondrial fraction (8.0 +/- 0.4 vs. 5.4 +/- 0.1 pmol N-acetyl farnesylcysteine methyl ester formed/min/mg protein by the carcinoma and by the normal endometrial preparations, respectively). As this fraction is enriched in plasma membranes, it appears that the elevated enzyme activity could be related to ras protein methylation; if so, selective methylation blockers might inhibit the growth of endometrial carcinomas.\n" ], "offsets": [ [ 0, 1827 ] ] } ]

[ { "id": "PMID-8054365_T1", "type": "Protein", "text": [ "prenylated protein methyltransferase" ], "offsets": [ [ 24, 60 ] ], "normalized": [] }, { "id": "PMID-8054365_T2", "type": "Protein", "text": [ "prenylated protein methyltransferase" ], "offsets": [ [ 261, 297 ] ], "normalized": [] }, { "id": "PMID-8054365_T3", "type": "Protein", "text": [ "PPMTase" ], "offsets": [ [ 299, 306 ] ], "normalized": [] }, { "id": "PMID-8054365_T4", "type": "Protein", "text": [ "PPMTase" ], "offsets": [ [ 366, 373 ] ], "normalized": [] }, { "id": "PMID-8054365_T5", "type": "Protein", "text": [ "PPMTase" ], "offsets": [ [ 447, 454 ] ], "normalized": [] }, { "id": "PMID-8054365_T6", "type": "Protein", "text": [ "PPMTase" ], "offsets": [ [ 582, 589 ] ], "normalized": [] }, { "id": "PMID-8054365_T7", "type": "Protein", "text": [ "PPMTase" ], "offsets": [ [ 819, 826 ] ], "normalized": [] }, { "id": "PMID-8054365_T8", "type": "Protein", "text": [ "PPMTase" ], "offsets": [ [ 980, 987 ] ], "normalized": [] }, { "id": "PMID-8054365_T9", "type": "Protein", "text": [ "PPMTase" ], "offsets": [ [ 1135, 1142 ] ], "normalized": [] }, { "id": "PMID-8054365_T10", "type": "Protein", "text": [ "PPMTase" ], "offsets": [ [ 1223, 1230 ] ], "normalized": [] } ]

[]

[ { "id": "PMID-8054365_1", "entity_ids": [ "PMID-8054365_T2", "PMID-8054365_T3" ] } ]

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[ { "id": "PMID-8064731__text", "type": "abstract", "text": [ "Serum ferritin and isoferritins are tools for diagnosis of active adult Still's disease. \nOBJECTIVE: Still's disease is an acute systemic inflammatory disorder. There are no pathognomonic symptoms or specific laboratory abnormalities. Serum ferritin concentration in rheumatoid arthritis together with some plasma glycoproteins such as alpha 2-glycoprotein and C-reactive protein are part of the response to inflammation. Ferritin in plasma is glycosylated and the sialoglycosylated forms increase its microheterogeneity. Our purpose was to confirm in a large series that high values of ferritin can be found in adult Still's disease (ASD) and to see if a specific isoferritin can be isolated in this disease compared with the other systemic diseases. METHOD: Thirty-one sera were investigated from 11 men and 9 women with ASD and compared with 27 sera from 27 patients with systemic diseases. We studied the course of one case of ASD for 15 months. Serum ferritin was determined by immunoenzymology (Abbott Ferrizin). The isoferritins were investigated by isoelectric focussing and the percentage of glycosylation by affinity for concanavalin A (Con-A). RESULTS: In patients with active ASD, the ferritin levels were higher than in patients with inactive ASD or other systemic diseases: p < 0.001. The glycoforms of ferritin were basic and the proportion of ferritin bound to Con-A was lower than other ASD: p < 0.001. CONCLUSIONS: Serum ferritin levels have a diagnostic value for acute ASD. The study of sialylation and abnormalities in the glycosylation of ferritin helps to discriminate ASD from arthritis or other systemic diseases. In conclusion, the glycoform of isoferritins and the percentage of glycosylation offers an additional tool for the diagnosis of Still's disease.\n" ], "offsets": [ [ 0, 1784 ] ] } ]

[ { "id": "PMID-8064731_T1", "type": "Protein", "text": [ "C-reactive protein" ], "offsets": [ [ 361, 379 ] ], "normalized": [] }, { "id": "PMID-8064731_T2", "type": "Protein", "text": [ "concanavalin A" ], "offsets": [ [ 1131, 1145 ] ], "normalized": [] }, { "id": "PMID-8064731_T3", "type": "Protein", "text": [ "Con-A" ], "offsets": [ [ 1147, 1152 ] ], "normalized": [] }, { "id": "PMID-8064731_T4", "type": "Protein", "text": [ "Con-A" ], "offsets": [ [ 1377, 1382 ] ], "normalized": [] } ]

[]

[ { "id": "PMID-8064731_1", "entity_ids": [ "PMID-8064731_T2", "PMID-8064731_T3" ] } ]

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[ { "id": "PMID-8090748__text", "type": "abstract", "text": [ "Subcellular localization of the UDP-N-acetyl-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase-mediated O-glycosylation reaction in the submaxillary gland. \nAddition of N-acetylgalactosamine to threonine and serine is the first step in the synthesis of O-glycosidically linked oligosaccharides. A UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase (EC 2.4.1.41) from porcine submaxillary glands was recently purified to electrophoretic homogeneity, and polyclonal antibodies against the purified transferase were raised. Immunoblots of porcine, bovine, and ovine submaxillary gland extracts with the anti-transferase antibodies gave a single band and the antibodies reacted equally well with the purified glycosylated and N-glycanase-treated transferase. Immunoelectron microscopic localization of the transferase was achieved in Lowicryl K4M thin sections and frozen-thawed thin sections of porcine and bovine submaxillary gland by using the protein A-gold technique. Specific gold particle labeling was observed in the cis Golgi apparatus and smooth-membraned vesicular structures in close topological relation with it. Labeling was undetectable in the rough endoplasmic reticulum, its transitional elements, and smooth-membraned structures close to them, the trans Golgi apparatus, mucin droplets, and the plasma membrane. The onset of labeling for peptide-bound GalNAc as detected with Vicia villosa isolectin G4 mirrored the transferase immunolocalization as directly shown by double labeling and extended into the trans Golgi apparatus and mucous droplets. Apomucin immunolabeling was found throughout the endoplasmic reticulum and the intermediate compartment and partially overlapped the region of transferase labeling in the Golgi apparatus as demonstrated by double immunolabeling. Thus, the initial step of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-mediated O-glycosylation in porcine and bovine submaxillary gland cells occurs in the cis Golgi apparatus. The possible involvement of the intermediate compartment remains to be clarified.\n" ], "offsets": [ [ 0, 2101 ] ] } ]

[ { "id": "PMID-8090748_T1", "type": "Protein", "text": [ "UDP-N-acetyl-D-galactosamine: polypeptide N-acetylgalactosaminyltransferase" ], "offsets": [ [ 32, 107 ] ], "normalized": [] }, { "id": "PMID-8090748_T2", "type": "Protein", "text": [ "UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase" ], "offsets": [ [ 310, 384 ] ], "normalized": [] }, { "id": "PMID-8090748_T3", "type": "Protein", "text": [ "isolectin G4" ], "offsets": [ [ 1441, 1453 ] ], "normalized": [] }, { "id": "PMID-8090748_T4", "type": "Protein", "text": [ "Apomucin" ], "offsets": [ [ 1600, 1608 ] ], "normalized": [] }, { "id": "PMID-8090748_T5", "type": "Protein", "text": [ "UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase" ], "offsets": [ [ 1855, 1911 ] ], "normalized": [] } ]

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[ { "id": "PMID-8178450__text", "type": "abstract", "text": [ "Sequence-specific methylation inhibits the activity of the Epstein-Barr virus LMP 1 and BCR2 enhancer-promoter regions. \nWe reported earlier that variable expression of the Epstein-Barr virus (EBV) encoded membrane protein LMP 1 in nasopharyngeal carcinoma and the host-cell-phenotype-dependent activity of the BCR2 promoter (one of the possible initiator sites for transcripts of Epstein-Barr nuclear antigens) in Burkitt's lymphoma (BL) lines can be related to the methylation status of the 5'-flanking regulatory regions of the BNLF 1 and BCR2 promoter, respectively. Here we report that clones of the BL line Mutu that differ in expression of LMP 1 also show a differential methylation pattern of the LMP 1 regulatory sequences: this region is hypomethylated in an LMP 1 expressing (group III) clone but methylated in a group I clone that does not express LMP 1. We introduced in vitro methylated reporter plasmids carrying BNLF 1 and BCR2 enhancer-promoter sequences into the BL line Raji and found that overall methylation of 5'-CG-3' sequences by the Spiroplasma methylase Sssl significantly reduced their activity compared to unmethylated or mock-methylated controls. Methylation of 5-CCGG-3' sequences by Hpall methyltransferase gave similar results. On the contrary, methylation of 5'GCGC-3' sequences by Hhall methyltransferase gave similar results. On the contrary, methylation of 5'-GCGC-3' sequences by Hpal methyltransferase resulted only in a moderate reduction of BNLF 1 enhancer-promoter activity. These data support the notion that methylation at discrete sites within control regions of latent, growth-transformation associated EBV genes may contribute to silencing their expression.\n" ], "offsets": [ [ 0, 1704 ] ] } ]

[ { "id": "PMID-8178450_T1", "type": "Protein", "text": [ "LMP 1" ], "offsets": [ [ 78, 83 ] ], "normalized": [] }, { "id": "PMID-8178450_T2", "type": "Protein", "text": [ "LMP 1" ], "offsets": [ [ 223, 228 ] ], "normalized": [] }, { "id": "PMID-8178450_T3", "type": "Protein", "text": [ "BNLF 1" ], "offsets": [ [ 531, 537 ] ], "normalized": [] }, { "id": "PMID-8178450_T4", "type": "Protein", "text": [ "LMP 1" ], "offsets": [ [ 647, 652 ] ], "normalized": [] }, { "id": "PMID-8178450_T5", "type": "Protein", "text": [ "LMP 1" ], "offsets": [ [ 705, 710 ] ], "normalized": [] }, { "id": "PMID-8178450_T6", "type": "Protein", "text": [ "LMP 1" ], "offsets": [ [ 769, 774 ] ], "normalized": [] }, { "id": "PMID-8178450_T7", "type": "Protein", "text": [ "LMP 1" ], "offsets": [ [ 860, 865 ] ], "normalized": [] }, { "id": "PMID-8178450_T8", "type": "Protein", "text": [ "BNLF 1" ], "offsets": [ [ 928, 934 ] ], "normalized": [] }, { "id": "PMID-8178450_T9", "type": "Protein", "text": [ "methylase Sssl" ], "offsets": [ [ 1070, 1084 ] ], "normalized": [] }, { "id": "PMID-8178450_T10", "type": "Protein", "text": [ "Hpall methyltransferase" ], "offsets": [ [ 1214, 1237 ] ], "normalized": [] }, { "id": "PMID-8178450_T11", "type": "Protein", "text": [ "Hhall methyltransferase" ], "offsets": [ [ 1315, 1338 ] ], "normalized": [] }, { "id": "PMID-8178450_T12", "type": "Protein", "text": [ "Hpal methyltransferase" ], "offsets": [ [ 1417, 1439 ] ], "normalized": [] }, { "id": "PMID-8178450_T13", "type": "Protein", "text": [ "BNLF 1" ], "offsets": [ [ 1481, 1487 ] ], "normalized": [] }, { "id": "PMID-8178450_T15", "type": "Entity", "text": [ "5'-flanking regulatory regions" ], "offsets": [ [ 493, 523 ] ], "normalized": [] }, { "id": "PMID-8178450_T16", "type": "Entity", "text": [ "BCR2 promoter" ], "offsets": [ [ 542, 555 ] ], "normalized": [] }, { "id": "PMID-8178450_T18", "type": "Entity", "text": [ "regulatory sequences" ], "offsets": [ [ 711, 731 ] ], "normalized": [] }, { "id": "PMID-8178450_T23", "type": "Entity", "text": [ "5'-CG-3'" ], "offsets": [ [ 1032, 1040 ] ], "normalized": [] }, { "id": "PMID-8178450_T26", "type": "Entity", "text": [ "5-CCGG-3'" ], "offsets": [ [ 1191, 1200 ] ], "normalized": [] }, { "id": "PMID-8178450_T29", "type": "Entity", "text": [ "5'GCGC-3'" ], "offsets": [ [ 1292, 1301 ] ], "normalized": [] }, { "id": "PMID-8178450_T32", "type": "Entity", "text": [ "5'-GCGC-3'" ], "offsets": [ [ 1393, 1403 ] ], "normalized": [] } ]

[ { "id": "PMID-8178450_E1", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 467, 478 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_T3" }, { "role": "Site", "ref_id": "PMID-8178450_T15" } ] }, { "id": "PMID-8178450_E2", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 467, 478 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_T3" }, { "role": "Site", "ref_id": "PMID-8178450_T16" } ] }, { "id": "PMID-8178450_E3", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 678, 689 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_T5" }, { "role": "Site", "ref_id": "PMID-8178450_T18" } ] }, { "id": "PMID-8178450_E4", "type": "DNA_demethylation", "trigger": { "text": [ "hypomethylated" ], "offsets": [ [ 748, 762 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_T5" }, { "role": "Site", "ref_id": "PMID-8178450_T18" } ] }, { "id": "PMID-8178450_E5", "type": "DNA_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 808, 818 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_T5" }, { "role": "Site", "ref_id": "PMID-8178450_T18" } ] }, { "id": "PMID-8178450_E6", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1017, 1028 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_T8" }, { "role": "Site", "ref_id": "PMID-8178450_T23" } ] }, { "id": "PMID-8178450_E7", "type": "Catalysis", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1017, 1028 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_E6" }, { "role": "Cause", "ref_id": "PMID-8178450_T9" } ] }, { "id": "PMID-8178450_E8", "type": "DNA_methylation", "trigger": { "text": [ "Methylation" ], "offsets": [ [ 1176, 1187 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_T8" }, { "role": "Site", "ref_id": "PMID-8178450_T26" } ] }, { "id": "PMID-8178450_E9", "type": "Catalysis", "trigger": { "text": [ "Methylation" ], "offsets": [ [ 1176, 1187 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_E8" }, { "role": "Cause", "ref_id": "PMID-8178450_T10" } ] }, { "id": "PMID-8178450_E10", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1277, 1288 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_T8" }, { "role": "Site", "ref_id": "PMID-8178450_T29" } ] }, { "id": "PMID-8178450_E11", "type": "Catalysis", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1277, 1288 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_E10" }, { "role": "Cause", "ref_id": "PMID-8178450_T11" } ] }, { "id": "PMID-8178450_E12", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1378, 1389 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_T8" }, { "role": "Site", "ref_id": "PMID-8178450_T32" } ] }, { "id": "PMID-8178450_E13", "type": "Catalysis", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1378, 1389 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8178450_E12" }, { "role": "Cause", "ref_id": "PMID-8178450_T12" } ] } ]

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[ { "id": "PMID-8226664__text", "type": "abstract", "text": [ "Cotranscription of two genes necessary for ribosomal protein L11 methylation (prmA) and pantothenate transport (panF) in Escherichia coli K-12. \nGenetic complementation and enzyme assays have shown that the DNA region between panF, which encodes pantothenate permease, and orf1, the first gene of the fis operon, encodes prmA, the genetic determinant for the ribosomal protein L11 methyltransferase. Sequencing of this region identified one long open reading frame that encodes a protein of 31,830 Da and corresponds to the prmA gene. We found, both in vivo and in vitro, that prmA is expressed from promoters located upstream of panF and thus that the panF and prmA genes constitute a bifunctional operon. We located the major 3' end of prmA transcripts 90 nucleotides downstream of the stop codon of prmA in the DNA region upstream of the fis operon, a region implicated in the control of the expression of the fis operon. Although no promoter activity was detected immediately upstream of prmA, S1 mapping detected 5' ends of mRNA in this region, implying that some mRNA processing occurs within the bicistronic panF-prmA mRNA.\n" ], "offsets": [ [ 0, 1131 ] ] } ]

[ { "id": "PMID-8226664_T1", "type": "Protein", "text": [ "ribosomal protein L11" ], "offsets": [ [ 43, 64 ] ], "normalized": [] }, { "id": "PMID-8226664_T2", "type": "Protein", "text": [ "prmA" ], "offsets": [ [ 78, 82 ] ], "normalized": [] }, { "id": "PMID-8226664_T3", "type": "Protein", "text": [ "panF" ], "offsets": [ [ 112, 116 ] ], "normalized": [] }, { "id": "PMID-8226664_T4", "type": "Protein", "text": [ "panF" ], "offsets": [ [ 226, 230 ] ], "normalized": [] }, { "id": "PMID-8226664_T5", "type": "Protein", "text": [ "pantothenate permease" ], "offsets": [ [ 246, 267 ] ], "normalized": [] }, { "id": "PMID-8226664_T6", "type": "Protein", "text": [ "prmA" ], "offsets": [ [ 321, 325 ] ], "normalized": [] }, { "id": "PMID-8226664_T7", "type": "Protein", "text": [ "ribosomal protein L11 methyltransferase" ], "offsets": [ [ 359, 398 ] ], "normalized": [] }, { "id": "PMID-8226664_T8", "type": "Protein", "text": [ "prmA" ], "offsets": [ [ 524, 528 ] ], "normalized": [] }, { "id": "PMID-8226664_T9", "type": "Protein", "text": [ "prmA" ], "offsets": [ [ 577, 581 ] ], "normalized": [] }, { "id": "PMID-8226664_T10", "type": "Protein", "text": [ "panF" ], "offsets": [ [ 630, 634 ] ], "normalized": [] }, { "id": "PMID-8226664_T11", "type": "Protein", "text": [ "panF" ], "offsets": [ [ 653, 657 ] ], "normalized": [] }, { "id": "PMID-8226664_T12", "type": "Protein", "text": [ "prmA" ], "offsets": [ [ 662, 666 ] ], "normalized": [] }, { "id": "PMID-8226664_T13", "type": "Protein", "text": [ "prmA" ], "offsets": [ [ 738, 742 ] ], "normalized": [] }, { "id": "PMID-8226664_T14", "type": "Protein", "text": [ "prmA" ], "offsets": [ [ 802, 806 ] ], "normalized": [] }, { "id": "PMID-8226664_T15", "type": "Protein", "text": [ "prmA" ], "offsets": [ [ 992, 996 ] ], "normalized": [] }, { "id": "PMID-8226664_T16", "type": "Protein", "text": [ "panF" ], "offsets": [ [ 1115, 1119 ] ], "normalized": [] }, { "id": "PMID-8226664_T17", "type": "Protein", "text": [ "prmA" ], "offsets": [ [ 1120, 1124 ] ], "normalized": [] } ]

[ { "id": "PMID-8226664_E1", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 65, 76 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8226664_T1" } ] } ]

[ { "id": "PMID-8226664_1", "entity_ids": [ "PMID-8226664_T4", "PMID-8226664_T5" ] }, { "id": "PMID-8226664_2", "entity_ids": [ "PMID-8226664_T6", "PMID-8226664_T7" ] } ]

[]

[ { "id": "PMID-8226858__text", "type": "abstract", "text": [ "The effect of aspartate hydroxylation on calcium binding to epidermal growth factor-like modules in coagulation factors IX and X. \nHydroxylation of aspartic acid to erythro-beta-aspartic acid (Hya) occurs in epidermal growth factor (EGF)-like modules in numerous extracellular proteins with diverse functions. Several EGF-like modules with the consensus sequence for hydroxylation bind Ca2+, and it has therefore been suggested that the hydroxyl group is essential for Ca2+ binding. To determine directly the influence of beta-hydroxylation on calcium binding in the EGF-like modules from coagulation factors IX and X, we have now measured calcium binding to both the fully beta-hydroxylated and the non-beta-hydroxylated modules of the two proteins. At low ionic strength, the Hya-containing module of factor X has a slightly higher Ca2+ affinity, but at physiological salt concentrations this difference is no longer significant for either factor IX or X. Analysis of the 1H NMR chemical shift differences between the hydroxylated and nonhydroxylated factor X modules show that hydroxylation has no effect on the domain fold. Furthermore, measurements on factor IX show that hydroxylation has no effect on the Ca2+/Mg2+ specificity of the ion binding site. We conclude that the hydroxyl group is not a direct ligand for the calcium ion in these EGF-like modules, nor is it essential for high-affinity Ca2+ binding.\n" ], "offsets": [ [ 0, 1417 ] ] } ]

[ { "id": "PMID-8226858_T1", "type": "Protein", "text": [ "coagulation factors IX" ], "offsets": [ [ 100, 122 ] ], "normalized": [] }, { "id": "PMID-8226858_T2", "type": "Protein", "text": [ "X" ], "offsets": [ [ 127, 128 ] ], "normalized": [] }, { "id": "PMID-8226858_T3", "type": "Protein", "text": [ "coagulation factors IX" ], "offsets": [ [ 589, 611 ] ], "normalized": [] }, { "id": "PMID-8226858_T4", "type": "Protein", "text": [ "X" ], "offsets": [ [ 616, 617 ] ], "normalized": [] }, { "id": "PMID-8226858_T5", "type": "Protein", "text": [ "factor X" ], "offsets": [ [ 803, 811 ] ], "normalized": [] }, { "id": "PMID-8226858_T6", "type": "Protein", "text": [ "factor IX" ], "offsets": [ [ 942, 951 ] ], "normalized": [] }, { "id": "PMID-8226858_T7", "type": "Protein", "text": [ "X" ], "offsets": [ [ 955, 956 ] ], "normalized": [] }, { "id": "PMID-8226858_T8", "type": "Protein", "text": [ "factor X" ], "offsets": [ [ 1053, 1061 ] ], "normalized": [] }, { "id": "PMID-8226858_T9", "type": "Protein", "text": [ "factor IX" ], "offsets": [ [ 1157, 1166 ] ], "normalized": [] }, { "id": "PMID-8226858_T10", "type": "Entity", "text": [ "aspartate" ], "offsets": [ [ 14, 23 ] ], "normalized": [] }, { "id": "PMID-8226858_T13", "type": "Entity", "text": [ "EGF-like modules" ], "offsets": [ [ 567, 583 ] ], "normalized": [] } ]

[ { "id": "PMID-8226858_E1", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 24, 37 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8226858_T1" }, { "role": "Site", "ref_id": "PMID-8226858_T10" } ] }, { "id": "PMID-8226858_E2", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 24, 37 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8226858_T2" }, { "role": "Site", "ref_id": "PMID-8226858_T10" } ] }, { "id": "PMID-8226858_E3", "type": "Hydroxylation", "trigger": { "text": [ "beta-hydroxylation" ], "offsets": [ [ 522, 540 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8226858_T3" }, { "role": "Site", "ref_id": "PMID-8226858_T13" } ] }, { "id": "PMID-8226858_E4", "type": "Hydroxylation", "trigger": { "text": [ "beta-hydroxylation" ], "offsets": [ [ 522, 540 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8226858_T4" }, { "role": "Site", "ref_id": "PMID-8226858_T13" } ] }, { "id": "PMID-8226858_E5", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylated" ], "offsets": [ [ 1020, 1032 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8226858_T8" } ] }, { "id": "PMID-8226858_E6", "type": "Hydroxylation", "trigger": { "text": [ "nonhydroxylated" ], "offsets": [ [ 1037, 1052 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8226858_T8" } ] }, { "id": "PMID-8226858_E7", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1080, 1093 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8226858_T8" } ] }, { "id": "PMID-8226858_E8", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 1177, 1190 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8226858_T9" } ] } ]

[]

[]

[ { "id": "PMID-8257853__text", "type": "abstract", "text": [ "Glycosylation of the thrombin-like serine protease ancrod from Agkistrodon rhodostoma venom. Oligosaccharide substitution pattern at each N-glycosylation site. \nIn a previous study, we determined the structures of the glycans present in ancrod, a thrombin-like serine protease from the venom of the Malayan pit viper Agkistrodon rhodostoma (Pfeiffer et al. (1992) Eur J Biochem 205:961-78). In order to allocate the various carbohydrate chains to distinct N-glycosylation sites of the molecule, we have now isolated individual glycopeptides. Peptide moieties were identified after deglycosylation with peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase F by amino acid analysis and sequencing. Liberated oligosaccharides were assigned to the previously deduced carbohydrate structures by high performance liquid chromatography. Although only quantitative differences were observed, the results indicate that each glycosylation site of ancrod carries its characteristic oligosaccharide pattern. Furthermore, all potential sites were shown to be substituted by carbohydrates.\n" ], "offsets": [ [ 0, 1082 ] ] } ]

[ { "id": "PMID-8257853_T1", "type": "Protein", "text": [ "ancrod" ], "offsets": [ [ 51, 57 ] ], "normalized": [] }, { "id": "PMID-8257853_T2", "type": "Protein", "text": [ "ancrod" ], "offsets": [ [ 238, 244 ] ], "normalized": [] }, { "id": "PMID-8257853_T3", "type": "Protein", "text": [ "peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase F" ], "offsets": [ [ 603, 662 ] ], "normalized": [] }, { "id": "PMID-8257853_T4", "type": "Protein", "text": [ "ancrod" ], "offsets": [ [ 943, 949 ] ], "normalized": [] }, { "id": "PMID-8257853_T6", "type": "Entity", "text": [ "glycosylation site" ], "offsets": [ [ 921, 939 ] ], "normalized": [] }, { "id": "PMID-8257853_T8", "type": "Entity", "text": [ "oligosaccharide" ], "offsets": [ [ 977, 992 ] ], "normalized": [] }, { "id": "PMID-8257853_T9", "type": "Entity", "text": [ "potential sites" ], "offsets": [ [ 1019, 1034 ] ], "normalized": [] }, { "id": "PMID-8257853_T11", "type": "Entity", "text": [ "carbohydrates" ], "offsets": [ [ 1067, 1080 ] ], "normalized": [] } ]

[ { "id": "PMID-8257853_E1", "type": "Glycosylation", "trigger": { "text": [ "Glycosylation" ], "offsets": [ [ 0, 13 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8257853_T1" } ] }, { "id": "PMID-8257853_E2", "type": "Glycosylation", "trigger": { "text": [ "carries" ], "offsets": [ [ 950, 957 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8257853_T4" }, { "role": "Site", "ref_id": "PMID-8257853_T6" }, { "role": "Sidechain", "ref_id": "PMID-8257853_T8" } ] }, { "id": "PMID-8257853_E3", "type": "Glycosylation", "trigger": { "text": [ "substituted" ], "offsets": [ [ 1052, 1063 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8257853_T4" }, { "role": "Site", "ref_id": "PMID-8257853_T9" }, { "role": "Sidechain", "ref_id": "PMID-8257853_T11" } ] } ]

[]

[]

[ { "id": "PMID-8276888__text", "type": "abstract", "text": [ "The role of CaaX-dependent modifications in membrane association of Xenopus nuclear lamin B3 during meiosis and the fate of B3 in transfected mitotic cells. \nRecent evidence shows that the COOH-terminal CaaX motif of lamins is necessary to target newly synthesized proteins to the nuclear envelope membranes. Isoprenylation at the CaaX-cysteine has been taken to explain the different fates of A- and B-type lamins during cell division. A-type lamins, which loose their isoprenylation shortly after incorporation into the lamina structure, become freely soluble upon mitotic nuclear envelope breakdown. Somatic B-type lamins, in contrast, are permanently isoprenylated and, although depolymerized during mitosis, remain associated with remnants of nuclear envelope membranes. However, Xenopus lamin B3, the major B-type lamin of amphibian oocytes and eggs, becomes soluble after nuclear envelope breakdown in meiotic metaphase. Here we show that Xenopus lamin B3 is permanently isoprenylated and carboxyl methylated in oocytes (interphase) and eggs (meiotic metaphase). When transfected into mouse L cells Xenopus lamin B3 is integrated into the host lamina and responds to cell cycle signals in a normal fashion. Notably, the ectopically expressed Xenopus lamin does not form heterooligomers with the endogenous lamins as revealed by a coprecipitation experiment with mitotic lamins. In contrast to the situation in amphibian eggs, a significant portion of lamin B3 remains associated with membranes during mitosis. We conclude from these data that the CaaX motif-mediated modifications, although necessary, are not sufficient for a stable association of lamins with membranes and that additional factors are involved in lamin-membrane binding.\n" ], "offsets": [ [ 0, 1746 ] ] } ]

[ { "id": "PMID-8276888_T1", "type": "Protein", "text": [ "lamin B3" ], "offsets": [ [ 84, 92 ] ], "normalized": [] }, { "id": "PMID-8276888_T2", "type": "Protein", "text": [ "B3" ], "offsets": [ [ 124, 126 ] ], "normalized": [] }, { "id": "PMID-8276888_T3", "type": "Protein", "text": [ "lamin B3" ], "offsets": [ [ 793, 801 ] ], "normalized": [] }, { "id": "PMID-8276888_T4", "type": "Protein", "text": [ "lamin B3" ], "offsets": [ [ 954, 962 ] ], "normalized": [] }, { "id": "PMID-8276888_T5", "type": "Protein", "text": [ "lamin B3" ], "offsets": [ [ 1114, 1122 ] ], "normalized": [] }, { "id": "PMID-8276888_T6", "type": "Protein", "text": [ "lamin B3" ], "offsets": [ [ 1458, 1466 ] ], "normalized": [] } ]

[ { "id": "PMID-8276888_E1", "type": "Methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 1005, 1015 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8276888_T4" } ] } ]

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[]

[ { "id": "PMID-8279517__text", "type": "abstract", "text": [ "Characterization of the beta-subunit of the H(+)-K(+)-ATPase using an inhibitory monoclonal antibody. \nThe gastric proton pump, H(+)-K(+)-ATPase, is composed of alpha- and beta-subunits. The 95-kDa alpha-subunit has been referred to as the catalytic subunit containing sites for ATP binding and phosphorylation. The beta-subunit is a glycoprotein with a 34-kDa core peptide that has a single transmembrane segment, a small cytoplasmic NH2-terminal, and a large extracellular COOH-terminal domain with seven potential N-linked glycosylation sites. To further study the beta-subunit, we developed monoclonal antibodies that identified a 52-kDa mannose-rich glycoprotein that was deglycosylated by endoglycosidase H such that six transient intermediates were identified, as well as a 34-kDa beta-subunit core peptide. These observations suggest that the beta-subunit is synthesized as a 52-kDa glycoprotein with seven N-linked precursor high-mannose oligosaccharides that mature into complex oligosaccharides. One antibody, 2G11, inhibits the K(+)-stimulated ATP hydrolysis as well as K(+)-stimulated p-nitrophenyl phosphatase (pNPPase) activity of the H(+)-K(+)-ATPase. Kinetic studies revealed that 2G11 inhibited maximum velocity (Vmax) of ATP hydrolysis by approximately 50% with no change in the Km for K+, whereas, for pNPPase both Vmax and Km were altered. These studies demonstrate a functional role for the beta-subunit in the H(+)-K(+)-ATPase activity, especially the K(+)-induced conformational states.\n" ], "offsets": [ [ 0, 1511 ] ] } ]

[ { "id": "PMID-8279517_T1", "type": "Protein", "text": [ "endoglycosidase H" ], "offsets": [ [ 695, 712 ] ], "normalized": [] } ]

[]

[]

[]

[ { "id": "PMID-8344280__text", "type": "abstract", "text": [ "Biosynthesis and secretion of human interleukin 2 glycoprotein variants from baculovirus-infected Sf21 cells. Characterization of polypeptides and posttranslational modifications. \nHuman interleukin 2 (IL-2) and human IL-2 mutant proteins, with artificially introduced N-glycosylation or O-glycosylation sites, have been expressed in a lepidopteran cell line (Sf21, Spodoptera frugiperda) using recombinant baculovirus vectors. Only approximately 25% of the total recombinant IL-2 protein synthesized by Sf21 cells was secreted into the culture medium. Significant N-terminal truncations were detected in the secreted polypeptides (up to 85% of the molecules). Alanine and proline were absent in the major truncated forms; the first 3-5 amino acids were also absent in a small proportion of the purified proteins. The introduction of potential artificial O-glycosylation peptide sequences (..GGKAPTPPPK..), to the C-terminus or between positions 80 and 81 of the IL-2 polypeptide chain, resulted in the secretion of unglycosylated and O-glycosylated variant forms. Fast atom bombardment mass spectrometry, compositional analysis and methylation analysis, of the tryptic glycopeptide APTPPPK, revealed the presence of either GalNAc or the disaccharide Gal(beta 1-3)GalNAc as the only carbohydrate constituents attached exclusively to Thr in this peptide, in a specific ratio for each individual IL-2 mutant protein. The Gal(beta 1-3)GalNAc protein forms could be partially altered in vitro to mammalian-type glycoforms by porcine liver beta-galactoside alpha-2,3-sialyltransferase in the presence of CMP-N-acetylneuraminic acid. An IL-2 mutant form, with an 11-amino-acid peptide of human interferon-beta at position 4, which includes its only N-glycosylation site, had exclusively truncated proximally fucosylated oligomannosidic glycans; Man3GlcNAc[Fuc(alpha 1-6)]GlcNAc or Man2GlcNAc[Fuc(alpha 1-6)]GlcNAc structures, in a ratio of 3:1, were detected in the secreted proteins. No evidence was obtained for the presence of secreted proteins with complex oligosaccharide chains, irrespective of the cell-culture conditions used or the harvesting time, for infected cells with recombinant baculovirus constructs.\n" ], "offsets": [ [ 0, 2213 ] ] } ]

[ { "id": "PMID-8344280_T1", "type": "Protein", "text": [ "interleukin 2" ], "offsets": [ [ 36, 49 ] ], "normalized": [] }, { "id": "PMID-8344280_T2", "type": "Protein", "text": [ "interleukin 2" ], "offsets": [ [ 188, 201 ] ], "normalized": [] }, { "id": "PMID-8344280_T3", "type": "Protein", "text": [ "IL-2" ], "offsets": [ [ 203, 207 ] ], "normalized": [] }, { "id": "PMID-8344280_T4", "type": "Protein", "text": [ "IL-2" ], "offsets": [ [ 219, 223 ] ], "normalized": [] }, { "id": "PMID-8344280_T5", "type": "Protein", "text": [ "IL-2" ], "offsets": [ [ 477, 481 ] ], "normalized": [] }, { "id": "PMID-8344280_T6", "type": "Protein", "text": [ "IL-2" ], "offsets": [ [ 964, 968 ] ], "normalized": [] }, { "id": "PMID-8344280_T7", "type": "Protein", "text": [ "IL-2" ], "offsets": [ [ 1395, 1399 ] ], "normalized": [] }, { "id": "PMID-8344280_T8", "type": "Protein", "text": [ "beta-galactoside alpha-2,3-sialyltransferase" ], "offsets": [ [ 1536, 1580 ] ], "normalized": [] }, { "id": "PMID-8344280_T9", "type": "Protein", "text": [ "IL-2" ], "offsets": [ [ 1632, 1636 ] ], "normalized": [] }, { "id": "PMID-8344280_T10", "type": "Protein", "text": [ "interferon-beta" ], "offsets": [ [ 1689, 1704 ] ], "normalized": [] }, { "id": "PMID-8344280_T13", "type": "Entity", "text": [ "GalNAc" ], "offsets": [ [ 1225, 1231 ] ], "normalized": [] }, { "id": "PMID-8344280_T14", "type": "Entity", "text": [ "Gal(beta 1-3)GalNAc" ], "offsets": [ [ 1252, 1271 ] ], "normalized": [] }, { "id": "PMID-8344280_T16", "type": "Entity", "text": [ "Thr" ], "offsets": [ [ 1334, 1337 ] ], "normalized": [] } ]

[ { "id": "PMID-8344280_E1", "type": "Glycosylation", "trigger": { "text": [ "unglycosylated" ], "offsets": [ [ 1017, 1031 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8344280_T4" } ] }, { "id": "PMID-8344280_E2", "type": "Glycosylation", "trigger": { "text": [ "O-glycosylated" ], "offsets": [ [ 1036, 1050 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8344280_T4" } ] }, { "id": "PMID-8344280_E3", "type": "Glycosylation", "trigger": { "text": [ "attached" ], "offsets": [ [ 1310, 1318 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8344280_T7" }, { "role": "Site", "ref_id": "PMID-8344280_T16" }, { "role": "Sidechain", "ref_id": "PMID-8344280_T13" } ] }, { "id": "PMID-8344280_E4", "type": "Glycosylation", "trigger": { "text": [ "attached" ], "offsets": [ [ 1310, 1318 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8344280_T7" }, { "role": "Site", "ref_id": "PMID-8344280_T16" }, { "role": "Sidechain", "ref_id": "PMID-8344280_T14" } ] } ]

[ { "id": "PMID-8344280_1", "entity_ids": [ "PMID-8344280_T2", "PMID-8344280_T3" ] } ]

[]

[ { "id": "PMID-8344951__text", "type": "abstract", "text": [ "The role of conserved amino acids in substrate binding and discrimination by photolyase. \nDNA photolyases catalyze the light-dependent repair of pyrimidine dimers in DNA. We have utilized chemical modification and site-directed mutagenesis to probe the interactions involved in substrate recognition by the yeast photolyase Phr1. Lys517 was protected from reductive methylation in the presence of substrate, but not in its absence, and the specific and nonspecific association constants for substrate binding by Phr1 (Lys517-->Ala) were decreased 10-fold. These results establish a role for Lys517 in substrate binding. Mutations at Arg507, Lys463, and Trp387 reduced both the overall affinity for substrate and substrate discrimination. Sites of altered interactions in ES complexes were identified by methylation and ethylation interference techniques. Interaction with the base immediately 3' to the dimer was altered in the Phr1(Lys517-->Ala). DNA complex, whereas interactions with the phosphate and base immediately 5' to the dimer were reduced when Phr1(Arg507-->Ala) bound substrate. Multiple interactions 5' and 3' to the dimer were perturbed in complexes containing Phr1(Trp387-->Ala) or Phr1(Lys463-->Ala). In addition the quantum yield for dimer photolysis by Phr1(Trp387-->Ala) was reduced 3-fold. The locations of these mutations establish that a portion of the DNA binding domain is comprised of residues in the highly conserved carboxyl-terminal half of the enzyme.\n" ], "offsets": [ [ 0, 1482 ] ] } ]

[ { "id": "PMID-8344951_T1", "type": "Protein", "text": [ "Phr1" ], "offsets": [ [ 324, 328 ] ], "normalized": [] }, { "id": "PMID-8344951_T2", "type": "Protein", "text": [ "Phr1" ], "offsets": [ [ 512, 516 ] ], "normalized": [] }, { "id": "PMID-8344951_T3", "type": "Protein", "text": [ "Phr1" ], "offsets": [ [ 928, 932 ] ], "normalized": [] }, { "id": "PMID-8344951_T4", "type": "Protein", "text": [ "Phr1" ], "offsets": [ [ 1056, 1060 ] ], "normalized": [] }, { "id": "PMID-8344951_T5", "type": "Protein", "text": [ "Phr1" ], "offsets": [ [ 1176, 1180 ] ], "normalized": [] }, { "id": "PMID-8344951_T6", "type": "Protein", "text": [ "Phr1" ], "offsets": [ [ 1198, 1202 ] ], "normalized": [] }, { "id": "PMID-8344951_T7", "type": "Protein", "text": [ "Phr1" ], "offsets": [ [ 1272, 1276 ] ], "normalized": [] }, { "id": "PMID-8344951_T8", "type": "Entity", "text": [ "Lys517" ], "offsets": [ [ 330, 336 ] ], "normalized": [] } ]

[ { "id": "PMID-8344951_E1", "type": "Methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 366, 377 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8344951_T1" }, { "role": "Site", "ref_id": "PMID-8344951_T8" } ] } ]

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[ { "id": "PMID-8389305__text", "type": "abstract", "text": [ "An anatomical and biochemical study of the pituitary proopiomelanocortin systems in the polypteriform fish Calamoichthys calabaricus. \nImmunohistochemical and biochemical analyses were performed on the pituitary Proopiomelanocortin (POMC) systems of the polypteriform fish Calamoichthys calabaricus. Immunohistochemical staining of the pituitary revealed a clustering of ACTH immunopositive cells within the rostral pars distalis. alpha-Melanocyte stimulating hormone (alpha-MSH)-related and beta-endorphin-related immunoreactivity were found colocalized in epithelial cells of the pars intermedia. Biochemical analyses included Sephadex G-50 column chromatography, reversed-phase HPLC, and cation exchange chromatography. These analyses revealed the presence of immunoreactive forms of ACTH which stimulated glucocorticoid release when tested on isolated Bufo marinus adrenocortical tissue. Three forms of alpha-MSH were detected, and the major form had the same HPLC chromatographic properties as synthetic monoacetylated alpha-MSH. Finally, five forms of beta-endorphin were detected, and all of these forms were N-acetylated. Based on these observations, it appears that N-acetylation is a major post-translational processing event within the melanotropic cells of C. calabaricus. Given the position of Order Cladistia in the phylogeny of actinopterygian fish, it appears that N-acetylation of POMC-related products is an ancestral trait of osteichthyean fish.\n" ], "offsets": [ [ 0, 1465 ] ] } ]

[ { "id": "PMID-8389305_T1", "type": "Protein", "text": [ "proopiomelanocortin" ], "offsets": [ [ 53, 72 ] ], "normalized": [] }, { "id": "PMID-8389305_T2", "type": "Protein", "text": [ "pituitary Proopiomelanocortin" ], "offsets": [ [ 202, 231 ] ], "normalized": [] }, { "id": "PMID-8389305_T3", "type": "Protein", "text": [ "POMC" ], "offsets": [ [ 233, 237 ] ], "normalized": [] }, { "id": "PMID-8389305_T4", "type": "Protein", "text": [ "ACTH" ], "offsets": [ [ 371, 375 ] ], "normalized": [] }, { "id": "PMID-8389305_T5", "type": "Protein", "text": [ "alpha-Melanocyte stimulating hormone" ], "offsets": [ [ 431, 467 ] ], "normalized": [] }, { "id": "PMID-8389305_T6", "type": "Protein", "text": [ "alpha-MSH" ], "offsets": [ [ 469, 478 ] ], "normalized": [] }, { "id": "PMID-8389305_T7", "type": "Protein", "text": [ "beta-endorphin" ], "offsets": [ [ 492, 506 ] ], "normalized": [] }, { "id": "PMID-8389305_T8", "type": "Protein", "text": [ "ACTH" ], "offsets": [ [ 787, 791 ] ], "normalized": [] }, { "id": "PMID-8389305_T9", "type": "Protein", "text": [ "alpha-MSH" ], "offsets": [ [ 907, 916 ] ], "normalized": [] }, { "id": "PMID-8389305_T10", "type": "Protein", "text": [ "alpha-MSH" ], "offsets": [ [ 1024, 1033 ] ], "normalized": [] }, { "id": "PMID-8389305_T11", "type": "Protein", "text": [ "beta-endorphin" ], "offsets": [ [ 1058, 1072 ] ], "normalized": [] }, { "id": "PMID-8389305_T12", "type": "Protein", "text": [ "POMC" ], "offsets": [ [ 1398, 1402 ] ], "normalized": [] } ]

[ { "id": "PMID-8389305_E1", "type": "Acetylation", "trigger": { "text": [ "monoacetylated" ], "offsets": [ [ 1009, 1023 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8389305_T10" } ] }, { "id": "PMID-8389305_E2", "type": "Acetylation", "trigger": { "text": [ "N-acetylated" ], "offsets": [ [ 1116, 1128 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8389305_T11" } ] } ]

[ { "id": "PMID-8389305_1", "entity_ids": [ "PMID-8389305_T2", "PMID-8389305_T3" ] }, { "id": "PMID-8389305_2", "entity_ids": [ "PMID-8389305_T5", "PMID-8389305_T6" ] } ]

[]

[ { "id": "PMID-8413307__text", "type": "abstract", "text": [ "Agonist-induced phosphorylation of the luteinizing hormone/chorionic gonadotropin receptor expressed in a stably transfected cell line. \nMuch of the definitive work on G-protein-coupled receptor phosphorylation and its impact on receptor function has been performed with the catecholamine receptors. Evidence for receptor phosphorylation is lacking, however, for G-protein-coupled receptors that bind larger ligands, such as LH/CG. Using immunoprecipitation techniques and a clonal cell line stably transfected with the LH/CG receptor, we show here for the first time that exposure of cells to hCG induces phosphorylation of its cognate receptor. The hCG-induced increase in receptor phosphorylation requires receptor activation because it cannot be elicited with a hCG antagonist and is mediated at least in part by the cAMP second messenger system. This hypothesis is supported by the finding that the hCG-induced receptor phosphorylation is greatly reduced (but not abolished) in a cell line that overexpresses cAMP phosphodiesterase and that receptor phosphorylation can be induced by activation of endogenous cAMP synthesis with prostaglandin E2 or by addition of 8-bromo-cAMP. Last, we show that LH/CG receptor phosphorylation can be induced with a phorbol ester, but not with a calcium ionophore. We also examined a potential correlation between LH/CG receptor phosphorylation and uncoupling of the receptor from its effector. Although the phorbol ester-induced phosphorylation of the LH/CG receptor can be correlated with uncoupling, other experiments indicate that hCG-induced uncoupling of the LH/CG receptor can occur under conditions where the cAMP-mediated receptor phosphorylation is greatly reduced (or abolished).\n" ], "offsets": [ [ 0, 1730 ] ] } ]

[ { "id": "PMID-8413307_T1", "type": "Protein", "text": [ "luteinizing hormone/chorionic gonadotropin receptor" ], "offsets": [ [ 39, 90 ] ], "normalized": [] }, { "id": "PMID-8413307_T2", "type": "Protein", "text": [ "LH/CG receptor" ], "offsets": [ [ 520, 534 ] ], "normalized": [] }, { "id": "PMID-8413307_T3", "type": "Protein", "text": [ "LH/CG receptor" ], "offsets": [ [ 1202, 1216 ] ], "normalized": [] }, { "id": "PMID-8413307_T4", "type": "Protein", "text": [ "LH/CG receptor" ], "offsets": [ [ 1353, 1367 ] ], "normalized": [] }, { "id": "PMID-8413307_T5", "type": "Protein", "text": [ "LH/CG receptor" ], "offsets": [ [ 1492, 1506 ] ], "normalized": [] }, { "id": "PMID-8413307_T6", "type": "Protein", "text": [ "LH/CG receptor" ], "offsets": [ [ 1604, 1618 ] ], "normalized": [] } ]

[ { "id": "PMID-8413307_E1", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 16, 31 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8413307_T1" } ] }, { "id": "PMID-8413307_E2", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 606, 621 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8413307_T2" } ] }, { "id": "PMID-8413307_E3", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 684, 699 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8413307_T2" } ] }, { "id": "PMID-8413307_E4", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 925, 940 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8413307_T2" } ] }, { "id": "PMID-8413307_E5", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1055, 1070 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8413307_T2" } ] }, { "id": "PMID-8413307_E6", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1217, 1232 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8413307_T3" } ] }, { "id": "PMID-8413307_E7", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1368, 1383 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8413307_T4" } ] }, { "id": "PMID-8413307_E8", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1469, 1484 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8413307_T5" } ] }, { "id": "PMID-8413307_E9", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 1679, 1694 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8413307_T6" } ] } ]

[]

[]

[ { "id": "PMID-8428977__text", "type": "abstract", "text": [ "Mechanisms of collagen trimer formation. Construction and expression of a recombinant minigene in HeLa cells reveals a direct effect of prolyl hydroxylation on chain assembly of type XII collagen. \nCollagen types IX, XII, and XIV are characterized by the presence of a highly conserved region comprising the most C-terminal triple helical domain (COL1, approximately 100 residues/chain) and 2 cysteines separated by 4 amino acid residues at the junction between this COL1 domain and the C-terminal non-triple helical domain (NC1). In order to better understand the functions of this conserved domain, we have constructed a recombinant minigene, comprising the sequence coding for an unrelated signal peptide and for the COL1 and NC1 domains of type XII collagen. This construct was placed under the control of the cytomegalovirus promoter and transfected into HeLa cells. The cells expressed the transfected minigene and the secreted chain, called alpha 1 (mini XII), could be detected by immunotransfer with an anti-peptide antibody recognizing an epitope found in the NC1 domain. Under conditions preventing the hydroxylation of prolyl residues (absence of ascorbate or presence of alpha alpha'-dipyridyl), interchain disulfide bridges did not form, while in the presence of ascorbate, disulfide-bonded (alpha 1 (mini XII))3 molecules were secreted. The collagenous nature and triple helical conformation of the trimeric molecule were ascertained by the differential resistances of the COL1 and NC1 domains to trypsin and collagenase digestions, respectively. Our data demonstrate that the NC1 and COL1 domains of type XII collagen contain the information necessary for trimer formation and that, contrary to the fibrillar collagen types, posttranslational modification of the triple helical domain is essential for assembly and disulfide bonding of the chains.\n" ], "offsets": [ [ 0, 1865 ] ] } ]

[ { "id": "PMID-8428977_T1", "type": "Protein", "text": [ "type XII collagen" ], "offsets": [ [ 179, 196 ] ], "normalized": [] }, { "id": "PMID-8428977_T2", "type": "Protein", "text": [ "XII" ], "offsets": [ [ 218, 221 ] ], "normalized": [] }, { "id": "PMID-8428977_T3", "type": "Protein", "text": [ "XIV" ], "offsets": [ [ 227, 230 ] ], "normalized": [] }, { "id": "PMID-8428977_T4", "type": "Protein", "text": [ "type XII collagen" ], "offsets": [ [ 745, 762 ] ], "normalized": [] }, { "id": "PMID-8428977_T5", "type": "Protein", "text": [ "type XII collagen" ], "offsets": [ [ 1617, 1634 ] ], "normalized": [] }, { "id": "PMID-8428977_T6", "type": "Entity", "text": [ "prolyl" ], "offsets": [ [ 137, 143 ] ], "normalized": [] } ]

[ { "id": "PMID-8428977_E1", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 144, 157 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8428977_T1" }, { "role": "Site", "ref_id": "PMID-8428977_T6" } ] } ]

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[]

[ { "id": "PMID-8435081__text", "type": "abstract", "text": [ "Fulvic acid supplementation and selenium deficiency disturb the structural integrity of mouse skeletal tissue. An animal model to study the molecular defects of Kashin-Beck disease. \nHigh concentrations of fulvic acid and selenium deficiency are the main causative factors of Kashin-Beck disease, an endemic, chronic and degenerative osteoarticular disorder found in China. In the search for an animal model of this disease, mice were exposed to these pathogenetic conditions for two generations and the collagen types from skin, bone and cartilage were analysed. The growth of the treated mice was slightly retarded, and the rate of reproduction was lower in animals maintained on a fulvic acid-supplemented and/or selenium-deficient diet. Irregular bone formation was seen by radiography and morphometry. Biochemical analysis indicated that lysine residues in collagen I from bone and in collagen II from cartilage were overmodified. The values of Hyl/(Hyl+Lys) in bone collagen alpha 1(I) chains from treated mice were about 0.434-0.484, i.e. substantially higher than that of the control (0.277). The values of this parameter for collagen II were 0.482 for control and 0.546-0.566 for treated mice. The melting temperature of collagen I from bones of treated mice was 1 degrees C lower than that of control collagen, indicating decreased thermal stability. The breakage point of the tibiae of treated mice occurred at a lower preload force than for controls, suggesting that the overmodified and thermally less stable collagen molecules are causally related to a lower mechanical strength of bones.\n" ], "offsets": [ [ 0, 1604 ] ] } ]

[ { "id": "PMID-8435081_T1", "type": "Protein", "text": [ "collagen II" ], "offsets": [ [ 891, 902 ] ], "normalized": [] }, { "id": "PMID-8435081_T2", "type": "Protein", "text": [ "collagen alpha 1(I)" ], "offsets": [ [ 973, 992 ] ], "normalized": [] }, { "id": "PMID-8435081_T3", "type": "Protein", "text": [ "collagen II" ], "offsets": [ [ 1135, 1146 ] ], "normalized": [] } ]

[]

[]

[]

[ { "id": "PMID-8457787__text", "type": "abstract", "text": [ "Recombinant human interleukin 3 in clinical oncology. \nInterleukin 3 (IL-3) is a multipotent hematopoietic growth factor which became available as a recombinant (rh) growth factor for use in the clinic a few years ago. In dose-finding studies, this hematopoietic growth factor has been evaluated without and after standard chemotherapy. Stimulatory effects on leukocytes, neutrophils, eosinophils, monocytes, reticulocytes and platelets were observed in some studies. Chemotherapy postponement due to insufficient bone marrow recovery was less frequent when IL-3 was administered. There are some clinical studies available in which rhIL-3 is combined with rh granulocyte-macrophage colony-stimulating factor (GM-CSF). The results do not clearly suggest superiority of these combinations over rhGM-CSF alone, but this may be partly due to the time scheduling of the growth factors. Administration s.c. is not inferior to i.v. Side effects mainly consist of flu-like symptoms and headache. The role of rhIL-3 after high-dose chemotherapy and autologous bone marrow reinfusion is still questionable. The addition of rhIL-3 to rhGM-CSF both administered after chemotherapy may allow a very high yield of peripheral stem cells suitable for bone marrow reconstitution after high-dose chemotherapy. rhIL-3 can stimulate leukemia tumor cell proliferation in vitro as well as proliferation of solid tumor cell lines. It is not yet clear in which way rhIL-3 combined with chemotherapy will effect tumor response and patient survival. It is too early to define the exact place of rhIL-3 in oncology. Additional studies with rhIL-3 alone and in combination with other growth factors are needed.\n" ], "offsets": [ [ 0, 1684 ] ] } ]

[ { "id": "PMID-8457787_T1", "type": "Protein", "text": [ "interleukin 3" ], "offsets": [ [ 18, 31 ] ], "normalized": [] }, { "id": "PMID-8457787_T2", "type": "Protein", "text": [ "Interleukin 3" ], "offsets": [ [ 55, 68 ] ], "normalized": [] }, { "id": "PMID-8457787_T3", "type": "Protein", "text": [ "IL-3" ], "offsets": [ [ 70, 74 ] ], "normalized": [] }, { "id": "PMID-8457787_T4", "type": "Protein", "text": [ "hematopoietic growth factor" ], "offsets": [ [ 93, 120 ] ], "normalized": [] }, { "id": "PMID-8457787_T5", "type": "Protein", "text": [ "hematopoietic growth factor" ], "offsets": [ [ 249, 276 ] ], "normalized": [] }, { "id": "PMID-8457787_T6", "type": "Protein", "text": [ "IL-3" ], "offsets": [ [ 558, 562 ] ], "normalized": [] }, { "id": "PMID-8457787_T7", "type": "Protein", "text": [ "IL-3" ], "offsets": [ [ 634, 638 ] ], "normalized": [] }, { "id": "PMID-8457787_T8", "type": "Protein", "text": [ "granulocyte-macrophage colony-stimulating factor" ], "offsets": [ [ 659, 707 ] ], "normalized": [] }, { "id": "PMID-8457787_T9", "type": "Protein", "text": [ "GM-CSF" ], "offsets": [ [ 709, 715 ] ], "normalized": [] }, { "id": "PMID-8457787_T10", "type": "Protein", "text": [ "GM-CSF" ], "offsets": [ [ 794, 800 ] ], "normalized": [] }, { "id": "PMID-8457787_T11", "type": "Protein", "text": [ "IL-3" ], "offsets": [ [ 1003, 1007 ] ], "normalized": [] }, { "id": "PMID-8457787_T12", "type": "Protein", "text": [ "IL-3" ], "offsets": [ [ 1116, 1120 ] ], "normalized": [] }, { "id": "PMID-8457787_T13", "type": "Protein", "text": [ "GM-CSF" ], "offsets": [ [ 1126, 1132 ] ], "normalized": [] }, { "id": "PMID-8457787_T14", "type": "Protein", "text": [ "IL-3" ], "offsets": [ [ 1295, 1299 ] ], "normalized": [] }, { "id": "PMID-8457787_T15", "type": "Protein", "text": [ "IL-3" ], "offsets": [ [ 1444, 1448 ] ], "normalized": [] }, { "id": "PMID-8457787_T16", "type": "Protein", "text": [ "IL-3" ], "offsets": [ [ 1572, 1576 ] ], "normalized": [] }, { "id": "PMID-8457787_T17", "type": "Protein", "text": [ "IL-3" ], "offsets": [ [ 1616, 1620 ] ], "normalized": [] } ]

[]

[ { "id": "PMID-8457787_1", "entity_ids": [ "PMID-8457787_T2", "PMID-8457787_T3", "PMID-8457787_T4" ] }, { "id": "PMID-8457787_2", "entity_ids": [ "PMID-8457787_T8", "PMID-8457787_T9" ] } ]

[]

[ { "id": "PMID-8507209__text", "type": "abstract", "text": [ "In vitro translation of the human insulin proreceptor results in N-linked glycosylation without dimer formation. \nThe heterotetrameric configuration of the cell surface human insulin receptor (hINSR) is important for mediating insulin action. Investigation of proreceptor dimerization, the quaternary processing event during biogenesis, offers the potential to examine interactions between disulfide-linked receptor subunits. Thus, dimer formation of the proreceptor was examined in a cell-free system that utilized a coupled transcription and translation method with rabbit reticulocyte lysate. Translation products were labeled with [35S]methionine and identified by non-reducing SDS-polyacrylamide gel electrophoresis and autoradiography. In vitro synthesis in the presence of oxidized glutathione failed to demonstrate dimerization of the nascent proreceptor. Co-translational processing with the addition of microsomal membranes resulted in N-linked glycosylation of the proreceptor but without dimer formation. Thus, similar to that observed in vivo, insulin proreceptor dimerization does not appear to be a co-translational or early post-translational event.\n" ], "offsets": [ [ 0, 1166 ] ] } ]

[ { "id": "PMID-8507209_T1", "type": "Protein", "text": [ "insulin proreceptor" ], "offsets": [ [ 34, 53 ] ], "normalized": [] }, { "id": "PMID-8507209_T2", "type": "Protein", "text": [ "insulin receptor" ], "offsets": [ [ 175, 191 ] ], "normalized": [] }, { "id": "PMID-8507209_T3", "type": "Protein", "text": [ "INSR" ], "offsets": [ [ 194, 198 ] ], "normalized": [] }, { "id": "PMID-8507209_T4", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 227, 234 ] ], "normalized": [] }, { "id": "PMID-8507209_T5", "type": "Protein", "text": [ "insulin proreceptor" ], "offsets": [ [ 1057, 1076 ] ], "normalized": [] } ]

[ { "id": "PMID-8507209_E1", "type": "Glycosylation", "trigger": { "text": [ "N-linked glycosylation" ], "offsets": [ [ 65, 87 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8507209_T1" } ] } ]

[ { "id": "PMID-8507209_1", "entity_ids": [ "PMID-8507209_T2", "PMID-8507209_T3" ] } ]

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[ { "id": "PMID-8576151__text", "type": "abstract", "text": [ "Biochemical characterization of human collagenase-3. \nThe cDNA of a novel matrix metalloproteinase, collagenase-3 (MMP-13) has been isolated from a breast tumor library (Freije, J. M. P., Dicz-Itza, I., Balbin, M., Sanchez, L. M., Blasco, R., Tolivia, J., and Lopez-Otin, C. (1994) J. Biol. Chem. 269, 16766-16773), and a potential role in tumor progression has been proposed for this enzyme. In order to establish the possible role of collagenase-3 in connective tissue turnover, we have expressed and purified recombinant human procollagenase-3 and characterized the enzyme biochemically. The purified procollagenase-3 was shown to be glycosylated and displayed a M(r) of 60,000, the N-terminal sequence being LPLPSGGD, which is consistent with the cDNA-predicted sequence. The proenzyme was activated by p-aminophenylmercuric acetate or stromelysin, yielding an intermediate form of M(r) 50,000, which displayed the N-terminal sequence L58EVTGK. Further processing resulted in cleavage of the Glu84-Tyr85 peptide bond to the final active enzyme (M(r) 48,000). Trypsin activation of procollagenase-3 also generated a Tyr85 N terminus, but it was evident that the C-terminal domain was rapidly lost, and hence the collagenolytic activity diminished. Analysis of the substrate specificity of collagenase-3 revealed that soluble type II collagen was preferentially hydrolyzed, while the enzyme was 5 or 6 times less efficient at cleaving type I or III collagen. Fibrillar type I collagen was cleaved with comparable efficiency to the fibroblast and neutrophil collagenases (MMP-1 and MMP-8), respectively. Unlike these collagenases, gelatin and the peptide substrates Mea-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2 and Mca-Pro-Cha-Gly-Nva-His-Ala-Dpa-NH2 were efficiently hydrolyzed as well, as would be predicted from the similarities between the active site sequence of collagenase-3 (MMP-13) and the gelatinases A and B. Active collagenase-3 was inhibited in a 1:1 stoichiometric fashion by the tissue inhibitors of metalloproteinases, TIMP-1, TIMP-2, and TIMP-3. These results suggest that in vivo collagenase-3 could play a significant role in the turnover of connective tissue matrix constituents.\n" ], "offsets": [ [ 0, 2192 ] ] } ]

[ { "id": "PMID-8576151_T1", "type": "Protein", "text": [ "collagenase-3" ], "offsets": [ [ 38, 51 ] ], "normalized": [] }, { "id": "PMID-8576151_T2", "type": "Protein", "text": [ "collagenase-3" ], "offsets": [ [ 100, 113 ] ], "normalized": [] }, { "id": "PMID-8576151_T3", "type": "Protein", "text": [ "MMP-13" ], "offsets": [ [ 115, 121 ] ], "normalized": [] }, { "id": "PMID-8576151_T4", "type": "Protein", "text": [ "collagenase-3" ], "offsets": [ [ 436, 449 ] ], "normalized": [] }, { "id": "PMID-8576151_T5", "type": "Protein", "text": [ "procollagenase-3" ], "offsets": [ [ 530, 546 ] ], "normalized": [] }, { "id": "PMID-8576151_T6", "type": "Protein", "text": [ "procollagenase-3" ], "offsets": [ [ 604, 620 ] ], "normalized": [] }, { "id": "PMID-8576151_T7", "type": "Protein", "text": [ "procollagenase-3" ], "offsets": [ [ 1085, 1101 ] ], "normalized": [] }, { "id": "PMID-8576151_T8", "type": "Protein", "text": [ "collagenase-3" ], "offsets": [ [ 1292, 1305 ] ], "normalized": [] }, { "id": "PMID-8576151_T9", "type": "Protein", "text": [ "type II collagen" ], "offsets": [ [ 1328, 1344 ] ], "normalized": [] }, { "id": "PMID-8576151_T10", "type": "Protein", "text": [ "MMP-1" ], "offsets": [ [ 1573, 1578 ] ], "normalized": [] }, { "id": "PMID-8576151_T11", "type": "Protein", "text": [ "MMP-8" ], "offsets": [ [ 1583, 1588 ] ], "normalized": [] }, { "id": "PMID-8576151_T12", "type": "Protein", "text": [ "collagenase-3" ], "offsets": [ [ 1860, 1873 ] ], "normalized": [] }, { "id": "PMID-8576151_T13", "type": "Protein", "text": [ "MMP-13" ], "offsets": [ [ 1875, 1881 ] ], "normalized": [] }, { "id": "PMID-8576151_T14", "type": "Protein", "text": [ "gelatinases A" ], "offsets": [ [ 1891, 1904 ] ], "normalized": [] }, { "id": "PMID-8576151_T15", "type": "Protein", "text": [ "B" ], "offsets": [ [ 1909, 1910 ] ], "normalized": [] }, { "id": "PMID-8576151_T16", "type": "Protein", "text": [ "collagenase-3" ], "offsets": [ [ 1919, 1932 ] ], "normalized": [] }, { "id": "PMID-8576151_T17", "type": "Protein", "text": [ "TIMP-1" ], "offsets": [ [ 2027, 2033 ] ], "normalized": [] }, { "id": "PMID-8576151_T18", "type": "Protein", "text": [ "TIMP-2" ], "offsets": [ [ 2035, 2041 ] ], "normalized": [] }, { "id": "PMID-8576151_T19", "type": "Protein", "text": [ "TIMP-3" ], "offsets": [ [ 2047, 2053 ] ], "normalized": [] }, { "id": "PMID-8576151_T20", "type": "Protein", "text": [ "collagenase-3" ], "offsets": [ [ 2090, 2103 ] ], "normalized": [] } ]

[ { "id": "PMID-8576151_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 637, 649 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8576151_T6" } ] } ]

[ { "id": "PMID-8576151_1", "entity_ids": [ "PMID-8576151_T2", "PMID-8576151_T3" ] }, { "id": "PMID-8576151_2", "entity_ids": [ "PMID-8576151_T12", "PMID-8576151_T13" ] } ]

[]

[ { "id": "PMID-8620017__text", "type": "abstract", "text": [ "Preferential transfer to truncated oligosaccharides to the first sequon of yeast exoglucanase in Saccharomyces cerevisiae alg3 cells. \nIn addition to the exoglucanases (Exg) secreted into the culture medium by wild type cells, ExgIa and ExgIb, which have oligosaccharides attached to both potential N-glycosylation sites, Saccharomyces cerevisiae alg3 mutant secreted substantial amounts (35--44%) of underglycosylated and unglycosylated forms. Quantification of these forms indicated that no more than 78% of the available N-sites were occupied. About 50% of the transferred oligosaccharides were endo H sensitive, indicating that the lipid-linked precursor had completed its synthesis to Glc3-Man9-GlcNAc2. The other 50% remained endo H-resistant and, accordingly, it should be derived from the precursor oligosaccharide Man5-GlcNAc2 synthesized by this mutant. A closer analysis of forms that have received two oligosaccharides (ExgIb) showed that the first sequon was enriched in truncated residues, whereas the second one was enriched in regular counterparts. Similarly, analysis of the individual underglycosylated glycoforms indicated that 38% of the oligosaccharides attached to the second site were regular. This percentage dropped to 20% for glycoforms carrying the oligosaccharide in the first sequon. The preferential transfer of truncated oligosaccharides to the first glycosylation site seems to be a consequence of (1) the low percentage of truncated lipid linked oligosaccharides that receives the glucotriose unit, and (2) the effect of the glucotriose unit on the selection of N-sites to be glycosylated.\n" ], "offsets": [ [ 0, 1623 ] ] } ]

[ { "id": "PMID-8620017_T1", "type": "Protein", "text": [ "ExgI" ], "offsets": [ [ 227, 231 ] ], "normalized": [] }, { "id": "PMID-8620017_T2", "type": "Protein", "text": [ "ExgI" ], "offsets": [ [ 237, 241 ] ], "normalized": [] }, { "id": "PMID-8620017_T3", "type": "Protein", "text": [ "ExgI" ], "offsets": [ [ 932, 936 ] ], "normalized": [] }, { "id": "PMID-8620017_T4", "type": "Entity", "text": [ "oligosaccharides" ], "offsets": [ [ 255, 271 ] ], "normalized": [] }, { "id": "PMID-8620017_T6", "type": "Entity", "text": [ "N-glycosylation sites" ], "offsets": [ [ 299, 320 ] ], "normalized": [] }, { "id": "PMID-8620017_T8", "type": "Entity", "text": [ "oligosaccharides" ], "offsets": [ [ 914, 930 ] ], "normalized": [] }, { "id": "PMID-8620017_T10", "type": "Entity", "text": [ "truncated oligosaccharides" ], "offsets": [ [ 1342, 1368 ] ], "normalized": [] }, { "id": "PMID-8620017_T11", "type": "Entity", "text": [ "first glycosylation site" ], "offsets": [ [ 1376, 1400 ] ], "normalized": [] } ]

[ { "id": "PMID-8620017_E1", "type": "Glycosylation", "trigger": { "text": [ "attached" ], "offsets": [ [ 272, 280 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8620017_T1" }, { "role": "Site", "ref_id": "PMID-8620017_T6" }, { "role": "Sidechain", "ref_id": "PMID-8620017_T4" } ] }, { "id": "PMID-8620017_E2", "type": "Glycosylation", "trigger": { "text": [ "attached" ], "offsets": [ [ 272, 280 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8620017_T2" }, { "role": "Site", "ref_id": "PMID-8620017_T6" }, { "role": "Sidechain", "ref_id": "PMID-8620017_T4" } ] }, { "id": "PMID-8620017_E3", "type": "Glycosylation", "trigger": { "text": [ "received" ], "offsets": [ [ 901, 909 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8620017_T3" }, { "role": "Sidechain", "ref_id": "PMID-8620017_T8" } ] }, { "id": "PMID-8620017_E4", "type": "Glycosylation", "trigger": { "text": [ "transfer" ], "offsets": [ [ 1330, 1338 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8620017_T3" }, { "role": "Site", "ref_id": "PMID-8620017_T11" }, { "role": "Sidechain", "ref_id": "PMID-8620017_T10" } ] } ]

[]

[]

[ { "id": "PMID-8638660__text", "type": "abstract", "text": [ "Role of glucosamine synthesis in the stimulation of TGF-alpha gene transcription by glucose and EGF. \nTransforming growth factor-alpha (TGF-alpha) gene transcription is regulated by both epidermal growth factor (EGF) and glucose. Previous studies have suggested that the metabolism of glucose to glucosamine through the enzyme L-glutamine: D-fructose-6-phosphate amidotransferase (GFAT) plays a critical role in the glucose signaling. In this paper, we compared the role of GFAT in the glucose and EGF signals. We found that, although EGF stimulates GFAT mRNA accumulation in MDA-MB-468 cells, this effect of EGF occurred several hours after TGF-alpha transcription increased. MDA-MB-468 cells also exhibited a TGF-alpha transcriptional response to low concentrations of glucose. The TGF-alpha response to glucose but not EGF could be inhibited by a blocker of GFAT activity. Blockade of GFAT was confirmed by using Western blotting with the RL2 antibody, which recognizes an epitope on proteins containing N-acetylglucosamine. Exposure of cells to glucose increased the RL2 signal on several polypeptides, but this change could be blocked by inhibition of GFAT. These results support the notion that glucose stimulation of TGF-alpha expression requires GFAT, but EGF stimulation does not.\n" ], "offsets": [ [ 0, 1290 ] ] } ]

[ { "id": "PMID-8638660_T1", "type": "Protein", "text": [ "TGF-alpha" ], "offsets": [ [ 52, 61 ] ], "normalized": [] }, { "id": "PMID-8638660_T2", "type": "Protein", "text": [ "EGF" ], "offsets": [ [ 96, 99 ] ], "normalized": [] }, { "id": "PMID-8638660_T3", "type": "Protein", "text": [ "Transforming growth factor-alpha" ], "offsets": [ [ 102, 134 ] ], "normalized": [] }, { "id": "PMID-8638660_T4", "type": "Protein", "text": [ "TGF-alpha" ], "offsets": [ [ 136, 145 ] ], "normalized": [] }, { "id": "PMID-8638660_T5", "type": "Protein", "text": [ "epidermal growth factor" ], "offsets": [ [ 187, 210 ] ], "normalized": [] }, { "id": "PMID-8638660_T6", "type": "Protein", "text": [ "EGF" ], "offsets": [ [ 212, 215 ] ], "normalized": [] }, { "id": "PMID-8638660_T7", "type": "Protein", "text": [ "L-glutamine: D-fructose-6-phosphate amidotransferase" ], "offsets": [ [ 327, 379 ] ], "normalized": [] }, { "id": "PMID-8638660_T8", "type": "Protein", "text": [ "GFAT" ], "offsets": [ [ 381, 385 ] ], "normalized": [] }, { "id": "PMID-8638660_T9", "type": "Protein", "text": [ "GFAT" ], "offsets": [ [ 474, 478 ] ], "normalized": [] }, { "id": "PMID-8638660_T10", "type": "Protein", "text": [ "EGF" ], "offsets": [ [ 498, 501 ] ], "normalized": [] }, { "id": "PMID-8638660_T11", "type": "Protein", "text": [ "EGF" ], "offsets": [ [ 535, 538 ] ], "normalized": [] }, { "id": "PMID-8638660_T12", "type": "Protein", "text": [ "GFAT" ], "offsets": [ [ 550, 554 ] ], "normalized": [] }, { "id": "PMID-8638660_T13", "type": "Protein", "text": [ "EGF" ], "offsets": [ [ 609, 612 ] ], "normalized": [] }, { "id": "PMID-8638660_T14", "type": "Protein", "text": [ "TGF-alpha" ], "offsets": [ [ 642, 651 ] ], "normalized": [] }, { "id": "PMID-8638660_T15", "type": "Protein", "text": [ "TGF-alpha" ], "offsets": [ [ 711, 720 ] ], "normalized": [] }, { "id": "PMID-8638660_T16", "type": "Protein", "text": [ "TGF-alpha" ], "offsets": [ [ 784, 793 ] ], "normalized": [] }, { "id": "PMID-8638660_T17", "type": "Protein", "text": [ "EGF" ], "offsets": [ [ 822, 825 ] ], "normalized": [] }, { "id": "PMID-8638660_T18", "type": "Protein", "text": [ "GFAT" ], "offsets": [ [ 861, 865 ] ], "normalized": [] }, { "id": "PMID-8638660_T19", "type": "Protein", "text": [ "GFAT" ], "offsets": [ [ 888, 892 ] ], "normalized": [] }, { "id": "PMID-8638660_T20", "type": "Protein", "text": [ "GFAT" ], "offsets": [ [ 1157, 1161 ] ], "normalized": [] }, { "id": "PMID-8638660_T21", "type": "Protein", "text": [ "TGF-alpha" ], "offsets": [ [ 1224, 1233 ] ], "normalized": [] }, { "id": "PMID-8638660_T22", "type": "Protein", "text": [ "GFAT" ], "offsets": [ [ 1254, 1258 ] ], "normalized": [] }, { "id": "PMID-8638660_T23", "type": "Protein", "text": [ "EGF" ], "offsets": [ [ 1264, 1267 ] ], "normalized": [] } ]

[]

[ { "id": "PMID-8638660_1", "entity_ids": [ "PMID-8638660_T3", "PMID-8638660_T4" ] }, { "id": "PMID-8638660_2", "entity_ids": [ "PMID-8638660_T5", "PMID-8638660_T6" ] }, { "id": "PMID-8638660_3", "entity_ids": [ "PMID-8638660_T7", "PMID-8638660_T8" ] } ]

[]

[ { "id": "PMID-8719938__text", "type": "abstract", "text": [ "Transforming growth factor beta 1 influences lysyl hydroxylation of collagen I and reduces steady-state levels of lysyl hydroxylase mRNA in human osteoblast-like cells. \nTransforming growth factor beta 1 (TGF-beta 1) is an osteotropic growth factor that is found in substantial concentration in bone. The authors studied the influence of TGF-beta 1 on the modification of lysine residues of collagen I. The degree of lysyl hydroxylation and lysyl glycosylation of newly synthesized collagen as well as steady-state levels of mRNA for both lysyl hydroxylase and collagens I and III were determined in human osteoblast-like cells in vitro. In normal human osteoblasts lysyl hydroxylation was decreased by TGF-beta 1 particularly in the collagen alpha 2-chain. This effect was paralleled by an increase in lysyl residues, whereas glycosylation was not affected. The mRNA for lysyl hydroxylase was reduced by one-third under the influence of TGF-beta 1. Additionally, the mRNAs for both procollagen I alpha-chains were stimulated by TGF-beta 1, whereas pro alpha 1 (III)-mRNA showed a decrease. Changes in the local regulatory activity of TGF-beta 1 may play a role in matrix maturation such as collagen type production and lysyl hydroxylation, the latter being altered in various pathological conditions, e.g. in generalized osteopenia.\n" ], "offsets": [ [ 0, 1334 ] ] } ]

[ { "id": "PMID-8719938_T1", "type": "Protein", "text": [ "Transforming growth factor beta 1" ], "offsets": [ [ 0, 33 ] ], "normalized": [] }, { "id": "PMID-8719938_T2", "type": "Protein", "text": [ "Transforming growth factor beta 1" ], "offsets": [ [ 170, 203 ] ], "normalized": [] }, { "id": "PMID-8719938_T3", "type": "Protein", "text": [ "TGF-beta 1" ], "offsets": [ [ 205, 215 ] ], "normalized": [] }, { "id": "PMID-8719938_T4", "type": "Protein", "text": [ "TGF-beta 1" ], "offsets": [ [ 338, 348 ] ], "normalized": [] }, { "id": "PMID-8719938_T5", "type": "Protein", "text": [ "III" ], "offsets": [ [ 577, 580 ] ], "normalized": [] }, { "id": "PMID-8719938_T6", "type": "Protein", "text": [ "TGF-beta 1" ], "offsets": [ [ 703, 713 ] ], "normalized": [] }, { "id": "PMID-8719938_T7", "type": "Protein", "text": [ "TGF-beta 1" ], "offsets": [ [ 938, 948 ] ], "normalized": [] }, { "id": "PMID-8719938_T8", "type": "Protein", "text": [ "TGF-beta 1" ], "offsets": [ [ 1029, 1039 ] ], "normalized": [] }, { "id": "PMID-8719938_T9", "type": "Protein", "text": [ "alpha 1 (III)" ], "offsets": [ [ 1053, 1066 ] ], "normalized": [] }, { "id": "PMID-8719938_T10", "type": "Protein", "text": [ "TGF-beta 1" ], "offsets": [ [ 1135, 1145 ] ], "normalized": [] }, { "id": "PMID-8719938_T11", "type": "Entity", "text": [ "lysyl" ], "offsets": [ [ 417, 422 ] ], "normalized": [] }, { "id": "PMID-8719938_T13", "type": "Entity", "text": [ "lysyl" ], "offsets": [ [ 441, 446 ] ], "normalized": [] } ]

[ { "id": "PMID-8719938_E1", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 423, 436 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8719938_T5" }, { "role": "Site", "ref_id": "PMID-8719938_T11" } ] }, { "id": "PMID-8719938_E2", "type": "Glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 447, 460 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-8719938_T5" }, { "role": "Site", "ref_id": "PMID-8719938_T13" } ] } ]

[ { "id": "PMID-8719938_1", "entity_ids": [ "PMID-8719938_T2", "PMID-8719938_T3" ] } ]

[]

[ { "id": "PMID-8810299__text", "type": "abstract", "text": [ "The related molecular chaperones calnexin and calreticulin differentially associate with nascent T cell antigen receptor proteins within the endoplasmic reticulum. \nAssembly of the multisubunit T cell antigen receptor (TCR) complex is an intricate process requiring coordinated regulation of at least six different gene products (alpha, beta, gamma, delta, epsilon, and zeta) and the ordered pairing of partner chains within the endoplasmic reticulum (ER). To date, two proteins have been implicated as functioning as molecular chaperones in the assembly of nascent TCR proteins: calnexin, a resident ER transmembrane protein, which associates with all TCR components except zeta, and T cell receptor-associated protein, which selectively associates with CD3gammaepsilon pairs. In this study, we examined the association of calreticulin, a soluble protein with significant sequence homology to calnexin, with newly synthesized TCR proteins. Analogous to calnexin, processing of glycan chains by glucosidase enzymes was required for initial association of TCRalpha and -beta proteins with calreticulin; however, several major differences were noted regarding interaction of calnexin and calreticulin chaperones with TCR proteins. First, TCRalpha and -beta proteins showed prolonged association with calnexin molecules compared with calreticulin; interaction of TCRalpha proteins with calreticulin was particularly transient, with most calreticulin-TCRalpha protein complexes dissociating within 15 min of their initial assembly. Second, we found that, unlike calnexin, which associated with clonotypic TCRalpha and -beta proteins and invariant CD3delta and -epsilon polypeptides, calreticulin associated specifically with clonotypic TCRalpha and -beta proteins. These studies identify calreticulin as a molecular chaperone for nascent clonotypic TCRalpha and -beta proteins and demonstrate that calreticulin and calnexin differentially associate with newly synthesized TCR proteins within the ER.\n" ], "offsets": [ [ 0, 1996 ] ] } ]

[ { "id": "PMID-8810299_T1", "type": "Protein", "text": [ "calnexin" ], "offsets": [ [ 33, 41 ] ], "normalized": [] }, { "id": "PMID-8810299_T2", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 46, 58 ] ], "normalized": [] }, { "id": "PMID-8810299_T3", "type": "Protein", "text": [ "calnexin" ], "offsets": [ [ 580, 588 ] ], "normalized": [] }, { "id": "PMID-8810299_T4", "type": "Protein", "text": [ "CD3gamma" ], "offsets": [ [ 755, 763 ] ], "normalized": [] }, { "id": "PMID-8810299_T5", "type": "Protein", "text": [ "epsilon" ], "offsets": [ [ 763, 770 ] ], "normalized": [] }, { "id": "PMID-8810299_T6", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 824, 836 ] ], "normalized": [] }, { "id": "PMID-8810299_T7", "type": "Protein", "text": [ "calnexin" ], "offsets": [ [ 894, 902 ] ], "normalized": [] }, { "id": "PMID-8810299_T8", "type": "Protein", "text": [ "calnexin" ], "offsets": [ [ 954, 962 ] ], "normalized": [] }, { "id": "PMID-8810299_T9", "type": "Protein", "text": [ "TCRalpha" ], "offsets": [ [ 1055, 1063 ] ], "normalized": [] }, { "id": "PMID-8810299_T10", "type": "Protein", "text": [ "-beta" ], "offsets": [ [ 1068, 1073 ] ], "normalized": [] }, { "id": "PMID-8810299_T11", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 1088, 1100 ] ], "normalized": [] }, { "id": "PMID-8810299_T12", "type": "Protein", "text": [ "calnexin" ], "offsets": [ [ 1173, 1181 ] ], "normalized": [] }, { "id": "PMID-8810299_T13", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 1186, 1198 ] ], "normalized": [] }, { "id": "PMID-8810299_T14", "type": "Protein", "text": [ "TCRalpha" ], "offsets": [ [ 1236, 1244 ] ], "normalized": [] }, { "id": "PMID-8810299_T15", "type": "Protein", "text": [ "-beta" ], "offsets": [ [ 1249, 1254 ] ], "normalized": [] }, { "id": "PMID-8810299_T16", "type": "Protein", "text": [ "calnexin" ], "offsets": [ [ 1298, 1306 ] ], "normalized": [] }, { "id": "PMID-8810299_T17", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 1331, 1343 ] ], "normalized": [] }, { "id": "PMID-8810299_T18", "type": "Protein", "text": [ "TCRalpha" ], "offsets": [ [ 1360, 1368 ] ], "normalized": [] }, { "id": "PMID-8810299_T19", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 1383, 1395 ] ], "normalized": [] }, { "id": "PMID-8810299_T20", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 1434, 1446 ] ], "normalized": [] }, { "id": "PMID-8810299_T21", "type": "Protein", "text": [ "TCRalpha" ], "offsets": [ [ 1447, 1455 ] ], "normalized": [] }, { "id": "PMID-8810299_T22", "type": "Protein", "text": [ "calnexin" ], "offsets": [ [ 1558, 1566 ] ], "normalized": [] }, { "id": "PMID-8810299_T23", "type": "Protein", "text": [ "TCRalpha" ], "offsets": [ [ 1601, 1609 ] ], "normalized": [] }, { "id": "PMID-8810299_T24", "type": "Protein", "text": [ "-beta" ], "offsets": [ [ 1614, 1619 ] ], "normalized": [] }, { "id": "PMID-8810299_T25", "type": "Protein", "text": [ "CD3delta" ], "offsets": [ [ 1643, 1651 ] ], "normalized": [] }, { "id": "PMID-8810299_T26", "type": "Protein", "text": [ "-epsilon" ], "offsets": [ [ 1656, 1664 ] ], "normalized": [] }, { "id": "PMID-8810299_T27", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 1679, 1691 ] ], "normalized": [] }, { "id": "PMID-8810299_T28", "type": "Protein", "text": [ "TCRalpha" ], "offsets": [ [ 1732, 1740 ] ], "normalized": [] }, { "id": "PMID-8810299_T29", "type": "Protein", "text": [ "-beta" ], "offsets": [ [ 1745, 1750 ] ], "normalized": [] }, { "id": "PMID-8810299_T30", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 1784, 1796 ] ], "normalized": [] }, { "id": "PMID-8810299_T31", "type": "Protein", "text": [ "TCRalpha" ], "offsets": [ [ 1845, 1853 ] ], "normalized": [] }, { "id": "PMID-8810299_T32", "type": "Protein", "text": [ "-beta" ], "offsets": [ [ 1858, 1863 ] ], "normalized": [] }, { "id": "PMID-8810299_T33", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 1894, 1906 ] ], "normalized": [] }, { "id": "PMID-8810299_T34", "type": "Protein", "text": [ "calnexin" ], "offsets": [ [ 1911, 1919 ] ], "normalized": [] } ]

[]

[]

[]

[ { "id": "PMID-8823614__text", "type": "abstract", "text": [ "Molecular requirements for polyamines binding to the antispermine monoclonal antibody Spm8-2. \nThe monoclonal antispermine antibody Spm8-2 was obtained by immunizing mice with a thyroglobulin-spermine conjugate. The molecular requirements for polyamines binding to this antibody were investigated by ELISA binding and inhibition tests, using a variety of natural polyamines and synthetic polyamine analogs. Four major structural determinants are important for the binding of polyamines by the antibody: (1) terminal amino groups: N-alkylation of both terminal amino groups of the polyamines leads to an important drop in the affinity for the antibody; (2) number of methylene groups spacing the amino groups: the four carbon chains appear to present the optimum length since the antibody binds polyamines with repeats of the aminobutyl moiety more actively than their homologues with shorter or longer carbon chains; (3) number of amino groups: the affinity of Spm8-2 for free homologous polyamines varied in the following order: pentamines > tetramines > triamines > diamines, showing the importance of the number of positive charges of the polyamines in the antibody-antigen reaction; the importance of charges is further emphasized by the dependence of antibody binding on the ionic strength of the medium; (4) N-acylation of one terminal amino group: the antibody binds more actively N1-acetylspermidine than spermidine or spermine. The binding properties of Spm8-2 suggest the presence of two recognition sequences, one selective for N-acylaminopropyl moieties, the second for the aminobutyl moiety.\n" ], "offsets": [ [ 0, 1605 ] ] } ]

[ { "id": "PMID-8823614_T1", "type": "Protein", "text": [ "thyroglobulin" ], "offsets": [ [ 178, 191 ] ], "normalized": [] } ]

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[]

[ { "id": "PMID-8990186__text", "type": "abstract", "text": [ "Conversion of inactive glycosylation inhibiting factor to bioactive derivatives by modification of a SH group. \nEscherichia coli-derived recombinant human glycosylation inhibiting factor (rhGIF) contains three cysteine residues (Cys-57, -60, and -81). All SH groups in the cysteine residues are free, and the GIF molecule had no biologic activity. Carboxymethylation of the SH group of Cys-60 in the molecule resulted in the generation of bioactivity, although the activity of the carboxymethylated GIF was 10- to 20-fold less than that of suppressor T cell (Ts)-derived GIF. However, treatment of the inactive rhGIF with ethylmercurithiosalicylate or 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) resulted in the generation of derivatives whose bioactivity was comparable to that of the Ts-derived bioactive GIF. The activity of these derivatives was lost by treatment with DTT. Isolation and chemical analysis of the DTNB-treated GIF derivative revealed that binding the 5-thio-2-nitrobenzoic acid group with Cys-60 was responsible for the generation of the highly bioactive derivative. Inactive cytosolic GIF from mammalian cells could also be converted to bioactive derivative by treatment with the SH reagent, while Ts-derived bioactive GIF was inactivated by DTT. These results, together with an x-ray crystal structure of GIF molecules, strongly suggest that the generation of bioactivity of GIF in Ts cells is due to posttranslational modifications that result in conformational changes in the molecule.\n" ], "offsets": [ [ 0, 1509 ] ] } ]

[ { "id": "PMID-8990186_T1", "type": "Protein", "text": [ "glycosylation inhibiting factor" ], "offsets": [ [ 23, 54 ] ], "normalized": [] }, { "id": "PMID-8990186_T2", "type": "Protein", "text": [ "glycosylation inhibiting factor" ], "offsets": [ [ 155, 186 ] ], "normalized": [] }, { "id": "PMID-8990186_T3", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 190, 193 ] ], "normalized": [] }, { "id": "PMID-8990186_T4", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 309, 312 ] ], "normalized": [] }, { "id": "PMID-8990186_T5", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 499, 502 ] ], "normalized": [] }, { "id": "PMID-8990186_T6", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 571, 574 ] ], "normalized": [] }, { "id": "PMID-8990186_T7", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 613, 616 ] ], "normalized": [] }, { "id": "PMID-8990186_T8", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 806, 809 ] ], "normalized": [] }, { "id": "PMID-8990186_T9", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 929, 932 ] ], "normalized": [] }, { "id": "PMID-8990186_T10", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 1105, 1108 ] ], "normalized": [] }, { "id": "PMID-8990186_T11", "type": "Protein", "text": [ "SH" ], "offsets": [ [ 1200, 1202 ] ], "normalized": [] }, { "id": "PMID-8990186_T12", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 1239, 1242 ] ], "normalized": [] }, { "id": "PMID-8990186_T13", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 1326, 1329 ] ], "normalized": [] }, { "id": "PMID-8990186_T14", "type": "Protein", "text": [ "GIF" ], "offsets": [ [ 1396, 1399 ] ], "normalized": [] } ]

[]

[ { "id": "PMID-8990186_1", "entity_ids": [ "PMID-8990186_T2", "PMID-8990186_T3" ] } ]

[]

[ { "id": "PMID-9006042__text", "type": "abstract", "text": [ "Reconstitution of trimethylamine-dependent coenzyme M methylation with the trimethylamine corrinoid protein and the isozymes of methyltransferase II from Methanosarcina barkeri. \nReconstitution of trimethylamine-dependent coenzyme M (CoM) methylation was achieved with three purified polypeptides. Two of these polypeptides copurified as a trimethylamine methyl transfer (TMA-MT) activity detected by stimulation of the TMA:CoM methyl transfer reaction in cell extracts. The purified TMA-MT fraction stimulated the rate of methyl-CoM formation sevenfold, up to 1.7 micromol/min/mg of TMA-MT protein. The TMA-MT polypeptides had molecular masses of 52 and 26 kDa. Gel permeation of the TMA-MT fraction demonstrated that the 52-kDa polypeptide eluted with an apparent molecular mass of 280 kDa. The 26-kDa protein eluted primarily as a monomer, but some 26-kDa polypeptides also eluted with the 280-kDa peak, indicating that the two proteins weakly associate. The two polypeptides could be completely separated using gel permeation in the presence of sodium dodecyl sulfate. The corrinoid remained associated with the 26-kDa polypeptide at a molar ratio of 1.1 corrin/26-kDa polypeptide. This polypeptide was therefore designated the TMA corrinoid protein, or TCP. The TMA-MT polypeptides, when supplemented with purified methylcorrinoid:CoM methyltransferase (MT2), could effect the demethylation of TMA with the subsequent methylation of CoM and the production of dimethylamine at specific activities of up to 600 nmol/min/mg of TMA-MT protein. Neither dimethylamine nor monomethylamine served as the substrate, and the activity required Ti(III) citrate and methyl viologen. TMA-MT could interact with either isozyme of MT2 but had the greatest affinity for the A isozyme. These results suggest that TCP is uniquely involved in TMA-dependent methanogenesis, that this corrinoid protein is methylated by the substrate and demethylated by either isozyme of MT2, and that the predominant isozyme of MT2 found in TMA-grown cells is the favored participant in the TMA:CoM methyl transfer reaction.\n" ], "offsets": [ [ 0, 2093 ] ] } ]

[ { "id": "PMID-9006042_T1", "type": "Protein", "text": [ "trimethylamine corrinoid protein" ], "offsets": [ [ 75, 107 ] ], "normalized": [] }, { "id": "PMID-9006042_T2", "type": "Protein", "text": [ "TMA corrinoid protein" ], "offsets": [ [ 1232, 1253 ] ], "normalized": [] }, { "id": "PMID-9006042_T3", "type": "Protein", "text": [ "TCP" ], "offsets": [ [ 1258, 1261 ] ], "normalized": [] }, { "id": "PMID-9006042_T4", "type": "Protein", "text": [ "methylcorrinoid:CoM methyltransferase" ], "offsets": [ [ 1320, 1357 ] ], "normalized": [] }, { "id": "PMID-9006042_T5", "type": "Protein", "text": [ "MT2" ], "offsets": [ [ 1359, 1362 ] ], "normalized": [] }, { "id": "PMID-9006042_T6", "type": "Protein", "text": [ "MT2" ], "offsets": [ [ 1720, 1723 ] ], "normalized": [] }, { "id": "PMID-9006042_T7", "type": "Protein", "text": [ "TCP" ], "offsets": [ [ 1800, 1803 ] ], "normalized": [] }, { "id": "PMID-9006042_T8", "type": "Protein", "text": [ "MT2" ], "offsets": [ [ 1955, 1958 ] ], "normalized": [] }, { "id": "PMID-9006042_T9", "type": "Protein", "text": [ "MT2" ], "offsets": [ [ 1996, 1999 ] ], "normalized": [] } ]

[]

[ { "id": "PMID-9006042_1", "entity_ids": [ "PMID-9006042_T2", "PMID-9006042_T3" ] }, { "id": "PMID-9006042_2", "entity_ids": [ "PMID-9006042_T4", "PMID-9006042_T5" ] } ]

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[ { "id": "PMID-9007280__text", "type": "abstract", "text": [ "Analysis of the binding specificities of oligomannoside-binding proteins using methylated monosaccharides. \nThe binding specificities of the closely related lectins from Canavalia ensiformis and Dioclea grandiflora were examined using specifically O-alkylated mono- and disaccharides. Both lectins accept any substitution at the monosaccharide C2 hydroxyl group. The binding energy of C2-alkylated ligands-concanavalin A complexes increases by 1 kcal mol-1 for the C2-O-ethyl ligand, while the binding energies of the corresponding complexes with the Dioclea lectin are identical. Both lectins accept methyl, but not ethyl, substitution of the C3 hydroxyl, in contrast to earlier reports. The results are interpreted in terms of existing models of the concanavalin A binding site. While the results are consistent with a model of the concanavalin A extended binding site that places the non-reducing terminus of all disaccharides in the monosaccharide binding site, they point to the dangers of interpreting the binding behavior of unnatural saccharide ligands on the basis of crystallographic data obtained with native ligands.\n" ], "offsets": [ [ 0, 1129 ] ] } ]

[ { "id": "PMID-9007280_T1", "type": "Protein", "text": [ "concanavalin A" ], "offsets": [ [ 406, 420 ] ], "normalized": [] }, { "id": "PMID-9007280_T2", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 559, 565 ] ], "normalized": [] }, { "id": "PMID-9007280_T3", "type": "Protein", "text": [ "concanavalin A" ], "offsets": [ [ 752, 766 ] ], "normalized": [] }, { "id": "PMID-9007280_T4", "type": "Protein", "text": [ "concanavalin A" ], "offsets": [ [ 834, 848 ] ], "normalized": [] } ]

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[]

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[ { "id": "PMID-9042224__text", "type": "abstract", "text": [ "Benzyl-alpha-GalNAc inhibits sialylation of O-glycosidic sugar chains on CD44 and enhances experimental metastatic capacity in B16BL6 melanoma cells. \nWe examined the effect of benzyl-alpha-N-acetylgalactosamine (benzyl-alpha-GalNAc), which specifically inhibits the synthesis of O-linked oligosaccharides, on the expression of the peanut agglutinin (PNA)-binding sugar chains (Gal beta 1-3GalNAc) of CD44 and on its experimental metastatic ability in B16BL6 melanoma. Benzyl-alpha-GalNAc increased the PNA-binding, but not Concanavalin A (Con A), wheat germ agglutinin (WGA), and leukoagglutinating phytohemaagglutinin (L-PHA)-binding to the cell surface. Benzyl-alpha-GalNAc markedly increased the PNA-binding to CD44 by decreasing the sialylation of these sugar chains. The experimental metastatic ability of B16BL6 cells was enhanced in association with this modulation of the sugar chains. These findings suggested that unsialylated Gal beta 1-3GalNAc sugar chains on the cell surface and/or CD44 are involved in the metastatic process of B16BL6 melanoma cells. On the other hand, the known functions of CD44, such as adhesion to hyaluronate, fibronectin, collagen, and endothelial cells, as well as homotypic aggregation, were not affected by benzyl-alpha-GalNAc regardless of the enhancement of metastatic ability induced by this glycosylation inhibitor. CD44 might have other metastasis related functions that remain to be elucidated.\n" ], "offsets": [ [ 0, 1443 ] ] } ]

[ { "id": "PMID-9042224_T1", "type": "Protein", "text": [ "CD44" ], "offsets": [ [ 73, 77 ] ], "normalized": [] }, { "id": "PMID-9042224_T2", "type": "Protein", "text": [ "agglutinin" ], "offsets": [ [ 339, 349 ] ], "normalized": [] }, { "id": "PMID-9042224_T3", "type": "Protein", "text": [ "PNA" ], "offsets": [ [ 351, 354 ] ], "normalized": [] }, { "id": "PMID-9042224_T4", "type": "Protein", "text": [ "CD44" ], "offsets": [ [ 401, 405 ] ], "normalized": [] }, { "id": "PMID-9042224_T5", "type": "Protein", "text": [ "PNA" ], "offsets": [ [ 503, 506 ] ], "normalized": [] }, { "id": "PMID-9042224_T6", "type": "Protein", "text": [ "Concanavalin A" ], "offsets": [ [ 524, 538 ] ], "normalized": [] }, { "id": "PMID-9042224_T7", "type": "Protein", "text": [ "Con A" ], "offsets": [ [ 540, 545 ] ], "normalized": [] }, { "id": "PMID-9042224_T8", "type": "Protein", "text": [ "PNA" ], "offsets": [ [ 700, 703 ] ], "normalized": [] }, { "id": "PMID-9042224_T9", "type": "Protein", "text": [ "CD44" ], "offsets": [ [ 715, 719 ] ], "normalized": [] }, { "id": "PMID-9042224_T10", "type": "Protein", "text": [ "CD44" ], "offsets": [ [ 997, 1001 ] ], "normalized": [] }, { "id": "PMID-9042224_T11", "type": "Protein", "text": [ "CD44" ], "offsets": [ [ 1109, 1113 ] ], "normalized": [] }, { "id": "PMID-9042224_T12", "type": "Protein", "text": [ "fibronectin" ], "offsets": [ [ 1148, 1159 ] ], "normalized": [] }, { "id": "PMID-9042224_T13", "type": "Protein", "text": [ "CD44" ], "offsets": [ [ 1362, 1366 ] ], "normalized": [] } ]

[ { "id": "PMID-9042224_E1", "type": "Glycosylation", "trigger": { "text": [ "O-glycosidic" ], "offsets": [ [ 44, 56 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9042224_T1" } ] } ]

[ { "id": "PMID-9042224_1", "entity_ids": [ "PMID-9042224_T2", "PMID-9042224_T3" ] }, { "id": "PMID-9042224_2", "entity_ids": [ "PMID-9042224_T6", "PMID-9042224_T7" ] } ]

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[ { "id": "PMID-9073553__text", "type": "abstract", "text": [ "Deglycosylation of serum vitamin D3-binding protein by alpha-N-acetylgalactosaminidase detected in the plasma of patients with systemic lupus erythematosus. \nA serum glycoprotein, Gc protein (vitamin D3-binding protein), can be converted by beta-galactosidase of B cells and sialidase of T cells to a potent macrophage-activating factor (MAF), a protein with N-acetylgalactosamine as the remaining sugar moiety. Thus, Gc protein is the precursor for MAF. Treatment of Gc protein with immobilized beta-galactosidase and sialidase generates a remarkably high titered macrophage-activating factor (GcMAF). When peripheral blood monocytes/ macrophages (designated macrophages) of 33 systemic lupus erythematosus patients were incubated with GcMAF (100 pg/ml), the macrophages of all patients were activated as determined by superoxide generation. However, the precursor activity of patient plasma Gc protein was lost or reduced in these patients. Loss of the precursor activity was the result of deglycosylation of plasma Gc protein by alpha-N-acetylgalactosaminidase activity found in the patient plasma. Levels of plasma alpha-N-acetylgalactosaminidase activity in individual patients had an inverse correlation with the MAF precursor activity of their plasma Gc protein. Deglycosylated Gc protein cannot be converted to macro-phage-activating factor. The resulting defect in macro-phage activation may lead to an inability to clear pathogenic immune complexes. Thus, elevated plasma alpha-N-acetylgalactosaminidase activity resulting in the loss of MAF precursor activity and reduced macro-phage activity may play a role in the pathogenesis of systemic lupus erythematosus.\n" ], "offsets": [ [ 0, 1673 ] ] } ]

[ { "id": "PMID-9073553_T1", "type": "Protein", "text": [ "vitamin D3-binding protein" ], "offsets": [ [ 25, 51 ] ], "normalized": [] }, { "id": "PMID-9073553_T2", "type": "Protein", "text": [ "alpha-N-acetylgalactosaminidase" ], "offsets": [ [ 55, 86 ] ], "normalized": [] }, { "id": "PMID-9073553_T3", "type": "Protein", "text": [ "Gc" ], "offsets": [ [ 180, 182 ] ], "normalized": [] }, { "id": "PMID-9073553_T4", "type": "Protein", "text": [ "vitamin D3-binding protein" ], "offsets": [ [ 192, 218 ] ], "normalized": [] }, { "id": "PMID-9073553_T5", "type": "Protein", "text": [ "beta-galactosidase" ], "offsets": [ [ 241, 259 ] ], "normalized": [] }, { "id": "PMID-9073553_T6", "type": "Protein", "text": [ "Gc" ], "offsets": [ [ 418, 420 ] ], "normalized": [] }, { "id": "PMID-9073553_T7", "type": "Protein", "text": [ "Gc" ], "offsets": [ [ 468, 470 ] ], "normalized": [] }, { "id": "PMID-9073553_T8", "type": "Protein", "text": [ "beta-galactosidase" ], "offsets": [ [ 496, 514 ] ], "normalized": [] }, { "id": "PMID-9073553_T9", "type": "Protein", "text": [ "Gc" ], "offsets": [ [ 595, 597 ] ], "normalized": [] }, { "id": "PMID-9073553_T10", "type": "Protein", "text": [ "Gc" ], "offsets": [ [ 737, 739 ] ], "normalized": [] }, { "id": "PMID-9073553_T11", "type": "Protein", "text": [ "Gc" ], "offsets": [ [ 893, 895 ] ], "normalized": [] }, { "id": "PMID-9073553_T12", "type": "Protein", "text": [ "Gc" ], "offsets": [ [ 1018, 1020 ] ], "normalized": [] }, { "id": "PMID-9073553_T13", "type": "Protein", "text": [ "alpha-N-acetylgalactosaminidase" ], "offsets": [ [ 1032, 1063 ] ], "normalized": [] }, { "id": "PMID-9073553_T14", "type": "Protein", "text": [ "alpha-N-acetylgalactosaminidase" ], "offsets": [ [ 1119, 1150 ] ], "normalized": [] }, { "id": "PMID-9073553_T15", "type": "Protein", "text": [ "Gc" ], "offsets": [ [ 1258, 1260 ] ], "normalized": [] }, { "id": "PMID-9073553_T16", "type": "Protein", "text": [ "Gc" ], "offsets": [ [ 1285, 1287 ] ], "normalized": [] }, { "id": "PMID-9073553_T17", "type": "Protein", "text": [ "alpha-N-acetylgalactosaminidase" ], "offsets": [ [ 1482, 1513 ] ], "normalized": [] } ]

[ { "id": "PMID-9073553_E1", "type": "Deglycosylation", "trigger": { "text": [ "Deglycosylation" ], "offsets": [ [ 0, 15 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9073553_T1" } ] }, { "id": "PMID-9073553_E2", "type": "Catalysis", "trigger": { "text": [ "Deglycosylation" ], "offsets": [ [ 0, 15 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9073553_E1" }, { "role": "Cause", "ref_id": "PMID-9073553_T2" } ] }, { "id": "PMID-9073553_E3", "type": "Deglycosylation", "trigger": { "text": [ "deglycosylation" ], "offsets": [ [ 992, 1007 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9073553_T12" } ] }, { "id": "PMID-9073553_E4", "type": "Catalysis", "trigger": { "text": [ "deglycosylation" ], "offsets": [ [ 992, 1007 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9073553_E3" }, { "role": "Cause", "ref_id": "PMID-9073553_T13" } ] }, { "id": "PMID-9073553_E5", "type": "Deglycosylation", "trigger": { "text": [ "Deglycosylated" ], "offsets": [ [ 1270, 1284 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9073553_T16" } ] } ]

[ { "id": "PMID-9073553_1", "entity_ids": [ "PMID-9073553_T3", "PMID-9073553_T4" ] } ]

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[ { "id": "PMID-9098857__text", "type": "abstract", "text": [ "Regulatory adaptation of isoprenoid biosynthesis and the LDL receptor pathway in fibroblasts from patients with mevalonate kinase deficiency. \nIn a search for the pathophysiologic mechanisms, we estimated isoprenoid synthesis and concentration, cellular growth, and the activity of the LDL receptor pathway in fibroblasts from patients with mevalonate kinase deficiency (MKD), a severe multisystemic disorder of cholesterol and non-sterol isoprenoid biosynthesis. In response to different concentrations of LDL and non-lipoprotein-bound cholesterol, MKD cells partially counteracted their enzyme defect by increased activities of 3-hydroxy-3-methylglutaryl (HMG)-CoA reductase (results from earlier studies) and the LDL receptor pathway, responses similar to the pharmacologic effects seen upon administration of HMG-CoA reductase inhibitors. Rates of N-linked protein glycosylation, estimated as the amount of [14C]galactose-labeled macromolecules secreted into cell culture medium, were significantly decreased in MKD fibroblasts in comparison with control cells which may indicate alterations in the dolichol or dolichol phosphate pool. In response to exogenous cholesterol, the major feedback inhibitor of isoprenoid biosynthesis, growth velocities of MKD fibroblasts declined in comparison with control cells, further suggesting an impairment of non-sterol isoprenoid biosynthesis in MKD. Our results suggest an imbalance in the multilevel regulation of the biosynthesis of cholesterol and non-sterol isoprenoids in MKD, representing an additional causative factor responsible for the pre- and postnatal pathology of MKD.\n" ], "offsets": [ [ 0, 1627 ] ] } ]

[ { "id": "PMID-9098857_T1", "type": "Protein", "text": [ "LDL receptor" ], "offsets": [ [ 57, 69 ] ], "normalized": [] }, { "id": "PMID-9098857_T2", "type": "Protein", "text": [ "mevalonate kinase" ], "offsets": [ [ 112, 129 ] ], "normalized": [] }, { "id": "PMID-9098857_T3", "type": "Protein", "text": [ "LDL receptor" ], "offsets": [ [ 286, 298 ] ], "normalized": [] }, { "id": "PMID-9098857_T4", "type": "Protein", "text": [ "mevalonate kinase" ], "offsets": [ [ 341, 358 ] ], "normalized": [] }, { "id": "PMID-9098857_T5", "type": "Protein", "text": [ "3-hydroxy-3-methylglutaryl (HMG)-CoA reductase" ], "offsets": [ [ 630, 676 ] ], "normalized": [] }, { "id": "PMID-9098857_T6", "type": "Protein", "text": [ "LDL receptor" ], "offsets": [ [ 716, 728 ] ], "normalized": [] }, { "id": "PMID-9098857_T7", "type": "Protein", "text": [ "HMG-CoA reductase" ], "offsets": [ [ 813, 830 ] ], "normalized": [] } ]

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[ { "id": "PMID-9125144__text", "type": "abstract", "text": [ "Protein glycosylation in a heat-resistant rat fibroblast cell model expressing human HSP70. \nThermotolerance and heat resistance are frequently associated with elevated levels of heat shock proteins (HSPs). Elevated heat resistance is also found to be associated with the overexpression of high levels of HSP70, as seen in M21 cells, derived from the Rat-1 line. In the present study, we report that M21 cells also feature an increase in general protein glycosylation and specific expression of the stress glycoprotein, GP62, both of which correlate with cellular heat resistance. The expression of GP50, a major stress glycoprotein in cell lines such as CHO, however, did not correlate with cellular heat resistance in M21 cells. Protein glycosylation that occurs during acute heat stress (\"prompt\" glycosylation) was associated with the glycosylation of a major \"prompt\" stress glycoprotein, P-SG64 (M(r) of 64,000), that was identified by immunoblotting as a glycosylated form of calreticulin. The higher level of protein glycosylation in M21 cells correlated well with increased D-[2-3H]mannose incorporation into precursor pools of dolichyl phosphomannose and dolichyl pyrophosphoryl oligosaccharides and into glycoproteins. Thus, heat resistance in M21 cells is associated not only with expression of high levels of HSP70, but also with a concomitant increase in protein glycosylation. These data support the hypothesis that stress-induced protein glycosylation is a component of cellular stress response, either in association with HSPs or as an independent mechanism.\n" ], "offsets": [ [ 0, 1576 ] ] } ]

[ { "id": "PMID-9125144_T1", "type": "Protein", "text": [ "HSP70" ], "offsets": [ [ 85, 90 ] ], "normalized": [] }, { "id": "PMID-9125144_T2", "type": "Protein", "text": [ "HSP70" ], "offsets": [ [ 305, 310 ] ], "normalized": [] }, { "id": "PMID-9125144_T3", "type": "Protein", "text": [ "GP62" ], "offsets": [ [ 520, 524 ] ], "normalized": [] }, { "id": "PMID-9125144_T4", "type": "Protein", "text": [ "GP50" ], "offsets": [ [ 599, 603 ] ], "normalized": [] }, { "id": "PMID-9125144_T5", "type": "Protein", "text": [ "P-SG64" ], "offsets": [ [ 894, 900 ] ], "normalized": [] }, { "id": "PMID-9125144_T6", "type": "Protein", "text": [ "calreticulin" ], "offsets": [ [ 983, 995 ] ], "normalized": [] }, { "id": "PMID-9125144_T7", "type": "Protein", "text": [ "HSP70" ], "offsets": [ [ 1322, 1327 ] ], "normalized": [] } ]

[ { "id": "PMID-9125144_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 962, 974 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9125144_T5" } ] } ]

[ { "id": "PMID-9125144_1", "entity_ids": [ "PMID-9125144_T5", "PMID-9125144_T6" ] } ]

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[ { "id": "PMID-9139867__text", "type": "abstract", "text": [ "The E-cadherin gene is silenced by CpG methylation in human hepatocellular carcinomas. \nOur study was designed to clarify the significance of silencing the E-cadherin gene, which is located on 16q22.1, due to CpG methylation during hepatocarcinogenesis. The CpG methylation status of primary hepatocellular carcinomas (HCCs) and corresponding liver tissues showing chronic hepatitis or cirrhosis, which are widely considered to be precancerous conditions, were assessed by digesting DNA with methylation-sensitive and non-sensitive restriction enzymes. CpG methylation around the promoter region of the E-cadherin gene was detected in 46% of liver tissues showing chronic hepatitis or cirrhosis and 67% of HCCs examined. Immunohistochemical examination revealed reduced E-cadherin expression in 59% of HCCs examined. CpG methylation around the promoter region correlated significantly with reduced E-cadherin expression in HCCs (p < 0.05). CpG methylation around the promoter region, which increases during the progression from a precancerous condition to HCC, may participate in hepatocarcinogenesis through reduction of E-cadherin expression, resulting in loss of intercellular adhesiveness and destruction of tissue morphology.\n" ], "offsets": [ [ 0, 1231 ] ] } ]

[ { "id": "PMID-9139867_T1", "type": "Protein", "text": [ "E-cadherin" ], "offsets": [ [ 4, 14 ] ], "normalized": [] }, { "id": "PMID-9139867_T2", "type": "Protein", "text": [ "E-cadherin" ], "offsets": [ [ 156, 166 ] ], "normalized": [] }, { "id": "PMID-9139867_T3", "type": "Protein", "text": [ "E-cadherin" ], "offsets": [ [ 603, 613 ] ], "normalized": [] }, { "id": "PMID-9139867_T4", "type": "Protein", "text": [ "E-cadherin" ], "offsets": [ [ 770, 780 ] ], "normalized": [] }, { "id": "PMID-9139867_T5", "type": "Protein", "text": [ "E-cadherin" ], "offsets": [ [ 898, 908 ] ], "normalized": [] }, { "id": "PMID-9139867_T6", "type": "Protein", "text": [ "E-cadherin" ], "offsets": [ [ 1122, 1132 ] ], "normalized": [] }, { "id": "PMID-9139867_T7", "type": "Entity", "text": [ "CpG" ], "offsets": [ [ 35, 38 ] ], "normalized": [] }, { "id": "PMID-9139867_T9", "type": "Entity", "text": [ "CpG" ], "offsets": [ [ 209, 212 ] ], "normalized": [] }, { "id": "PMID-9139867_T11", "type": "Entity", "text": [ "CpG" ], "offsets": [ [ 553, 556 ] ], "normalized": [] }, { "id": "PMID-9139867_T13", "type": "Entity", "text": [ "CpG" ], "offsets": [ [ 817, 820 ] ], "normalized": [] }, { "id": "PMID-9139867_T15", "type": "Entity", "text": [ "CpG" ], "offsets": [ [ 940, 943 ] ], "normalized": [] } ]

[ { "id": "PMID-9139867_E1", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 39, 50 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9139867_T1" }, { "role": "Site", "ref_id": "PMID-9139867_T7" } ] }, { "id": "PMID-9139867_E2", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 213, 224 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9139867_T2" }, { "role": "Site", "ref_id": "PMID-9139867_T9" } ] }, { "id": "PMID-9139867_E3", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 557, 568 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9139867_T3" }, { "role": "Site", "ref_id": "PMID-9139867_T11" } ] }, { "id": "PMID-9139867_E4", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 821, 832 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9139867_T5" }, { "role": "Site", "ref_id": "PMID-9139867_T13" } ] }, { "id": "PMID-9139867_E5", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 944, 955 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9139867_T6" }, { "role": "Site", "ref_id": "PMID-9139867_T15" } ] } ]

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[ { "id": "PMID-9145315__text", "type": "abstract", "text": [ "Characterization of the ETSA-21 antigen, a glycosylphosphatidyl-inositol anchor glycoprotein identified in breast cancer cells using monoclonal antibody B21. \nMab B21 is a monoclonal antibody (Mab) that recognizes an epithelial tumor surface antigen (ETSA-B21) from diverse human tumor cell lines including breast, ovary, uterus, and their cognate carcinoma tissues. A lower reactivity has been observed in normal breast tissue and benign hyperplesia. In this study, the characteristics of the ETSA-B21 antigen have been examined in greater detail in the MCF-7, SK-BR-3, and MDA-MB-453 breast cancer cell lines. Treatment with phosphatidylinositol-phospholipase C, but no neuraminidase were found to partially remove the ETSA-B21 signal from the cell surface as revealed by immunofluorescence microscopy. Inhibition of the N-glycosylation pathway by tunicamycin resulted in a decreased ETSA-B21 signal on the cell membrane. In addition, the antigen-antibody complex was internalized in breast cancer cells as demonstrated by an acidic was internalization assay evaluated using immunofluorescence. In conclusion, this study suggests that ETSA-B21 is a GPI anchor N-glycosylated protein promoting specific antibody internalization in breast cancer cells.\n" ], "offsets": [ [ 0, 1253 ] ] } ]

[ { "id": "PMID-9145315_T1", "type": "Protein", "text": [ "phosphatidylinositol-phospholipase C" ], "offsets": [ [ 627, 663 ] ], "normalized": [] } ]

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[ { "id": "PMID-9173084__text", "type": "abstract", "text": [ "Posttranscriptional aspects of the biosynthesis of type 1 collagen pro-alpha chains: the effects of posttranslational modifications on synthesis pauses during elongation of the pro alpha 1 (I) chain. \nEarly studies indicated that chain elongation pauses were prominent during the in vivo synthesis of type I procollagen chains, and it was postulated [Kirk et al., (1987): J Biol Chem 262:5540-5545.] that these might have a role in the coordination of procollagen I molecular assembly. To examine this postulate, polysomes isolated from [(14)C]-Pro-labeled 3T6 cells were subjected to SDS-PAGE. The resulting gels were Western blotted and screened with a monoclonal antibody (SP1 .D8) directed against the N-terminal region of the pro alpha 1 (I) chain. The blots were fluorographed, which also permitted analysis of the pro alpha 2 (I) chain. There was a prominent pro alpha1 synthesis pause near the completion of full-length chain elongation, not matched by a pro alpha 2 pause. The amount of labeled polysome-associated near-full length pro alpha 1 (I) chains increased in parallel with labeling time. After 24 h in culture -[(14)C-Pro], collagen synthesis ceased but unlabeled polysome-associated pro alpha1 chains were readily detected by SP1 .D8. Change to fresh culture medium +[(14)C-Pro] reinitiated synthesis and permitted tracing of the newly synthesized labeled pro a chains through the polysome and intracellular compartments. The secreted procollagen molecules had a 2:1 pro alpha 1 (1):pro alpha 2 (I) chain ratio but the polysome-bound peptides did not. Pulse-chase experiments showed that near-full length pro alpha 1 (I) chains remained bound to polysomes as long as 4 h after reinitiation of translation but there was no evidence for pro alpha 2 (I) chain accumulation. The hydroxylation inhibitor alpha, alpha'-dipyridyl, and triple-helix inhibitors cis-hydroxyproline and 3,4 dehydroproline had minimal effects on the buildup of polysome-associated pro al chains. The glycosylation inhibitor tunicamycin also failed to change the final pro alpha 1 chain pausing, but it did cause the appearance of several discrete lower molecular weight pro alpha 1-related polypeptides that could not be accounted for simply as the result of lack of N-linked glycosylation in the C-propeptide regions. Disulfide bond experiments showed that some of the paused nascent polysome-associated pro alpha 1 (I) chains were disulfide bonded. Thus, while synthesis of pro alpha 1 (I) and pro alpha 2 (I) chains proceeds in parallel within the same ER compartments, their elongation rates are not coordinated. Interactions leading to heterotrimer formation are a late event which may affect the rate of release of the completed pro alpha 1 (I) chain from the polysome. The release of completed nascent pro alpha 1 (I) chains from their polysomal complexes is regulated by a mechanism not operating in the synthesis of pro alpha 2 (I) chains. The pro alpha 1 (I) chain release process is not connected directly with hydroxylation, glycosylation or triple-helix formation.\n" ], "offsets": [ [ 0, 3068 ] ] } ]

[ { "id": "PMID-9173084_T1", "type": "Protein", "text": [ "alpha 1 (I)" ], "offsets": [ [ 181, 192 ] ], "normalized": [] }, { "id": "PMID-9173084_T2", "type": "Protein", "text": [ "alpha 1 (I)" ], "offsets": [ [ 735, 746 ] ], "normalized": [] }, { "id": "PMID-9173084_T3", "type": "Protein", "text": [ "alpha 2 (I)" ], "offsets": [ [ 825, 836 ] ], "normalized": [] }, { "id": "PMID-9173084_T4", "type": "Protein", "text": [ "alpha 1 (I)" ], "offsets": [ [ 1045, 1056 ] ], "normalized": [] }, { "id": "PMID-9173084_T5", "type": "Protein", "text": [ "alpha 1 (1)" ], "offsets": [ [ 1490, 1501 ] ], "normalized": [] }, { "id": "PMID-9173084_T6", "type": "Protein", "text": [ "alpha 2 (I)" ], "offsets": [ [ 1506, 1517 ] ], "normalized": [] }, { "id": "PMID-9173084_T7", "type": "Protein", "text": [ "alpha 1 (I)" ], "offsets": [ [ 1628, 1639 ] ], "normalized": [] }, { "id": "PMID-9173084_T8", "type": "Protein", "text": [ "alpha 2 (I)" ], "offsets": [ [ 1758, 1769 ] ], "normalized": [] }, { "id": "PMID-9173084_T9", "type": "Protein", "text": [ "alpha 1 (I)" ], "offsets": [ [ 2399, 2410 ] ], "normalized": [] }, { "id": "PMID-9173084_T10", "type": "Protein", "text": [ "alpha 1 (I)" ], "offsets": [ [ 2470, 2481 ] ], "normalized": [] }, { "id": "PMID-9173084_T11", "type": "Protein", "text": [ "alpha 2 (I)" ], "offsets": [ [ 2490, 2501 ] ], "normalized": [] }, { "id": "PMID-9173084_T12", "type": "Protein", "text": [ "alpha 1 (I)" ], "offsets": [ [ 2729, 2740 ] ], "normalized": [] }, { "id": "PMID-9173084_T13", "type": "Protein", "text": [ "alpha 1 (I)" ], "offsets": [ [ 2803, 2814 ] ], "normalized": [] }, { "id": "PMID-9173084_T14", "type": "Protein", "text": [ "alpha 2 (I)" ], "offsets": [ [ 2919, 2930 ] ], "normalized": [] }, { "id": "PMID-9173084_T15", "type": "Protein", "text": [ "pro alpha 1 (I)" ], "offsets": [ [ 2943, 2958 ] ], "normalized": [] } ]

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[ { "id": "PMID-9184925__text", "type": "abstract", "text": [ "Cytotoxic T lymphocytes derived from bone marrow mononuclear cells of multiple myeloma patients recognize an underglycosylated form of MUC1 mucin. \nMUC1 is a highly immunogenic epithelial mucin and serves as a tumor-associated antigen in breast, pancreatic and ovarian carcinomas. We previously reported the expression of MUC1 on myeloma cells and the establishment of an HLA-unrestricted cytotoxic T lymphocyte (CTL) line TN that recognized MUC1 from peripheral blood mononuclear cells in a multiple myeloma patient. In this study, we attempted to induce such CTL from six other multiple myeloma patients consecutively in order to show that the induction of the CTL line TN had not resulted from some idiosyncrasy of the first patient. Bone marrow mononuclear cells were used to induce CTL, because they contain myeloma cells that might stimulate the autologous lymphocytes. Bulk CTL lines were induced from two out of six patients. The CTL line TS was CD8+ cell dominant and KY was CD4+ cell dominant. Both CTL lines lysed MUC1+ myeloma and breast carcinoma cell lines. The cytotoxicity of the CTL lines was inhibited by anti-CD3, anti-alpha beta TCR and anti-MUC1 mAb. It was also inhibited by a MUC1 transfectant, but not by a mock transfectant in cold target inhibition assays. MUC1 was transfected into a human colonic carcinoma cell line. The reactivity of anti-MUC1 core protein mAb and the cytotoxicity of the CTL against the transfectant was enhanced by the treatment of the cells with an O-glycosylation inhibitor. Thus it is generally accepted that the HLA-unrestricted CTL which directly recognize the underglycosylated from of MUC1 using their TCR could be induced from a certain proportion (approximately 30%) of untreated multiple myeloma patients.\n" ], "offsets": [ [ 0, 1765 ] ] } ]

[ { "id": "PMID-9184925_T1", "type": "Protein", "text": [ "MUC1" ], "offsets": [ [ 135, 139 ] ], "normalized": [] }, { "id": "PMID-9184925_T2", "type": "Protein", "text": [ "MUC1" ], "offsets": [ [ 148, 152 ] ], "normalized": [] }, { "id": "PMID-9184925_T3", "type": "Protein", "text": [ "MUC1" ], "offsets": [ [ 322, 326 ] ], "normalized": [] }, { "id": "PMID-9184925_T4", "type": "Protein", "text": [ "MUC1" ], "offsets": [ [ 442, 446 ] ], "normalized": [] }, { "id": "PMID-9184925_T5", "type": "Protein", "text": [ "CD8" ], "offsets": [ [ 954, 957 ] ], "normalized": [] }, { "id": "PMID-9184925_T6", "type": "Protein", "text": [ "CD4" ], "offsets": [ [ 984, 987 ] ], "normalized": [] }, { "id": "PMID-9184925_T7", "type": "Protein", "text": [ "MUC1" ], "offsets": [ [ 1025, 1029 ] ], "normalized": [] }, { "id": "PMID-9184925_T8", "type": "Protein", "text": [ "alpha" ], "offsets": [ [ 1138, 1143 ] ], "normalized": [] }, { "id": "PMID-9184925_T9", "type": "Protein", "text": [ "beta TCR" ], "offsets": [ [ 1144, 1152 ] ], "normalized": [] }, { "id": "PMID-9184925_T10", "type": "Protein", "text": [ "MUC1" ], "offsets": [ [ 1162, 1166 ] ], "normalized": [] }, { "id": "PMID-9184925_T11", "type": "Protein", "text": [ "MUC1" ], "offsets": [ [ 1199, 1203 ] ], "normalized": [] }, { "id": "PMID-9184925_T12", "type": "Protein", "text": [ "MUC1" ], "offsets": [ [ 1283, 1287 ] ], "normalized": [] }, { "id": "PMID-9184925_T13", "type": "Protein", "text": [ "MUC1" ], "offsets": [ [ 1369, 1373 ] ], "normalized": [] }, { "id": "PMID-9184925_T14", "type": "Protein", "text": [ "MUC1" ], "offsets": [ [ 1641, 1645 ] ], "normalized": [] } ]

[ { "id": "PMID-9184925_E1", "type": "Glycosylation", "trigger": { "text": [ "underglycosylated" ], "offsets": [ [ 109, 126 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9184925_T1" } ] }, { "id": "PMID-9184925_E2", "type": "Glycosylation", "trigger": { "text": [ "underglycosylated" ], "offsets": [ [ 1615, 1632 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9184925_T14" } ] } ]

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[ { "id": "PMID-9204977__text", "type": "abstract", "text": [ "DNA methylation patterns in the calcitonin gene region at first diagnosis and at relapse of acute lymphoblastic leukemia (ALL). \nAberrant DNA methylation can occur early in neoplastic transformation and may lead to the development of cancer. We describe the alterations of methylation patterns at the DNA sequence level which occurred in the 5' region of the calcitonin gene in lymphoblasts from 14 pediatric patients with acute lymphoblastic leukemia (ALL). The DNA methylation status of 25 CpG sites was determined by sequence analysis after bisulfite treatment of the DNA. This method showed that 13 out of 14 patients had increased numbers of methylated CpG sites in the calcitonin gene region at initial diagnosis when compared to control DNA from healthy individuals. The 5' region of the calcitonin gene appears to be methylated to a significantly higher degree in T lineage ALL compared to B lineage ALL (P < 0.01). Each of six ALL patients who were investigated at initial diagnosis and at relapse showed alterations in DNA methylation between the two stages. These six cases were also investigated by Southern blot analysis with methylcytosine-sensitive restriction enzymes and this method showed an increase in DNA methylation in only four of the six cases. The DNA sequencing method thus appears to be better suited to assess alterations of DNA methylation than Southern blot analysis. There are marked regional differences in the frequency of methylation of individual CpG sites and in the frequency of alterations between the two stages. Our results show that alterations in DNA methylation continue to occur from the initial stage to the relapse stage of ALL, suggesting that aberrant DNA methylation may play a role in tumor progression.\n" ], "offsets": [ [ 0, 1754 ] ] } ]

[ { "id": "PMID-9204977_T1", "type": "Protein", "text": [ "calcitonin" ], "offsets": [ [ 32, 42 ] ], "normalized": [] }, { "id": "PMID-9204977_T2", "type": "Protein", "text": [ "calcitonin" ], "offsets": [ [ 359, 369 ] ], "normalized": [] }, { "id": "PMID-9204977_T3", "type": "Protein", "text": [ "calcitonin" ], "offsets": [ [ 675, 685 ] ], "normalized": [] }, { "id": "PMID-9204977_T4", "type": "Protein", "text": [ "calcitonin" ], "offsets": [ [ 795, 805 ] ], "normalized": [] }, { "id": "PMID-9204977_T7", "type": "Entity", "text": [ "5' region" ], "offsets": [ [ 342, 351 ] ], "normalized": [] }, { "id": "PMID-9204977_T9", "type": "Entity", "text": [ "25 CpG sites" ], "offsets": [ [ 489, 501 ] ], "normalized": [] }, { "id": "PMID-9204977_T11", "type": "Entity", "text": [ "CpG sites" ], "offsets": [ [ 658, 667 ] ], "normalized": [] }, { "id": "PMID-9204977_T12", "type": "Entity", "text": [ "5' region" ], "offsets": [ [ 778, 787 ] ], "normalized": [] }, { "id": "PMID-9204977_T17", "type": "Entity", "text": [ "CpG sites" ], "offsets": [ [ 1482, 1491 ] ], "normalized": [] } ]

[ { "id": "PMID-9204977_E1", "type": "DNA_methylation", "trigger": { "text": [ "DNA methylation" ], "offsets": [ [ 0, 15 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9204977_T1" } ] }, { "id": "PMID-9204977_E2", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 273, 284 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9204977_T2" }, { "role": "Site", "ref_id": "PMID-9204977_T7" } ] }, { "id": "PMID-9204977_E3", "type": "DNA_methylation", "trigger": { "text": [ "DNA methylation" ], "offsets": [ [ 463, 478 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9204977_T2" }, { "role": "Site", "ref_id": "PMID-9204977_T9" } ] }, { "id": "PMID-9204977_E4", "type": "DNA_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 647, 657 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9204977_T3" }, { "role": "Site", "ref_id": "PMID-9204977_T11" } ] }, { "id": "PMID-9204977_E5", "type": "DNA_methylation", "trigger": { "text": [ "methylated" ], "offsets": [ [ 825, 835 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9204977_T4" }, { "role": "Site", "ref_id": "PMID-9204977_T12" } ] }, { "id": "PMID-9204977_E6", "type": "DNA_methylation", "trigger": { "text": [ "DNA methylation" ], "offsets": [ [ 1029, 1044 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9204977_T4" } ] }, { "id": "PMID-9204977_E7", "type": "DNA_methylation", "trigger": { "text": [ "DNA methylation" ], "offsets": [ [ 1222, 1237 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9204977_T4" } ] }, { "id": "PMID-9204977_E8", "type": "DNA_methylation", "trigger": { "text": [ "methylation" ], "offsets": [ [ 1456, 1467 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9204977_T4" }, { "role": "Site", "ref_id": "PMID-9204977_T17" } ] }, { "id": "PMID-9204977_E9", "type": "DNA_methylation", "trigger": { "text": [ "DNA methylation" ], "offsets": [ [ 1589, 1604 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9204977_T4" } ] } ]

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[ { "id": "PMID-9212783__text", "type": "abstract", "text": [ "Structural specificity requirements in the binding of beta lactam antibiotics to human serum albumin. \nThe binding of some cephalosporins of pharmacological interest, to human serum albumin was studied using ultrafiltration method. The identification of the binding sites in albumin was also performed using probes for the so-called sites I, II, bilirubin and fatty acids binding sites. Cephalosporins were classified into three groups according to their affinity for albumin: low affinity (K = 10-10(2) M-1), medium affinity (K = 10(3) M-1) and high affinity (K = 10(4) M-1). Cephalosporin binding to albumin produced a perturbation of several basic amino acids of the protein such as histidine and lysine. It was found that only cefuroxime, ceftazidime and cefoperazone interact slightly with site I on serum albumin, while site II possesses capacity to bind: cephradine, cephalexin, ceftazidime, ceftriaxone, cefoperazone, cefaclor and cefsulodin. The bilirubin binding site showed capacity to interact with a great number of cephalosporins: ceftriaxone, cefazolin, cephaloglycin, cefamandole, cefotaxime, cefoxitin, cefuroxime, cefoperazone and cefadroxil. Ceftriaxone showed capacity to bind to the fatty acid binding site on HSA. No relation was found between the displacement of the marker and the chemical nature of the substituents at R1 and R2. Cephalosporins interact with HSA at the binding region that involves: tyrosyl 411, histidyl 146 and lysyls 195, 199, 225, 240 and 525 residues. The chemical modification of specific amino acids showed that the interaction of these amino acids with beta lactam antibiotics is not carried out to the same extent for all the cephalosporins tested. The results obtained revealed that the binding sites for cephalosporins on albumin are structurally heterogeneous, having different amino acids in the vicinity of the ligand molecule.\n" ], "offsets": [ [ 0, 1884 ] ] } ]

[ { "id": "PMID-9212783_T1", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 87, 100 ] ], "normalized": [] }, { "id": "PMID-9212783_T2", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 176, 189 ] ], "normalized": [] }, { "id": "PMID-9212783_T3", "type": "Protein", "text": [ "albumin" ], "offsets": [ [ 275, 282 ] ], "normalized": [] }, { "id": "PMID-9212783_T4", "type": "Protein", "text": [ "albumin" ], "offsets": [ [ 468, 475 ] ], "normalized": [] }, { "id": "PMID-9212783_T5", "type": "Protein", "text": [ "albumin" ], "offsets": [ [ 602, 609 ] ], "normalized": [] }, { "id": "PMID-9212783_T6", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 805, 818 ] ], "normalized": [] }, { "id": "PMID-9212783_T7", "type": "Protein", "text": [ "albumin" ], "offsets": [ [ 1775, 1782 ] ], "normalized": [] } ]

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[ { "id": "PMID-9222494__text", "type": "abstract", "text": [ "A strategy of tRNA recognition that includes determinants of RNA structure. \nRecognition of tRNAs by aminoacyl tRNA synthetases establishes the connection between amino acids and anticodon triplets of the genetic code. Although anticodons and nucleotides adjacent to the amino acid attachment site are generally important, the tertiary structural framework of tRNAs has recently been implicated to have a role in tRNA recognition. A G15:G48 tertiary hydrogen base pair of E. coli tRNA(Cys) is important for recognition of the tRNA by cysteine tRNA synthetase. This base pair is proposed to consist of N2:N3, rather than N1:O6, hydrogen bonds. The reproduction of the hydrogen pairing scheme of tRNA(Gly). This reproduction required an A13:A22 mismatch in the dihyrouridine stem. To determine if A13:A22 is a determinant of the structural features of G15:G48, we investigated the A15:U48 and A15:A48 variants of tRNA(Gly) which harbored specific substitutions of A13:A22. We show here that introduction of A13:A22 to both tRNA frameworks confers structural features similar to those of G15:G48 in E. coli tRNA(Cys). These structural features are accompanied by efficient recognition of both tRNAs by cysteine tRNA synthetase. Substitution of A13:A22 with U13:A22 alters the structural features at 15:48 and impairs tRNA recognition. The dependence on A13:22 for tRNA recognition has a distinct similarity to that of E. coli tRNA(Cys) and to that of the G15:G48 variant of tRNA(Gly). The results have implications for the design and manipulation of RNA structural elements as the basis for tRNA recognition.\n" ], "offsets": [ [ 0, 1606 ] ] } ]

[ { "id": "PMID-9222494_T1", "type": "Protein", "text": [ "cysteine tRNA synthetase" ], "offsets": [ [ 534, 558 ] ], "normalized": [] }, { "id": "PMID-9222494_T2", "type": "Protein", "text": [ "cysteine tRNA synthetase" ], "offsets": [ [ 1199, 1223 ] ], "normalized": [] } ]

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[ { "id": "PMID-9259992__text", "type": "abstract", "text": [ "The role of oxidative stress in the long-term glycation of LDL. \nAdvanced glycation is a major pathway for the posttranslational modification of plasma and tissue proteins. The initiating reaction is the nonenzymatic addition of sugars such as glucose to the primary amino groups of proteins, i.e., mainly to lysine residues. These \"early\" Schiff base and Amadori products then undergo a series of inter- and intramolecular rearrangements to produce the \"late\" products termed advanced glycation end products (AGEs). Incubation of LDL with glucose or glucose-6-phosphate produces AGE moieties on both the lipid and apolipoprotein B components. In addition, we tried to generate AGE-LDL by reaction with AGE-peptides (< 10 kD) obtained by enzymatic digestion of long-term glycated fibronectin as a model for connective tissue AGE-peptides. AGE-formation can be assessed by monitoring of fluorescence (370/440 nm) which is easily differentiated from the much lower autofluorescence of oxidized low density lipoproteins (oxLDL). Alternatively, AGE formation was detected by an AGE-specific ELISA using antibodies elicited in rabbits against bovine AGE-RNAse. In the present study we investigated the influence of oxidative stress on the long-term glycation of LDL and the modulation of LDL-oxidation by AGE-modification. We observed (a) that the rate of AGE formation is reduced by BHT/EDTA both on LDL and serum albumin (glycation vs. glycoxidation), (b) long-term glycated LDL is more readily oxidized than unglycated LDL, (c) oxLDL is more prone to AGE-modification, (d) AGE-modification of LDL strongly alters its epitope spectrum and (e) that aminoguanidine at higher concentrations (1-10 mM) inhibits copper-catalyzed LDL oxidation in the way of a classical antioxidant.\n" ], "offsets": [ [ 0, 1774 ] ] } ]

[ { "id": "PMID-9259992_T1", "type": "Protein", "text": [ "apolipoprotein B" ], "offsets": [ [ 615, 631 ] ], "normalized": [] }, { "id": "PMID-9259992_T2", "type": "Protein", "text": [ "fibronectin" ], "offsets": [ [ 780, 791 ] ], "normalized": [] }, { "id": "PMID-9259992_T3", "type": "Protein", "text": [ "serum albumin" ], "offsets": [ [ 1404, 1417 ] ], "normalized": [] } ]

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[ { "id": "PMID-9276678__text", "type": "abstract", "text": [ "Glycosylation of human bone collagen I in relation to lysylhydroxylation and fibril diameter. \nPosttranslational modifications (lysylhydroxylation, glycosylation, and crosslink formation) of collagen I and the trabecular bone volume (TBV) as well as the supramolecular organization of human vertebrae were studied by analyzing vertebral bones of 55 individuals (22-93 years of age). The degree of lysylhydroxylation of both a-chains of collagen I showed a significant inverse correlation with the TBV, while only a weak correlation between lysylhydroxylation of alpha2(I) and the age of the donor was observed. The degree of glycosylation of collagen I was significantly correlated with both the level of lysylhydroxylation and the degree of osteopenia. Electron microscopic evaluation did not show any relationship between the level of collagen glycosylation and the diameter of in vivo formed fibrils or in vitro formed fibrillar aggregates. In our study the molar ratio of the mature collagen crosslinks, pyridinoline and deoxypyridinoline, showed a slight tendency to be higher, in particular in the samples with a high level of lysylhydroxylation. This ratio was recently found to be significantly increased in avian osteoporotic bone. Our data suggest that the increased level of lysylhydroxylation in human osteopenia is related to the glycosylation of collagen I, while it seems to have little impact on the formation of the mature, non-reducible collagen crosslinks investigated. Based on our observations it appears unlikely that the different diameters of collagen fibrils contribute greatly to the reduced biomechanical stability reported for overhydroxylated, osteopenic bone tissue.\n" ], "offsets": [ [ 0, 1697 ] ] } ]

[ { "id": "PMID-9276678_T1", "type": "Protein", "text": [ "alpha2(I)" ], "offsets": [ [ 562, 571 ] ], "normalized": [] }, { "id": "PMID-9276678_T2", "type": "Entity", "text": [ "lysyl" ], "offsets": [ [ 540, 545 ] ], "normalized": [] } ]

[ { "id": "PMID-9276678_E1", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylation" ], "offsets": [ [ 545, 558 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9276678_T1" }, { "role": "Site", "ref_id": "PMID-9276678_T2" } ] } ]

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[ { "id": "PMID-9375892__text", "type": "abstract", "text": [ "Alterations in the O-linked glycosylation of IgA1 in children with Henoch-Schonlein purpura. \nOBJECTIVE: To examine O-linked glycosylation of serum IgA1 in children with acute Henoch-Schonlein purpura (HSP). METHODS: The O-linked oligosaccharides of serum IgA1 from 28 children with acute HSP and 26 control children were examined by enzyme immunoassay using plant lectins with well defined carbohydrate binding specificities. The lectins included Artocarpus integrifolia (jacalin), Arachis hypogaea (peanut lectin), and Sambucus nigra (elderberry lectin). Jacalin binds to galactose-N-acetylgalactosamine (Gal-GalNAc). Jacalin interaction with this oligosaccharide is not influenced by the presence of sialic acid on the galactose moiety. Peanut lectin also interacts with Gal-GalNAc, but binding is inhibited if the galactose residue is sialylated. Elderberry lectin binds to N-acetylneuraminic acid (sialic acid). RESULTS: There was no difference in the binding of jacalin to IgA1 from patients with HSP compared to controls (p = 0.5). The binding of peanut lectin to IgA1 was significantly higher in HSP compared to controls (p = 0.007). Since peanut lectin binding is inhibited by the presence of sialylated galactose, these results suggest diminished sialic content of the O-linked oligosaccharides of IgA1 in HSP compared to controls. Indeed, the binding of the sialic acid-specific elderberry lectin to IgA1 was significantly lower in HSP compared to controls (p = 0.004). CONCLUSION: The O-linked oligosaccharides of serum IgA1 from children with acute HSP are deficient in salic acid compared to serum IgA1 from control children.\n" ], "offsets": [ [ 0, 1640 ] ] } ]

[ { "id": "PMID-9375892_T1", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 747, 753 ] ], "normalized": [] }, { "id": "PMID-9375892_T2", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 1061, 1067 ] ], "normalized": [] }, { "id": "PMID-9375892_T3", "type": "Protein", "text": [ "lectin" ], "offsets": [ [ 1155, 1161 ] ], "normalized": [] } ]

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[ { "id": "PMID-9379032__text", "type": "abstract", "text": [ "Alteration of glycosylation renders HIV sensitive to inactivation by normal human serum. \nRetroviruses from various mammalian species, excluding humans, are effectively inactivated in normal human serum (NHS). Recent studies have shown that NHS inactivation of retroviruses occurs through natural Ab recognition of a terminal glycosidic moiety on the viral envelope that is acquired during replication in the host cell. This carbohydrate structure (the alpha-galactosyl epitope) is expressed on the cells of most mammals, with the exception of humans and other Old World primates. In this study, NHS sensitivity of HIV was assessed following viral propagation in human cells that were manipulated to express the alpha-galactosyl epitope. HUT-78 cells were transduced with an exogenous alpha1-3-galactosyl transferase gene, which codes for the terminal glycosyl transferase responsible for generation of the alpha-galactosyl epitope. The transduced HUT-78 cells expressed high levels of the alpha-galactosyl epitope on their membrane surface, rendering them sensitive to killing in NHS. Similarly, HIV passaged through these cells acquired the alpha-galactosyl epitope in association with the envelope glycoprotein gp120 and was also effectively inactivated in NHS. Viral inactivation was abolished by the addition of a synthetic disaccharide that contains the alpha-galactosyl epitope, indicating that virolysis is mediated by anti-alpha-galactosyl natural Ab. These results demonstrate that, like other retroviruses bearing the alpha-galactosyl epitope, HIV modified to express this epitope is inactivated in NHS. Furthermore, these data suggest that expression of the alpha-galactosyl epitope on the surface of viruses may have implications in the interspecies transmission of such viruses to humans.\n" ], "offsets": [ [ 0, 1803 ] ] } ]

[ { "id": "PMID-9379032_T1", "type": "Protein", "text": [ "gp120" ], "offsets": [ [ 1214, 1219 ] ], "normalized": [] } ]

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[ { "id": "PMID-9425240__text", "type": "abstract", "text": [ "A point mutation in the neu-1 locus causes the neuraminidase defect in the SM/J mouse. \nLysosomal neuraminidase (sialidase) occurs in a high molecular weight complex with the glycosidase beta-galactosidase and the serine carboxypeptidase protective protein/cathepsin A (PPCA). Association of the enzyme with PPCA is crucial for its correct targeting and lysosomal activation. In man two genetically distinct storage disorders are associated with either a primary or a secondary deficiency of lysosomal neuraminidase: sialidosis and galactosialidosis. In the mouse the naturally occurring inbred strain SM/J presents with a number of phenotypic abnormalities that have been attributed to reduced neuraminidase activity. SM/J mice were originally characterized by their altered sialylation of several lysosomal glycoproteins. This defect was linked to a single gene, neu-1 , on chromosome 17, which was mapped by linkage analysis to the H-2 locus. In addition, these mice have an altered immune response that has also been coupled to a deficiency of the Neu-1 neuraminidase. Here we report the identification in SM/J mice of a single amino acid substitution (L209I) in the Neu-1 protein which is responsible for the partial deficiency of lysosomal neuraminidase. We propose that the reduced activity is caused by the enzyme's altered affinity for its substrate, rather than a change in substrate specificity or turnover rate. The mutant enzyme is correctly compartmentalized in lysosomes and maintains the ability to associate with its activating protein, PPCA. We propose that it is this mutation that is responsible for the SM/J phenotype.\n" ], "offsets": [ [ 0, 1640 ] ] } ]

[ { "id": "PMID-9425240_T1", "type": "Protein", "text": [ "neu-1" ], "offsets": [ [ 24, 29 ] ], "normalized": [] }, { "id": "PMID-9425240_T2", "type": "Protein", "text": [ "Lysosomal neuraminidase" ], "offsets": [ [ 88, 111 ] ], "normalized": [] }, { "id": "PMID-9425240_T3", "type": "Protein", "text": [ "beta-galactosidase" ], "offsets": [ [ 187, 205 ] ], "normalized": [] }, { "id": "PMID-9425240_T4", "type": "Protein", "text": [ "protective protein/cathepsin A" ], "offsets": [ [ 238, 268 ] ], "normalized": [] }, { "id": "PMID-9425240_T5", "type": "Protein", "text": [ "PPCA" ], "offsets": [ [ 270, 274 ] ], "normalized": [] }, { "id": "PMID-9425240_T6", "type": "Protein", "text": [ "PPCA" ], "offsets": [ [ 308, 312 ] ], "normalized": [] }, { "id": "PMID-9425240_T7", "type": "Protein", "text": [ "lysosomal neuraminidase" ], "offsets": [ [ 492, 515 ] ], "normalized": [] }, { "id": "PMID-9425240_T8", "type": "Protein", "text": [ "neu-1" ], "offsets": [ [ 865, 870 ] ], "normalized": [] }, { "id": "PMID-9425240_T9", "type": "Protein", "text": [ "Neu-1" ], "offsets": [ [ 1052, 1057 ] ], "normalized": [] }, { "id": "PMID-9425240_T10", "type": "Protein", "text": [ "Neu-1" ], "offsets": [ [ 1171, 1176 ] ], "normalized": [] }, { "id": "PMID-9425240_T11", "type": "Protein", "text": [ "lysosomal neuraminidase" ], "offsets": [ [ 1236, 1259 ] ], "normalized": [] }, { "id": "PMID-9425240_T12", "type": "Protein", "text": [ "PPCA" ], "offsets": [ [ 1554, 1558 ] ], "normalized": [] } ]

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[ { "id": "PMID-9425240_1", "entity_ids": [ "PMID-9425240_T4", "PMID-9425240_T5" ] } ]

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[ { "id": "PMID-9513082__text", "type": "abstract", "text": [ "Expression and purification of biologically active porcine follicle-stimulating hormone in insect cells bearing a baculovirus vector. \nBiologically active recombinant porcine FSH (rec-pFSH) free from the cognate pituitary glycoprotein hormone LH was produced. It was synthesized by a baculovirus vector-insect cell system using two cDNAs encoding the glycoprotein alpha and FSH beta subunits. Its antigenicity was the same as that of pFSH prepared from the pituitary. Glycosylation of rec-pFSH was shown by tunicamycin treatment but the molecular mass of each subunit was lower than that of pituitary-derived FSH, because of the absence of trimming of terminal sugars in insect cells. Rec-pFSH was secreted into the culture medium at about 1 mg/l and purified in six fractions, because of the heterogeneity of the sugar group, by S-Sepharose and concanavalin A-Sepharose column chromatography. The biological activity of rec-pFSH was examined by measuring its effect on progesterone secretion from porcine granulosa cells and germinal vesicle breakdown (GVBD) of porcine oocytes. It showed adequate activity with respect to progesterone secretion, although some fractions rich in the sugar group showed lower activity than that of pituitary-derived FSH. It exhibited higher GVBD activity than that of pituitary-derived FSH at concentrations as low as 1 ng/ml. These results demonstrate that the baculovirus vector-insect cell system can provide biologically active rec-pFSH.\n" ], "offsets": [ [ 0, 1475 ] ] } ]

[ { "id": "PMID-9513082_T1", "type": "Protein", "text": [ "FSH beta" ], "offsets": [ [ 374, 382 ] ], "normalized": [] } ]

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[ { "id": "PMID-9545296__text", "type": "abstract", "text": [ "Protein disulfide isomerase acts as a molecular chaperone during the assembly of procollagen. \nProtein-disulfide isomerase (PDI) has been shown to be a multifunctional enzyme catalyzing the formation of disulfide bonds, as well as being a component of the enzymes prolyl 4-hydroxylase (P4-H) and microsomal triglyceride transfer protein. It has also been proposed to function as a molecular chaperone during the refolding of denatured proteins in vitro. To investigate the role of this multifunctional protein within a cellular context, we have established a semi-permeabilized cell system that reconstitutes the synthesis, folding, modification, and assembly of procollagen as they would occur in the cell. We demonstrate here that P4-H associates transiently with the triple helical domain during the assembly of procollagen. The release of P4-H from the triple helical domain coincides with assembly into a thermally stable triple helix. However, if triple helix formation is prevented, P4-H remains associated, suggesting a role for this enzyme in preventing aggregation of this domain. We also show that PDI associates independently with the C-propeptide of monomeric procollagen chains prior to trimer formation, indicating a role for this protein in coordinating the assembly of heterotrimeric molecules. This demonstrates that PDI has multiple functions in the folding of the same protein, that is, as a catalyst for disulfide bond formation, as a subunit of P4-H during proline hydroxylation, and independently as a molecular chaperone during chain assembly.\n" ], "offsets": [ [ 0, 1568 ] ] } ]

[ { "id": "PMID-9545296_T1", "type": "Protein", "text": [ "Protein disulfide isomerase" ], "offsets": [ [ 0, 27 ] ], "normalized": [] }, { "id": "PMID-9545296_T2", "type": "Protein", "text": [ "Protein-disulfide isomerase" ], "offsets": [ [ 95, 122 ] ], "normalized": [] }, { "id": "PMID-9545296_T3", "type": "Protein", "text": [ "PDI" ], "offsets": [ [ 124, 127 ] ], "normalized": [] }, { "id": "PMID-9545296_T4", "type": "Protein", "text": [ "PDI" ], "offsets": [ [ 1109, 1112 ] ], "normalized": [] }, { "id": "PMID-9545296_T5", "type": "Protein", "text": [ "PDI" ], "offsets": [ [ 1335, 1338 ] ], "normalized": [] } ]

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[ { "id": "PMID-9545296_1", "entity_ids": [ "PMID-9545296_T2", "PMID-9545296_T3" ] } ]

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[ { "id": "PMID-9641684__text", "type": "abstract", "text": [ "The antigenic structure of the HIV gp120 envelope glycoprotein. \nThe human immunodeficiency virus HIV-1 establishes persistent infections in humans which lead to acquired immunodeficiency syndrome (AIDS). The HIV-1 envelope glycoproteins, gp120 and gp41, are assembled into a trimeric complex that mediates virus entry into target cells. HIV-1 entry depends on the sequential interaction of the gp120 exterior envelope glycoprotein with the receptors on the cell, CD4 and members of the chemokine receptor family. The gp120 glycoprotein, which can be shed from the envelope complex, elicits both virus-neutralizing and non-neutralizing antibodies during natural infection. Antibodies that lack neutralizing activity are often directed against the gp120 regions that are occluded on the assembled trimer and which are exposed only upon shedding. Neutralizing antibodies, by contrast, must access the functional envelope glycoprotein complex and typically recognize conserved or variable epitopes near the receptor-binding regions. Here we describe the spatial organization of conserved neutralization epitopes on gp120, using epitope maps in conjunction with the X-ray crystal structure of a ternary complex that includes a gp120 core, CD4 and a neutralizing antibody. A large fraction of the predicted accessible surface of gp120 in the trimer is composed of variable, heavily glycosylated core and loop structures that surround the receptor-binding regions. Understanding the structural basis for the ability of HIV-1 to evade the humoral immune response should assist in the design of a vaccine.\n" ], "offsets": [ [ 0, 1598 ] ] } ]

[ { "id": "PMID-9641684_T1", "type": "Protein", "text": [ "gp120" ], "offsets": [ [ 35, 40 ] ], "normalized": [] }, { "id": "PMID-9641684_T2", "type": "Protein", "text": [ "gp120" ], "offsets": [ [ 239, 244 ] ], "normalized": [] }, { "id": "PMID-9641684_T3", "type": "Protein", "text": [ "gp41" ], "offsets": [ [ 249, 253 ] ], "normalized": [] }, { "id": "PMID-9641684_T4", "type": "Protein", "text": [ "gp120" ], "offsets": [ [ 395, 400 ] ], "normalized": [] }, { "id": "PMID-9641684_T5", "type": "Protein", "text": [ "CD4" ], "offsets": [ [ 464, 467 ] ], "normalized": [] }, { "id": "PMID-9641684_T6", "type": "Protein", "text": [ "gp120" ], "offsets": [ [ 518, 523 ] ], "normalized": [] }, { "id": "PMID-9641684_T7", "type": "Protein", "text": [ "gp120" ], "offsets": [ [ 747, 752 ] ], "normalized": [] }, { "id": "PMID-9641684_T8", "type": "Protein", "text": [ "gp120" ], "offsets": [ [ 1112, 1117 ] ], "normalized": [] }, { "id": "PMID-9641684_T9", "type": "Protein", "text": [ "gp120" ], "offsets": [ [ 1223, 1228 ] ], "normalized": [] }, { "id": "PMID-9641684_T10", "type": "Protein", "text": [ "CD4" ], "offsets": [ [ 1235, 1238 ] ], "normalized": [] }, { "id": "PMID-9641684_T11", "type": "Protein", "text": [ "gp120" ], "offsets": [ [ 1324, 1329 ] ], "normalized": [] }, { "id": "PMID-9641684_T13", "type": "Entity", "text": [ "core" ], "offsets": [ [ 1390, 1394 ] ], "normalized": [] } ]

[ { "id": "PMID-9641684_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 1377, 1389 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9641684_T11" }, { "role": "Site", "ref_id": "PMID-9641684_T13" } ] } ]

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[ { "id": "PMID-9655244__text", "type": "abstract", "text": [ "Production of recombinant hydroxylated human type III collagen fragment in Saccharomyces cerevisiae. \nA recombinant hydroxylated fragment of human type III collagen has been produced in Saccharomyces cerevisiae by coordinated coexpression of a collagen gene fragment together with both the alpha- and beta-subunit genes for prolyl-4-hydroxylase (EC 1.14.11.2). The collagen fragment consisted of 255 residues of the helical domain and the complete C-telopeptide and C-propeptide domains. It was inserted under the control of the ethanol-inducible ADH2 promoter in a multicopy, TRP1-selectable, yeast expression vector, YEpFlag1. The prolyihydroxylase subunit genes were cloned on either side of a bidirectional galactose-inducible promoter in a low-copy minichromosome yeast expression vector, pYEUra3, which is URA3 selectable. Coordinated expression of the three different gene products after cotransformation into S. cerevisiae was detected by immunoblotting. Amino acid analysis of an immunoreactive collagen fraction demonstrated the presence of hydroxyproline, while the presence of a triple-helical domain in the collagen fragment was demonstrated by its resistance to pepsin proteolysis.\n" ], "offsets": [ [ 0, 1196 ] ] } ]

[ { "id": "PMID-9655244_T1", "type": "Protein", "text": [ "type III collagen" ], "offsets": [ [ 45, 62 ] ], "normalized": [] }, { "id": "PMID-9655244_T2", "type": "Protein", "text": [ "type III collagen" ], "offsets": [ [ 147, 164 ] ], "normalized": [] }, { "id": "PMID-9655244_T3", "type": "Protein", "text": [ "ADH2" ], "offsets": [ [ 547, 551 ] ], "normalized": [] }, { "id": "PMID-9655244_T4", "type": "Protein", "text": [ "TRP1" ], "offsets": [ [ 577, 581 ] ], "normalized": [] }, { "id": "PMID-9655244_T5", "type": "Protein", "text": [ "URA3" ], "offsets": [ [ 812, 816 ] ], "normalized": [] } ]

[ { "id": "PMID-9655244_E1", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylated" ], "offsets": [ [ 26, 38 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9655244_T1" } ] }, { "id": "PMID-9655244_E2", "type": "Hydroxylation", "trigger": { "text": [ "hydroxylated" ], "offsets": [ [ 116, 128 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9655244_T2" } ] } ]

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[ { "id": "PMID-9669673__text", "type": "abstract", "text": [ "CD34 molecule epitope distribution on cells of haematopoietic origin. \nThe CD34 molecule belongs to the mucin membrane molecule family and is expressed on virtually all normal haematopoietic progenitor cells (HPC). Due to its heavy glycosylation, several different epitopes exist on the molecule. Based on the sensitivity of the glycosylated molecule to degradation with a glycoprotease from Pasteurella haemolytica and neuraminidase, three classes of epitopes have been identified. The class I and II epitopes are probably related to the glycosylated part of the molecule while class III epitopes are core protein related. It has been known for some time that CD34 class I epitopes are absent on CD34 molecules expressed on high endothelial venules. Here we review recent observations that expression of both class I and II epitopes, but not class III epitopes, is impaired on mature myeloid CD34-pos. HPC while no diverse class epitope expression was observed on immature HPC. In addition, cells from patients with CD34-pos. acute myeloid leukaemia of FAB classification M4-M5, i.e., leukaemic blast cells of relatively mature morphologic phenotype, also express less class I and II epitopes than class III epitopes. It therefore seems that HPC maturation and class I and II epitope deprivation are concomitant events and that CD34 class I and II epitopes are lost prior to downregulation of the CD34 molecule per se. The biological significance of this observation is discussed as well as the need to carefully select CD34-specific monoclonal antibodies for research and clinical purposes.\n" ], "offsets": [ [ 0, 1593 ] ] } ]

[ { "id": "PMID-9669673_T1", "type": "Protein", "text": [ "CD34" ], "offsets": [ [ 0, 4 ] ], "normalized": [] }, { "id": "PMID-9669673_T2", "type": "Protein", "text": [ "CD34" ], "offsets": [ [ 75, 79 ] ], "normalized": [] }, { "id": "PMID-9669673_T3", "type": "Protein", "text": [ "glycoprotease" ], "offsets": [ [ 373, 386 ] ], "normalized": [] }, { "id": "PMID-9669673_T4", "type": "Protein", "text": [ "CD34" ], "offsets": [ [ 661, 665 ] ], "normalized": [] }, { "id": "PMID-9669673_T5", "type": "Protein", "text": [ "CD34" ], "offsets": [ [ 697, 701 ] ], "normalized": [] }, { "id": "PMID-9669673_T6", "type": "Protein", "text": [ "CD34" ], "offsets": [ [ 893, 897 ] ], "normalized": [] }, { "id": "PMID-9669673_T7", "type": "Protein", "text": [ "CD34" ], "offsets": [ [ 1017, 1021 ] ], "normalized": [] }, { "id": "PMID-9669673_T8", "type": "Protein", "text": [ "CD34" ], "offsets": [ [ 1329, 1333 ] ], "normalized": [] }, { "id": "PMID-9669673_T9", "type": "Protein", "text": [ "CD34" ], "offsets": [ [ 1398, 1402 ] ], "normalized": [] }, { "id": "PMID-9669673_T10", "type": "Protein", "text": [ "CD34" ], "offsets": [ [ 1521, 1525 ] ], "normalized": [] } ]

[ { "id": "PMID-9669673_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 232, 245 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9669673_T2" } ] }, { "id": "PMID-9669673_E2", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 329, 341 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9669673_T2" } ] }, { "id": "PMID-9669673_E3", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 539, 551 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9669673_T2" } ] } ]

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[ { "id": "PMID-9692970__text", "type": "abstract", "text": [ "Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins. \nThe R2 protein of ribonucleotide reductase catalyzes the dioxygen-dependent one-electron oxidation of Tyr122 at a diiron-carboxylate site. Methane monooxygenase and related hydroxylases catalyze hydrocarbon hydroxylation at diiron sites structurally related to the one in R2. In protein R2, the likely reaction site for dioxygen is close to Phe208. The crystal structure of an iron ligand mutant R2, Y122F/E238A, reveals the hydroxylation of Phe208 at the meta, or epsilon-, ring position and the subsequent coordination of this residue to the diiron site. In another mutant, F208Y, the \"foreign\" residue Tyr208 is hydroxylated to Dopa. The structures of apo and diferrous F208Y presented here suggest that Tyr208 is coordinated to the iron site of F208Y throughout the Dopa generation cycle. Together, the structural data on these two mutants suggest two possible reaction geometries for the hydroxylation reaction catalyzed by these modified R2 diiron sites, geometries which might be relevant for the hydroxylation reaction catalyzed by other diiron sites such as methane monooxygenase. A critical role for residue Glu238 in directing the oxidative power of the reactive intermediate toward oxidation of Tyr122 is proposed.\n" ], "offsets": [ [ 0, 1422 ] ] } ]

[ { "id": "PMID-9692970_T1", "type": "Protein", "text": [ "R2" ], "offsets": [ [ 78, 80 ] ], "normalized": [] }, { "id": "PMID-9692970_T2", "type": "Protein", "text": [ "R2" ], "offsets": [ [ 199, 201 ] ], "normalized": [] }, { "id": "PMID-9692970_T3", "type": "Protein", "text": [ "R2" ], "offsets": [ [ 467, 469 ] ], "normalized": [] }, { "id": "PMID-9692970_T4", "type": "Protein", "text": [ "R2" ], "offsets": [ [ 482, 484 ] ], "normalized": [] }, { "id": "PMID-9692970_T5", "type": "Protein", "text": [ "R2" ], "offsets": [ [ 591, 593 ] ], "normalized": [] }, { "id": "PMID-9692970_T6", "type": "Protein", "text": [ "R2" ], "offsets": [ [ 1139, 1141 ] ], "normalized": [] } ]

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[ { "id": "PMID-9764481__text", "type": "abstract", "text": [ "Expression of recombinant human acid sphingomyelinase in insect Sf21 cells: purification, processing and enzymatic characterization. \nBiochemical and structural studies on human acid sphingomyelinase (haSMase) depend on the access to homogeneous biologically active enzyme. Due to the low abundance of native haSMase (n-haSMase) in human tissue, conventional purification strategies are not suitable for the isolation of preparative amounts of the enzyme. We describe a novel approach to the functional expression and purification of haSMase employing the baculovirus expression vector system. Infection of Spodoptera frugiperda 21 cells with recombinant baculovirus encoding haSMase leads to the expression of a glycosylated 75 kDa precursor protein, which is subsequently processed to an enzymatically active secreted 72 kDa haSMase. Variations in N-glycosylation and proteolytic maturation account for the difference in molecular mass between mature recombinant (72 kDa) and human placental haSMase (75 kDa). N-terminal amino acid sequencing of recombinant haSMase (r-haSMase) reveals a 23-residue N-terminal extension compared to the placental enzyme. The apparent K(m) and Vmax values for sphingomyelin degradation by r-haSMase in a micellar assay system are 32 microM and 0.56 mmol h-1 mg-1, respectively. In conclusion, the established baculovirus expression vector system provides an efficient tool for the expression and functional characterization of haSMase.\n" ], "offsets": [ [ 0, 1470 ] ] } ]

[ { "id": "PMID-9764481_T1", "type": "Protein", "text": [ "acid sphingomyelinase" ], "offsets": [ [ 32, 53 ] ], "normalized": [] }, { "id": "PMID-9764481_T2", "type": "Protein", "text": [ "acid sphingomyelinase" ], "offsets": [ [ 178, 199 ] ], "normalized": [] }, { "id": "PMID-9764481_T3", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 202, 208 ] ], "normalized": [] }, { "id": "PMID-9764481_T4", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 310, 316 ] ], "normalized": [] }, { "id": "PMID-9764481_T5", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 321, 327 ] ], "normalized": [] }, { "id": "PMID-9764481_T6", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 535, 541 ] ], "normalized": [] }, { "id": "PMID-9764481_T7", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 677, 683 ] ], "normalized": [] }, { "id": "PMID-9764481_T8", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 828, 834 ] ], "normalized": [] }, { "id": "PMID-9764481_T9", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 995, 1001 ] ], "normalized": [] }, { "id": "PMID-9764481_T10", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 1061, 1067 ] ], "normalized": [] }, { "id": "PMID-9764481_T11", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 1072, 1078 ] ], "normalized": [] }, { "id": "PMID-9764481_T12", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 1226, 1232 ] ], "normalized": [] }, { "id": "PMID-9764481_T13", "type": "Protein", "text": [ "aSMase" ], "offsets": [ [ 1462, 1468 ] ], "normalized": [] } ]

[ { "id": "PMID-9764481_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 713, 725 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9764481_T7" } ] }, { "id": "PMID-9764481_E2", "type": "Glycosylation", "trigger": { "text": [ "N-glycosylation" ], "offsets": [ [ 850, 865 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9764481_T9" } ] } ]

[ { "id": "PMID-9764481_1", "entity_ids": [ "PMID-9764481_T2", "PMID-9764481_T3" ] } ]

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[ { "id": "PMID-9774646__text", "type": "abstract", "text": [ "Persistent interactions of core histone tails with nucleosomal DNA following acetylation and transcription factor binding. \nIn this study, we examined the effect of acetylation of the NH2 tails of core histones on their binding to nucleosomal DNA in the absence or presence of bound transcription factors. To do this, we used a novel UV laser-induced protein-DNA cross-linking technique, combined with immunochemical and molecular biology approaches. Nucleosomes containing one or five GAL4 binding sites were reconstituted with hypoacetylated or hyperacetylated core histones. Within these reconstituted particles, UV laser-induced histone-DNA cross-linking was found to occur only via the nonstructured histone tails and thus presented a unique tool for studying histone tail interactions with nucleosomal DNA. Importantly, these studies demonstrated that the NH2 tails were not released from nucleosomal DNA upon histone acetylation, although some weakening of their interactions was observed at elevated ionic strengths. Moreover, the binding of up to five GAL4-AH dimers to nucleosomes occupying the central 90 bp occurred without displacement of the histone NH2 tails from DNA. GAL4-AH binding perturbed the interaction of each histone tail with nucleosomal DNA to different degrees. However, in all cases, greater than 50% of the interactions between the histone tails and DNA was retained upon GAL4-AH binding, even if the tails were highly acetylated. These data illustrate an interaction of acetylated or nonacetylated histone tails with DNA that persists in the presence of simultaneously bound transcription factors.\n" ], "offsets": [ [ 0, 1629 ] ] } ]

[ { "id": "PMID-9774646_T1", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 32, 39 ] ], "normalized": [] }, { "id": "PMID-9774646_T2", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 202, 210 ] ], "normalized": [] }, { "id": "PMID-9774646_T3", "type": "Protein", "text": [ "GAL4" ], "offsets": [ [ 486, 490 ] ], "normalized": [] }, { "id": "PMID-9774646_T4", "type": "Protein", "text": [ "histones" ], "offsets": [ [ 568, 576 ] ], "normalized": [] }, { "id": "PMID-9774646_T5", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 633, 640 ] ], "normalized": [] }, { "id": "PMID-9774646_T6", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 705, 712 ] ], "normalized": [] }, { "id": "PMID-9774646_T7", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 765, 772 ] ], "normalized": [] }, { "id": "PMID-9774646_T8", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 916, 923 ] ], "normalized": [] }, { "id": "PMID-9774646_T9", "type": "Protein", "text": [ "GAL4" ], "offsets": [ [ 1061, 1065 ] ], "normalized": [] }, { "id": "PMID-9774646_T10", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 1156, 1163 ] ], "normalized": [] }, { "id": "PMID-9774646_T11", "type": "Protein", "text": [ "GAL4" ], "offsets": [ [ 1184, 1188 ] ], "normalized": [] }, { "id": "PMID-9774646_T12", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 1234, 1241 ] ], "normalized": [] }, { "id": "PMID-9774646_T13", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 1362, 1369 ] ], "normalized": [] }, { "id": "PMID-9774646_T14", "type": "Protein", "text": [ "GAL4" ], "offsets": [ [ 1402, 1406 ] ], "normalized": [] }, { "id": "PMID-9774646_T15", "type": "Protein", "text": [ "histone" ], "offsets": [ [ 1529, 1536 ] ], "normalized": [] }, { "id": "PMID-9774646_T16", "type": "Entity", "text": [ "tails" ], "offsets": [ [ 40, 45 ] ], "normalized": [] }, { "id": "PMID-9774646_T19", "type": "Entity", "text": [ "NH2 tails" ], "offsets": [ [ 184, 193 ] ], "normalized": [] }, { "id": "PMID-9774646_T23", "type": "Entity", "text": [ "tails" ], "offsets": [ [ 1431, 1436 ] ], "normalized": [] }, { "id": "PMID-9774646_T27", "type": "Entity", "text": [ "tails" ], "offsets": [ [ 1537, 1542 ] ], "normalized": [] } ]

[ { "id": "PMID-9774646_E1", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 77, 88 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9774646_T1" }, { "role": "Site", "ref_id": "PMID-9774646_T16" } ] }, { "id": "PMID-9774646_E2", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 165, 176 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9774646_T2" }, { "role": "Site", "ref_id": "PMID-9774646_T19" } ] }, { "id": "PMID-9774646_E3", "type": "Acetylation", "trigger": { "text": [ "hypoacetylated" ], "offsets": [ [ 529, 543 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9774646_T4" } ] }, { "id": "PMID-9774646_E4", "type": "Acetylation", "trigger": { "text": [ "hyperacetylated" ], "offsets": [ [ 547, 562 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9774646_T4" } ] }, { "id": "PMID-9774646_E5", "type": "Acetylation", "trigger": { "text": [ "acetylation" ], "offsets": [ [ 924, 935 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9774646_T8" } ] }, { "id": "PMID-9774646_E6", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 1449, 1459 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9774646_T13" }, { "role": "Site", "ref_id": "PMID-9774646_T23" } ] }, { "id": "PMID-9774646_E7", "type": "Acetylation", "trigger": { "text": [ "acetylated" ], "offsets": [ [ 1501, 1511 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9774646_T15" }, { "role": "Site", "ref_id": "PMID-9774646_T27" } ] }, { "id": "PMID-9774646_E8", "type": "Acetylation", "trigger": { "text": [ "nonacetylated" ], "offsets": [ [ 1515, 1528 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9774646_T15" }, { "role": "Site", "ref_id": "PMID-9774646_T27" } ] } ]

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[ { "id": "PMID-9799232__text", "type": "abstract", "text": [ "CpG-DNA-specific activation of antigen-presenting cells requires stress kinase activity and is preceded by non-specific endocytosis and endosomal maturation. \nUnmethylated CpG motifs in bacterial DNA, plasmid DNA and synthetic oligodeoxynucleotides (CpG ODN) activate dendritic cells (DC) and macrophages in a CD40-CD40 ligand-independent fashion. To understand the molecular mechanisms involved we focused on the cellular uptake of CpG ODN, the need for endosomal maturation and the role of the stress kinase pathway. Here we demonstrate that CpG-DNA induces phosphorylation of Jun N-terminal kinase kinase 1 (JNKK1/SEK/MKK4) and subsequent activation of the stress kinases JNK1/2 and p38 in murine macrophages and dendritic cells. This leads to activation of the transcription factor activating protein-1 (AP-1) via phosphorylation of its constituents c-Jun and ATF2. Moreover, stress kinase activation is essential for CpG-DNA-induced cytokine release of tumor necrosis factor alpha (TNFalpha) and interleukin-12 (IL-12), as inhibition of p38 results in severe impairment of this biological response. We further demonstrate that cellular uptake via endocytosis and subsequent endosomal maturation is essential for signalling, since competition by non-CpG-DNA or compounds blocking endosomal maturation such as chloroquine or bafilomycin A prevent all aspects of cellular activation. The data suggest that endosomal maturation is required for translation of intraendosomal CpG ODN sequences into signalling via the stress kinase pathway, where p38 kinase activation represents an essential step in CpG-ODN-triggered activation of antigen-presenting cells.\n" ], "offsets": [ [ 0, 1658 ] ] } ]

[ { "id": "PMID-9799232_T1", "type": "Protein", "text": [ "CD40" ], "offsets": [ [ 310, 314 ] ], "normalized": [] }, { "id": "PMID-9799232_T2", "type": "Protein", "text": [ "CD40 ligand" ], "offsets": [ [ 315, 326 ] ], "normalized": [] }, { "id": "PMID-9799232_T3", "type": "Protein", "text": [ "Jun N-terminal kinase kinase 1" ], "offsets": [ [ 579, 609 ] ], "normalized": [] }, { "id": "PMID-9799232_T4", "type": "Protein", "text": [ "JNKK1" ], "offsets": [ [ 611, 616 ] ], "normalized": [] }, { "id": "PMID-9799232_T5", "type": "Protein", "text": [ "SEK" ], "offsets": [ [ 617, 620 ] ], "normalized": [] }, { "id": "PMID-9799232_T6", "type": "Protein", "text": [ "MKK4" ], "offsets": [ [ 621, 625 ] ], "normalized": [] }, { "id": "PMID-9799232_T7", "type": "Protein", "text": [ "JNK1" ], "offsets": [ [ 675, 679 ] ], "normalized": [] }, { "id": "PMID-9799232_T8", "type": "Protein", "text": [ "2" ], "offsets": [ [ 680, 681 ] ], "normalized": [] }, { "id": "PMID-9799232_T9", "type": "Protein", "text": [ "activating protein-1" ], "offsets": [ [ 786, 806 ] ], "normalized": [] }, { "id": "PMID-9799232_T10", "type": "Protein", "text": [ "AP-1" ], "offsets": [ [ 808, 812 ] ], "normalized": [] }, { "id": "PMID-9799232_T11", "type": "Protein", "text": [ "c-Jun" ], "offsets": [ [ 854, 859 ] ], "normalized": [] }, { "id": "PMID-9799232_T12", "type": "Protein", "text": [ "ATF2" ], "offsets": [ [ 864, 868 ] ], "normalized": [] }, { "id": "PMID-9799232_T13", "type": "Protein", "text": [ "tumor necrosis factor alpha" ], "offsets": [ [ 958, 985 ] ], "normalized": [] }, { "id": "PMID-9799232_T14", "type": "Protein", "text": [ "TNFalpha" ], "offsets": [ [ 987, 995 ] ], "normalized": [] } ]

[ { "id": "PMID-9799232_E1", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 560, 575 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9799232_T3" } ] }, { "id": "PMID-9799232_E2", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 818, 833 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9799232_T11" } ] }, { "id": "PMID-9799232_E3", "type": "Phosphorylation", "trigger": { "text": [ "phosphorylation" ], "offsets": [ [ 818, 833 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9799232_T12" } ] } ]

[ { "id": "PMID-9799232_1", "entity_ids": [ "PMID-9799232_T3", "PMID-9799232_T4", "PMID-9799232_T5", "PMID-9799232_T6" ] }, { "id": "PMID-9799232_2", "entity_ids": [ "PMID-9799232_T9", "PMID-9799232_T10" ] }, { "id": "PMID-9799232_3", "entity_ids": [ "PMID-9799232_T13", "PMID-9799232_T14" ] } ]

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[ { "id": "PMID-9817751__text", "type": "abstract", "text": [ "A role for the DnaJ homologue Scj1p in protein folding in the yeast endoplasmic reticulum. \nMembers of the eukaryotic heat shock protein 70 family (Hsp70s) are regulated by protein cofactors that contain domains homologous to bacterial DnaJ. Of the three DnaJ homologues in the yeast rough endoplasmic reticulum (RER; Scj1p, Sec63p, and Jem1p), Scj1p is most closely related to DnaJ, hence it is a probable cofactor for Kar2p, the major Hsp70 in the yeast RER. However, the physiological role of Scj1p has remained obscure due to the lack of an obvious defect in Kar2p-mediated pathways in scj1 null mutants. Here, we show that the Deltascj1 mutant is hypersensitive to tunicamycin or mutations that reduce N-linked glycosylation of proteins. Although maturation of glycosylated carboxypeptidase Y occurs with wild-type kinetics in Deltascj1 cells, the transport rate for an unglycosylated mutant carboxypeptidase Y (CPY) is markedly reduced. Loss of Scj1p induces the unfolded protein response pathway, and results in a cell wall defect when combined with an oligosaccharyltransferase mutation. The combined loss of both Scj1p and Jem1p exaggerates the sensitivity to hypoglycosylation stress, leads to further induction of the unfolded protein response pathway, and drastically delays maturation of an unglycosylated reporter protein in the RER. We propose that the major role for Scj1p is to cooperate with Kar2p to mediate maturation of proteins in the RER lumen.\n" ], "offsets": [ [ 0, 1468 ] ] } ]

[ { "id": "PMID-9817751_T1", "type": "Protein", "text": [ "DnaJ" ], "offsets": [ [ 15, 19 ] ], "normalized": [] }, { "id": "PMID-9817751_T2", "type": "Protein", "text": [ "Scj1p" ], "offsets": [ [ 30, 35 ] ], "normalized": [] }, { "id": "PMID-9817751_T3", "type": "Protein", "text": [ "DnaJ" ], "offsets": [ [ 236, 240 ] ], "normalized": [] }, { "id": "PMID-9817751_T4", "type": "Protein", "text": [ "DnaJ" ], "offsets": [ [ 255, 259 ] ], "normalized": [] }, { "id": "PMID-9817751_T5", "type": "Protein", "text": [ "Scj1p" ], "offsets": [ [ 318, 323 ] ], "normalized": [] }, { "id": "PMID-9817751_T6", "type": "Protein", "text": [ "Sec63p" ], "offsets": [ [ 325, 331 ] ], "normalized": [] }, { "id": "PMID-9817751_T7", "type": "Protein", "text": [ "Jem1p" ], "offsets": [ [ 337, 342 ] ], "normalized": [] }, { "id": "PMID-9817751_T8", "type": "Protein", "text": [ "Scj1p" ], "offsets": [ [ 345, 350 ] ], "normalized": [] }, { "id": "PMID-9817751_T9", "type": "Protein", "text": [ "DnaJ" ], "offsets": [ [ 378, 382 ] ], "normalized": [] }, { "id": "PMID-9817751_T10", "type": "Protein", "text": [ "Kar2p" ], "offsets": [ [ 420, 425 ] ], "normalized": [] }, { "id": "PMID-9817751_T11", "type": "Protein", "text": [ "Scj1p" ], "offsets": [ [ 496, 501 ] ], "normalized": [] }, { "id": "PMID-9817751_T12", "type": "Protein", "text": [ "Kar2p" ], "offsets": [ [ 563, 568 ] ], "normalized": [] }, { "id": "PMID-9817751_T13", "type": "Protein", "text": [ "scj1" ], "offsets": [ [ 590, 594 ] ], "normalized": [] }, { "id": "PMID-9817751_T14", "type": "Protein", "text": [ "scj1" ], "offsets": [ [ 637, 641 ] ], "normalized": [] }, { "id": "PMID-9817751_T15", "type": "Protein", "text": [ "carboxypeptidase Y" ], "offsets": [ [ 779, 797 ] ], "normalized": [] }, { "id": "PMID-9817751_T16", "type": "Protein", "text": [ "scj1" ], "offsets": [ [ 837, 841 ] ], "normalized": [] }, { "id": "PMID-9817751_T17", "type": "Protein", "text": [ "carboxypeptidase Y" ], "offsets": [ [ 897, 915 ] ], "normalized": [] }, { "id": "PMID-9817751_T18", "type": "Protein", "text": [ "CPY" ], "offsets": [ [ 917, 920 ] ], "normalized": [] }, { "id": "PMID-9817751_T19", "type": "Protein", "text": [ "Scj1p" ], "offsets": [ [ 951, 956 ] ], "normalized": [] }, { "id": "PMID-9817751_T20", "type": "Protein", "text": [ "Scj1p" ], "offsets": [ [ 1122, 1127 ] ], "normalized": [] }, { "id": "PMID-9817751_T21", "type": "Protein", "text": [ "Jem1p" ], "offsets": [ [ 1132, 1137 ] ], "normalized": [] }, { "id": "PMID-9817751_T22", "type": "Protein", "text": [ "Scj1p" ], "offsets": [ [ 1383, 1388 ] ], "normalized": [] }, { "id": "PMID-9817751_T23", "type": "Protein", "text": [ "Kar2p" ], "offsets": [ [ 1410, 1415 ] ], "normalized": [] } ]

[ { "id": "PMID-9817751_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylated" ], "offsets": [ [ 766, 778 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9817751_T15" } ] }, { "id": "PMID-9817751_E2", "type": "Glycosylation", "trigger": { "text": [ "unglycosylated" ], "offsets": [ [ 875, 889 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9817751_T17" } ] } ]

[ { "id": "PMID-9817751_1", "entity_ids": [ "PMID-9817751_T17", "PMID-9817751_T18" ] } ]

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[ { "id": "PMID-9837786__text", "type": "abstract", "text": [ "The attachment protein of Hendra virus has high structural similarity but limited primary sequence homology compared with viruses in the genus Paramyxovirus. \nThe complete nucleotide sequence of the attachment protein gene of Hendra virus, a new member of the subfamily Paramyxovirinae, has been determined from cDNA clones derived from viral genomic RNA. The deduced mRNA is 2565 nucleotides long with one open reading frame encoding a protein of 604 amino acids, which is similar in size to the attachment protein of the members of the subfamily. However, the mRNA transcript is >600 nucleotides longer than others in the subfamily due to the presence of long untranslated regions at both the 5' and 3' ends. The protein is designated G because it lacks both hemagglutination and neuraminidase activities. It contains a hydrophobic transmembrane domain close to the N terminus, eight potential N-linked glycosylation sites, and 18 cysteine residues. Although the HeV G protein had low sequence homology with Paramyxovirinae members, the predicted folding pattern of its extracellular globular head was very similar to that of members of the genus Paramyxovirus, with the location of seven potential pairs of sulfide bonds absolutely conserved. On the other hand, among the seven residues known to be critical for neuraminidase activity, only one was conserved in the Hendra virus G protein compared with at least six in HN proteins of paramyxoviruses and rubulaviruses and four in H proteins of morbilliviruses. The biological significance of this finding is discussed.\n" ], "offsets": [ [ 0, 1572 ] ] } ]

[ { "id": "PMID-9837786_T1", "type": "Protein", "text": [ "G" ], "offsets": [ [ 737, 738 ] ], "normalized": [] }, { "id": "PMID-9837786_T2", "type": "Protein", "text": [ "G" ], "offsets": [ [ 969, 970 ] ], "normalized": [] }, { "id": "PMID-9837786_T3", "type": "Protein", "text": [ "G" ], "offsets": [ [ 1382, 1383 ] ], "normalized": [] }, { "id": "PMID-9837786_T4", "type": "Protein", "text": [ "HN" ], "offsets": [ [ 1422, 1424 ] ], "normalized": [] }, { "id": "PMID-9837786_T5", "type": "Protein", "text": [ "H" ], "offsets": [ [ 1483, 1484 ] ], "normalized": [] } ]

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[ { "id": "PMID-9837804__text", "type": "abstract", "text": [ "Human herpesvirus-8 glycoprotein B interacts with Epstein-Barr virus (EBV) glycoprotein 110 but fails to complement the infectivity of EBV mutants. \nTo characterize human herpesvirus 8 (HHV-8) gB, the open reading frame was PCR amplified from the HHV-8-infected cell line BCBL-1 and cloned into an expression vector. To facilitate detection of expressed HHV-8 gB, the cytoplasmic tail of the glycoprotein was tagged with the influenza hemagglutinin (HA) epitope. Expression of tagged HHV-8 gB (gB-HA), as well as the untagged form, was readily detected in CHO-K1 cells and several lymphoblastoid cell lines (LCLs). HHV-8 gB-HA was sensitive to endoglycosidase H treatment, and immunofluorescence revealed that HHV-8 gB-HA was detectable in the perinuclear region of CHO-K1 cells. These observations suggest that HHV-8 gB is not processed in the Golgi and localizes to the endoplasmic reticulum or nuclear membrane. Because both HHV-8 and EBV are gamma-herpesviruses, the ability of HHV-8 gB to interact with and functionally complement EBV gp110 was examined. HHV-8 gB-HA and EBV gp110 co-immunoprecipitated, indicating formation of hetero-oligomers. However, HHV-8 gB-HA and HHV-8 gB failed to restore the infectivity of gp110-negative EBV mutants. These findings indicate that although HHV-8 gB and EBV gp110 have similar patterns of intracellular localization and can interact, there is not sufficient functional homology to allow efficient complementation.\n" ], "offsets": [ [ 0, 1461 ] ] } ]

[ { "id": "PMID-9837804_T1", "type": "Protein", "text": [ "B" ], "offsets": [ [ 33, 34 ] ], "normalized": [] }, { "id": "PMID-9837804_T2", "type": "Protein", "text": [ "glycoprotein 110" ], "offsets": [ [ 75, 91 ] ], "normalized": [] }, { "id": "PMID-9837804_T3", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 193, 195 ] ], "normalized": [] }, { "id": "PMID-9837804_T4", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 360, 362 ] ], "normalized": [] }, { "id": "PMID-9837804_T5", "type": "Protein", "text": [ "hemagglutinin" ], "offsets": [ [ 435, 448 ] ], "normalized": [] }, { "id": "PMID-9837804_T6", "type": "Protein", "text": [ "HA" ], "offsets": [ [ 450, 452 ] ], "normalized": [] }, { "id": "PMID-9837804_T7", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 490, 492 ] ], "normalized": [] }, { "id": "PMID-9837804_T8", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 494, 496 ] ], "normalized": [] }, { "id": "PMID-9837804_T9", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 621, 623 ] ], "normalized": [] }, { "id": "PMID-9837804_T10", "type": "Protein", "text": [ "endoglycosidase H" ], "offsets": [ [ 644, 661 ] ], "normalized": [] }, { "id": "PMID-9837804_T11", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 716, 718 ] ], "normalized": [] }, { "id": "PMID-9837804_T12", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 818, 820 ] ], "normalized": [] }, { "id": "PMID-9837804_T13", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 988, 990 ] ], "normalized": [] }, { "id": "PMID-9837804_T14", "type": "Protein", "text": [ "gp110" ], "offsets": [ [ 1040, 1045 ] ], "normalized": [] }, { "id": "PMID-9837804_T15", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 1066, 1068 ] ], "normalized": [] }, { "id": "PMID-9837804_T16", "type": "Protein", "text": [ "gp110" ], "offsets": [ [ 1080, 1085 ] ], "normalized": [] }, { "id": "PMID-9837804_T17", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 1166, 1168 ] ], "normalized": [] }, { "id": "PMID-9837804_T18", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 1182, 1184 ] ], "normalized": [] }, { "id": "PMID-9837804_T19", "type": "Protein", "text": [ "gp110" ], "offsets": [ [ 1222, 1227 ] ], "normalized": [] }, { "id": "PMID-9837804_T20", "type": "Protein", "text": [ "gB" ], "offsets": [ [ 1294, 1296 ] ], "normalized": [] }, { "id": "PMID-9837804_T21", "type": "Protein", "text": [ "gp110" ], "offsets": [ [ 1305, 1310 ] ], "normalized": [] } ]

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[ { "id": "PMID-9837804_1", "entity_ids": [ "PMID-9837804_T5", "PMID-9837804_T6" ] } ]

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[ { "id": "PMID-9848395__text", "type": "abstract", "text": [ "Inhibitory effect of ginsenoside on the mediator release in the guinea pig lung mast cells activated by specific antigen-antibody reactions. \nWe reported that some components of ginsenosides decreased mediator release which was evoked by the activation of mast cells caused by specific antigen-antibody reactions. This study aimed to assess the effects of ginsenoside, Rb1, which belongs to the protopanaxadiol, on the mechanism of mediator release during mast cell activation. Pretreatment of Rb1 (100 microg) significantly decreased histamine and leukotriene in a dose-dependent manner during mast cell activation. The PLD activity during mast cell activation decreased in the pretreatment of Rb1 (300 microg). The amount of DAG produced by PLC activity decreased because of Rb1 pretreatment. The amount of mass DAG decreased due to Rb1 pretreatment during mast cell activation. Rb1 (300 microg) pretreatment strongly inhibited the incorporation of the [3H]methyl moiety into phospholipids. The data suggest that Rb1, purified from Korean Red Ginseng Radix, inhibits an increase of DAG production during mast cell activation caused by antigen-antibody reactions, which is mediated via phosphatidylcholine-PLD and phosphatidylinositol-PLC systems. This is then followed by the inhibition of histamine releases. Furthermore, Rb1 reduces the phosphatidylcholine production by inhibiting the methyl-transferase I and II, and the reduction of phosphatidylcholine production inhibits leukotriene release.\n" ], "offsets": [ [ 0, 1501 ] ] } ]

[ { "id": "PMID-9848395_T1", "type": "Protein", "text": [ "PLD" ], "offsets": [ [ 621, 624 ] ], "normalized": [] }, { "id": "PMID-9848395_T2", "type": "Protein", "text": [ "PLD" ], "offsets": [ [ 1207, 1210 ] ], "normalized": [] } ]

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[ { "id": "PMID-9877231__text", "type": "abstract", "text": [ "Purine nucleotide- and sugar phosphate-induced inhibition of the carboxyl methylation and catalysis of protein phosphatase-2A in insulin-secreting cells: protection by divalent cations. \nRecently, we demonstrated that the 36 kDa catalytic subunit of protein phosphatase 2A (PP2Ac) undergoes methylation at its C-terminal leucine in normal rat islets, human islets and isolated beta cells; this modification increases the catalytic activity of PP2A [Kowluru et al. Endocrinology. 137:2315-2323, 1996]. Previous studies have suggested that adenine and guanine nucleotides or glycolytic intermediates [which are critical mediators in beta cell function] also modulate phosphatase activity in the pancreatic beta cell. Therefore, we examined whether these phosphorylated molecules specifically regulate the carboxyl methylation and the catalytic activity of PP2A in beta cells. Micromolar concentrations of ATP, ADP, GTP or GDP each inhibited the carboxyl methylation of PP2Ac and, to a lesser degree, the catalytic activity of PP2A. Likewise, the carboxyl methylation of PP2Ac and its catalytic activity were inhibited by [mono- or di-] phosphates of glucose or fructose. Additionally, however, the carboxyl methylation of PP2Ac was significantly stimulated by divalent metal ions (Mn2+ > Mg2+ > Ca2+ > control). The nucleotide or sugar phosphate-mediated inhibition of carboxyl methylation of PP2Ac and the catalytic activity of PP2A were completely prevented by Mn2+ or Mg2+. These data indicate that divalent metal ions protect against the inhibition by purine nucleotides or sugar phosphates of the carboxyl methylation of PP2Ac perhaps permitting PP2A to function under physiologic conditions. Therefore, these data warrant caution in interpretation of extant data on the regulation of phosphatase function by purine nucleotides.\n" ], "offsets": [ [ 0, 1832 ] ] } ]

[ { "id": "PMID-9877231_T1", "type": "Protein", "text": [ "insulin" ], "offsets": [ [ 129, 136 ] ], "normalized": [] } ]

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[ { "id": "PMID-9880569__text", "type": "abstract", "text": [ "Enzymatic characteristics of recombinant medium isozyme of 2'-5' oligoadenylate synthetase. \nP69 is an isozyme of the medium size class of human 2'-5' oligoadenylate synthetases. In this study, recombinant P69 was expressed and used for enzymological and structural investigations. Bacterially expressed P69 was inactive whereas the same protein expressed in insect cells was highly active. Whether this difference could be due to differential post-translational modifications of the protein was investigated. Mutations of appropriate residues showed that myristoylation of the protein was not necessary for enzyme activity. In contrast, inhibition of glycosylation of P69, by tunicamycin treatment of the insect cells, produced an enzymatically inactive protein. Recombinant P69 produced in insect cells was purified by affinity chromatography. It was a dimeric glycoprotein, very stable and completely dependent on double stranded (ds) RNA for activity. The enzyme catalyzed the non-processive synthesis of 2'-5'-linked oligoadenylate products containing up to 30 residues. 2'-O-Methylated dsRNA was incapable of activating P69 and a 25-base pair dsRNA was as effective as larger dsRNA. This expression system will be useful for large scale production of P69 and its mutants for structural studies.\n" ], "offsets": [ [ 0, 1301 ] ] } ]

[ { "id": "PMID-9880569_T1", "type": "Protein", "text": [ "P69" ], "offsets": [ [ 93, 96 ] ], "normalized": [] }, { "id": "PMID-9880569_T2", "type": "Protein", "text": [ "P69" ], "offsets": [ [ 206, 209 ] ], "normalized": [] }, { "id": "PMID-9880569_T3", "type": "Protein", "text": [ "P69" ], "offsets": [ [ 304, 307 ] ], "normalized": [] }, { "id": "PMID-9880569_T4", "type": "Protein", "text": [ "P69" ], "offsets": [ [ 669, 672 ] ], "normalized": [] }, { "id": "PMID-9880569_T5", "type": "Protein", "text": [ "P69" ], "offsets": [ [ 776, 779 ] ], "normalized": [] }, { "id": "PMID-9880569_T6", "type": "Protein", "text": [ "P69" ], "offsets": [ [ 1126, 1129 ] ], "normalized": [] }, { "id": "PMID-9880569_T7", "type": "Protein", "text": [ "P69" ], "offsets": [ [ 1257, 1260 ] ], "normalized": [] } ]

[ { "id": "PMID-9880569_E1", "type": "Glycosylation", "trigger": { "text": [ "glycosylation" ], "offsets": [ [ 652, 665 ] ] }, "arguments": [ { "role": "Theme", "ref_id": "PMID-9880569_T4" } ] } ]

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