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0 | PMID-10190553 | [
{
"id": "PMID-10190553__text",
"type": "abstract",
"text": [
"Regulation of connexin32 and connexin43 gene expression by DNA methylation in rat liver cells. \nGap junction proteins (connexins) are expressed in a cell-specific manner and expression is often reduced in neoplastic cells. We investigated the mechanisms of connexin32 (Cx32) and connexin43 (Cx43) expression in hepatic cells using MH1C1 rat hepatoma cells and freshly isolated, adult rat hepatocytes that express Cx32 but not Cx43 and WB-F344 rat liver epithelial cells that express Cx43 but not Cx32. Southern blotting after DNA restriction with MspI and HpaII indicated that two MspI/HpaII restriction sites in the Cx32 promoter (positions -147 and -847) were methylated in WB-F344 cells, but not in MH1C1 cells or hepatocytes. In contrast, an MspI/HpaII restriction site in the Cx43 promoter (position -38) was methylated in MH1C1 cells, but not in WB-F344 cells or hepatocytes. Transient transfection of the cell lines with connexin promoter-luciferase constructs indicated that the Cx32 promoter was 7-fold more active in MH1C1 cells and the Cx43 promoter was 5-fold more active in WB-F344 cells. These results suggest that transcription of Cx32 and Cx43 in hepatic cells is controlled by promoter methylation and by cell-specific transcription factors. Similar mechanisms may be involved in the reduced expression of these genes frequently observed in neoplastic cells.\n"
],
"offsets": [
[
0,
1376
]
]
}
] | [
{
"id": "PMID-10190553_T1",
"type": "Protein",
"text": [
"connexin32"
],
"offsets": [
[
14,
24
]
],
"normalized": []
},
{
"id": "PMID-10190553_T2",
"type": "Protein",
"text": [
"connexin43"
],
"offsets": [
[
29,
39
]
],
"normalized": []
},
{
"id": "PMID-10190553_T3",
"type": "Protein",
"text": [
"connexin32"
],
"offsets": [
[
257,
267
]
],
"normalized": []
},
{
"id": "PMID-10190553_T4",
"type": "Protein",
"text": [
"Cx32"
],
"offsets": [
[
269,
273
]
],
"normalized": []
},
{
"id": "PMID-10190553_T5",
"type": "Protein",
"text": [
"connexin43"
],
"offsets": [
[
279,
289
]
],
"normalized": []
},
{
"id": "PMID-10190553_T6",
"type": "Protein",
"text": [
"Cx43"
],
"offsets": [
[
291,
295
]
],
"normalized": []
},
{
"id": "PMID-10190553_T7",
"type": "Protein",
"text": [
"Cx32"
],
"offsets": [
[
413,
417
]
],
"normalized": []
},
{
"id": "PMID-10190553_T8",
"type": "Protein",
"text": [
"Cx43"
],
"offsets": [
[
426,
430
]
],
"normalized": []
},
{
"id": "PMID-10190553_T9",
"type": "Protein",
"text": [
"Cx43"
],
"offsets": [
[
483,
487
]
],
"normalized": []
},
{
"id": "PMID-10190553_T10",
"type": "Protein",
"text": [
"Cx32"
],
"offsets": [
[
496,
500
]
],
"normalized": []
},
{
"id": "PMID-10190553_T11",
"type": "Protein",
"text": [
"MspI"
],
"offsets": [
[
547,
551
]
],
"normalized": []
},
{
"id": "PMID-10190553_T12",
"type": "Protein",
"text": [
"HpaII"
],
"offsets": [
[
556,
561
]
],
"normalized": []
},
{
"id": "PMID-10190553_T13",
"type": "Protein",
"text": [
"MspI"
],
"offsets": [
[
581,
585
]
],
"normalized": []
},
{
"id": "PMID-10190553_T14",
"type": "Protein",
"text": [
"HpaII"
],
"offsets": [
[
586,
591
]
],
"normalized": []
},
{
"id": "PMID-10190553_T15",
"type": "Protein",
"text": [
"Cx32"
],
"offsets": [
[
617,
621
]
],
"normalized": []
},
{
"id": "PMID-10190553_T16",
"type": "Protein",
"text": [
"MspI"
],
"offsets": [
[
746,
750
]
],
"normalized": []
},
{
"id": "PMID-10190553_T17",
"type": "Protein",
"text": [
"HpaII"
],
"offsets": [
[
751,
756
]
],
"normalized": []
},
{
"id": "PMID-10190553_T18",
"type": "Protein",
"text": [
"Cx43"
],
"offsets": [
[
781,
785
]
],
"normalized": []
},
{
"id": "PMID-10190553_T19",
"type": "Protein",
"text": [
"luciferase"
],
"offsets": [
[
946,
956
]
],
"normalized": []
},
{
"id": "PMID-10190553_T20",
"type": "Protein",
"text": [
"Cx32"
],
"offsets": [
[
987,
991
]
],
"normalized": []
},
{
"id": "PMID-10190553_T21",
"type": "Protein",
"text": [
"Cx43"
],
"offsets": [
[
1047,
1051
]
],
"normalized": []
},
{
"id": "PMID-10190553_T22",
"type": "Protein",
"text": [
"Cx32"
],
"offsets": [
[
1146,
1150
]
],
"normalized": []
},
{
"id": "PMID-10190553_T23",
"type": "Protein",
"text": [
"Cx43"
],
"offsets": [
[
1155,
1159
]
],
"normalized": []
},
{
"id": "PMID-10190553_T24",
"type": "Entity",
"text": [
"positions -147"
],
"offsets": [
[
632,
646
]
],
"normalized": []
},
{
"id": "PMID-10190553_T25",
"type": "Entity",
"text": [
"-847"
],
"offsets": [
[
651,
655
]
],
"normalized": []
},
{
"id": "PMID-10190553_T27",
"type": "Entity",
"text": [
"position -38"
],
"offsets": [
[
796,
808
]
],
"normalized": []
},
{
"id": "PMID-10190553_T29",
"type": "Entity",
"text": [
"promoter"
],
"offsets": [
[
1194,
1202
]
],
"normalized": []
}
] | [
{
"id": "PMID-10190553_E1",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
662,
672
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10190553_T15"
},
{
"role": "Site",
"ref_id": "PMID-10190553_T24"
}
]
},
{
"id": "PMID-10190553_E2",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
662,
672
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10190553_T15"
},
{
"role": "Site",
"ref_id": "PMID-10190553_T25"
}
]
},
{
"id": "PMID-10190553_E3",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
662,
672
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10190553_T15"
},
{
"role": "Site",
"ref_id": "PMID-10190553_T24"
}
]
},
{
"id": "PMID-10190553_E4",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
662,
672
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10190553_T15"
},
{
"role": "Site",
"ref_id": "PMID-10190553_T25"
}
]
},
{
"id": "PMID-10190553_E5",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
814,
824
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10190553_T18"
},
{
"role": "Site",
"ref_id": "PMID-10190553_T27"
}
]
},
{
"id": "PMID-10190553_E6",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
814,
824
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10190553_T18"
},
{
"role": "Site",
"ref_id": "PMID-10190553_T27"
}
]
},
{
"id": "PMID-10190553_E7",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1203,
1214
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10190553_T22"
},
{
"role": "Site",
"ref_id": "PMID-10190553_T29"
}
]
},
{
"id": "PMID-10190553_E8",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1203,
1214
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10190553_T23"
},
{
"role": "Site",
"ref_id": "PMID-10190553_T29"
}
]
}
] | [
{
"id": "PMID-10190553_1",
"entity_ids": [
"PMID-10190553_T3",
"PMID-10190553_T4"
]
},
{
"id": "PMID-10190553_2",
"entity_ids": [
"PMID-10190553_T5",
"PMID-10190553_T6"
]
}
] | [] |
1 | PMID-10196193 | [
{
"id": "PMID-10196193__text",
"type": "abstract",
"text": [
"CheY-dependent methylation of the asparagine receptor, McpB, during chemotaxis in Bacillus subtilis. \nFor the Gram-positive organism Bacillus subtilis, chemotaxis to the attractant asparagine is mediated by the chemoreceptor McpB. In this study, we show that rapid net demethylation of B. subtilis McpB results in the immediate production of methanol, presumably due to the action of CheB. We also show that net demethylation of McpB occurs upon both addition and removal of asparagine. After each demethylation event, McpB is remethylated to nearly prestimulus levels. Both remethylation events are attributable to CheR using S-adenosylmethionine as a substrate. Therefore, no methyl transfer to an intermediate carrier need be postulated to occur during chemotaxis in B. subtilis as was previously suggested. Furthermore, we show that the remethylation of asparagine-bound McpB requires the response regulator, CheY-P, suggesting that CheY-P acts in a feedback mechanism to facilitate adaptation to positive stimuli during chemotaxis in B. subtilis. This hypothesis is supported by two observations: a cheRBCD mutant is capable of transient excitation and subsequent oscillations that bring the flagellar rotational bias below the prestimulus value in the tethered cell assay, and the cheRBCD mutant is capable of swarming in a Tryptone swarm plate.\n"
],
"offsets": [
[
0,
1352
]
]
}
] | [
{
"id": "PMID-10196193_T1",
"type": "Protein",
"text": [
"CheY"
],
"offsets": [
[
0,
4
]
],
"normalized": []
},
{
"id": "PMID-10196193_T2",
"type": "Protein",
"text": [
"McpB"
],
"offsets": [
[
55,
59
]
],
"normalized": []
},
{
"id": "PMID-10196193_T3",
"type": "Protein",
"text": [
"McpB"
],
"offsets": [
[
225,
229
]
],
"normalized": []
},
{
"id": "PMID-10196193_T4",
"type": "Protein",
"text": [
"McpB"
],
"offsets": [
[
298,
302
]
],
"normalized": []
},
{
"id": "PMID-10196193_T5",
"type": "Protein",
"text": [
"CheB"
],
"offsets": [
[
384,
388
]
],
"normalized": []
},
{
"id": "PMID-10196193_T6",
"type": "Protein",
"text": [
"McpB"
],
"offsets": [
[
429,
433
]
],
"normalized": []
},
{
"id": "PMID-10196193_T7",
"type": "Protein",
"text": [
"McpB"
],
"offsets": [
[
519,
523
]
],
"normalized": []
},
{
"id": "PMID-10196193_T8",
"type": "Protein",
"text": [
"CheR"
],
"offsets": [
[
616,
620
]
],
"normalized": []
},
{
"id": "PMID-10196193_T9",
"type": "Protein",
"text": [
"McpB"
],
"offsets": [
[
875,
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]
],
"normalized": []
},
{
"id": "PMID-10196193_T10",
"type": "Protein",
"text": [
"CheY"
],
"offsets": [
[
913,
917
]
],
"normalized": []
},
{
"id": "PMID-10196193_T11",
"type": "Protein",
"text": [
"CheY"
],
"offsets": [
[
937,
941
]
],
"normalized": []
},
{
"id": "PMID-10196193_T12",
"type": "Protein",
"text": [
"cheR"
],
"offsets": [
[
1104,
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]
],
"normalized": []
},
{
"id": "PMID-10196193_T13",
"type": "Protein",
"text": [
"B"
],
"offsets": [
[
1108,
1109
]
],
"normalized": []
},
{
"id": "PMID-10196193_T14",
"type": "Protein",
"text": [
"C"
],
"offsets": [
[
1109,
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]
],
"normalized": []
},
{
"id": "PMID-10196193_T15",
"type": "Protein",
"text": [
"D"
],
"offsets": [
[
1110,
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]
],
"normalized": []
},
{
"id": "PMID-10196193_T16",
"type": "Protein",
"text": [
"cheR"
],
"offsets": [
[
1287,
1291
]
],
"normalized": []
},
{
"id": "PMID-10196193_T17",
"type": "Protein",
"text": [
"B"
],
"offsets": [
[
1291,
1292
]
],
"normalized": []
},
{
"id": "PMID-10196193_T18",
"type": "Protein",
"text": [
"C"
],
"offsets": [
[
1292,
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]
],
"normalized": []
},
{
"id": "PMID-10196193_T19",
"type": "Protein",
"text": [
"D"
],
"offsets": [
[
1293,
1294
]
],
"normalized": []
}
] | [
{
"id": "PMID-10196193_E1",
"type": "Methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
15,
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]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10196193_T2"
}
]
},
{
"id": "PMID-10196193_E2",
"type": "Demethylation",
"trigger": {
"text": [
"demethylation"
],
"offsets": [
[
269,
282
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10196193_T4"
}
]
},
{
"id": "PMID-10196193_E3",
"type": "Demethylation",
"trigger": {
"text": [
"demethylation"
],
"offsets": [
[
412,
425
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10196193_T6"
}
]
},
{
"id": "PMID-10196193_E4",
"type": "Methylation",
"trigger": {
"text": [
"remethylated"
],
"offsets": [
[
527,
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]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10196193_T7"
}
]
},
{
"id": "PMID-10196193_E5",
"type": "Methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
575,
588
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10196193_T7"
}
]
},
{
"id": "PMID-10196193_E6",
"type": "Catalysis",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
575,
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]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10196193_E5"
},
{
"role": "Cause",
"ref_id": "PMID-10196193_T8"
}
]
},
{
"id": "PMID-10196193_E7",
"type": "Methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
841,
854
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10196193_T9"
}
]
}
] | [] | [] |
2 | PMID-10209866 | [
{
"id": "PMID-10209866__text",
"type": "abstract",
"text": [
"Transglycosylation reactions of Bacillus stearothermophilus maltogenic amylase with acarbose and various acceptors. \nIt was observed that Bacillus stearothermophilus maltogenic amylase cleaved the first glycosidic bond of acarbose to produce glucose and a pseudotrisaccharide (PTS) that was transferred to C-6 of the glucose to give an alpha-(1-->6) glycosidic linkage and the formation of isoacarbose. The addition of a number of different carbohydrates to the digest gave transfer products in which PTS was primarily attached alpha-(1-->6) to D-glucose, D-mannose, D-galactose, and methyl alpha-D-glucopyranoside. With D-fructopyranose and D-xylopyranose, PTS was linked alpha-(1-->5) and alpha-(1-->4), respectively. PTS was primarily transferred to C-6 of the nonreducing residue of maltose, cellobiose, lactose, and gentiobiose. Lesser amounts of alpha-(1-->3) and/or alpha-(1-->4) transfer products were also observed for these carbohydrate acceptors. The major transfer product to sucrose gave PTS linked alpha-(1-->4) to the glucose residue. alpha,alpha-Trehalose gave two major products with PTS linked alpha-(1-->6) and alpha-(1-->4). Maltitol gave two major products with PTS linked alpha-(1-->6) and alpha-(1-->4) to the glucopyranose residue. Raffinose gave two major products with PTS linked alpha-(1-->6) and alpha-(1-->4) to the D-galactopyranose residue. Maltotriose gave two major products with PTS linked alpha-(1-->6) and alpha-(1-->4) to the nonreducing end glucopyranose residue. Xylitol gave PTS linked alpha-(1-->5) as the major product and D-glucitol gave PTS linked alpha-(1-->6) as the only product. The structures of the transfer products were determined using thin-layer chromatography, high-performance ion chromatography, enzyme hydrolysis, methylation analysis and 13C NMR spectroscopy. The best acceptor was gentiobiose, followed closely by maltose and cellobiose, and the weakest acceptor was D-glucitol.\n"
],
"offsets": [
[
0,
1939
]
]
}
] | [
{
"id": "PMID-10209866_T1",
"type": "Protein",
"text": [
"maltogenic amylase"
],
"offsets": [
[
60,
78
]
],
"normalized": []
},
{
"id": "PMID-10209866_T2",
"type": "Protein",
"text": [
"maltogenic amylase"
],
"offsets": [
[
166,
184
]
],
"normalized": []
}
] | [] | [] | [] |
3 | PMID-10219568 | [
{
"id": "PMID-10219568__text",
"type": "abstract",
"text": [
"A Plasmodium chabaudi chabaudi high molecular mass glycoprotein translocated to the host cell membrane by a non-classical secretory pathway. \nWe have purified and characterized a novel high molecular mass glycoprotein of P. chabaudi chabaudi (Pc550gp) that is transported to the erythrocyte membrane during the intraerythrocytic cycle. Immuno fluorescence assays with polyclonal monospecific antibodies against Pc550gp show that the protein to be localized in the periphery of young trophozoite stages i.e., on the plasma membrane or parasitophorous vacuole membrane. However, in late trophozoites and schizonts the antigen is distributed in both parasite and host cell membranes. These results were confirmed by immunoblotting of isolated parasites and infected host cell membranes at different stages of parasite development. Moreover, alkali extraction of purified infected erythrocyte membranes at mature stages of parasite development does not solubilize Pc550gp, suggesting that it is an integral membrane protein. In addition proteinase K digestion of intact infected host cells induced the disappearance of Pc550gp. Further indicating its transmembrane nature and that it presents extracellular domains susceptible to proteolysis. Brefeldin A or low temperature (15 degrees C) treatment did not affect the translocation of Pc550gp from the parasite compartments to the erythrocyte membrane, indicating that the secretion of Pc550gp does not follow the classical transport pathway described in most eukaryotic cells.\n"
],
"offsets": [
[
0,
1524
]
]
}
] | [
{
"id": "PMID-10219568_T1",
"type": "Protein",
"text": [
"Pc550gp"
],
"offsets": [
[
243,
250
]
],
"normalized": []
},
{
"id": "PMID-10219568_T2",
"type": "Protein",
"text": [
"Pc550gp"
],
"offsets": [
[
411,
418
]
],
"normalized": []
},
{
"id": "PMID-10219568_T3",
"type": "Protein",
"text": [
"Pc550gp"
],
"offsets": [
[
960,
967
]
],
"normalized": []
},
{
"id": "PMID-10219568_T4",
"type": "Protein",
"text": [
"Pc550gp"
],
"offsets": [
[
1115,
1122
]
],
"normalized": []
},
{
"id": "PMID-10219568_T5",
"type": "Protein",
"text": [
"Pc550gp"
],
"offsets": [
[
1331,
1338
]
],
"normalized": []
},
{
"id": "PMID-10219568_T6",
"type": "Protein",
"text": [
"Pc550gp"
],
"offsets": [
[
1432,
1439
]
],
"normalized": []
}
] | [] | [] | [] |
4 | PMID-10360176 | [
{
"id": "PMID-10360176__text",
"type": "abstract",
"text": [
"Novel roles for classical factors at the interface between translation termination and initiation. \nThe pathway of bacterial ribosome recycling following translation termination has remained obscure. Here, we elucidate two essential steps and describe the roles played by the three translation factors EF-G, RRF, and IF3. Release factor RF3 is known to catalyze the dissociation of RF1 or RF2 from ribosomes after polypeptide release. We show that the next step is dissociation of 50S subunits from the 70S posttermination complex and that it is catalyzed by RRF and EF-G and requires GTP hydrolysis. Removal of deacylated tRNA from the resulting 30S:mRNA:tRNA posttermination complex is then necessary to permit rapid 30S subunit recycling. We show that this step requires initiation factor IF3, whose role was previously thought to be restricted to promoting specific 30S initiation complex formation from free 30S subunits.\n"
],
"offsets": [
[
0,
927
]
]
}
] | [
{
"id": "PMID-10360176_T1",
"type": "Protein",
"text": [
"EF-G"
],
"offsets": [
[
302,
306
]
],
"normalized": []
},
{
"id": "PMID-10360176_T2",
"type": "Protein",
"text": [
"RRF"
],
"offsets": [
[
308,
311
]
],
"normalized": []
},
{
"id": "PMID-10360176_T3",
"type": "Protein",
"text": [
"IF3"
],
"offsets": [
[
317,
320
]
],
"normalized": []
},
{
"id": "PMID-10360176_T4",
"type": "Protein",
"text": [
"RF3"
],
"offsets": [
[
337,
340
]
],
"normalized": []
},
{
"id": "PMID-10360176_T5",
"type": "Protein",
"text": [
"RF1"
],
"offsets": [
[
382,
385
]
],
"normalized": []
},
{
"id": "PMID-10360176_T6",
"type": "Protein",
"text": [
"RF2"
],
"offsets": [
[
389,
392
]
],
"normalized": []
},
{
"id": "PMID-10360176_T7",
"type": "Protein",
"text": [
"RRF"
],
"offsets": [
[
559,
562
]
],
"normalized": []
},
{
"id": "PMID-10360176_T8",
"type": "Protein",
"text": [
"EF-G"
],
"offsets": [
[
567,
571
]
],
"normalized": []
},
{
"id": "PMID-10360176_T9",
"type": "Protein",
"text": [
"IF3"
],
"offsets": [
[
792,
795
]
],
"normalized": []
}
] | [] | [] | [] |
5 | PMID-10428866 | [
{
"id": "PMID-10428866__text",
"type": "abstract",
"text": [
"Effect of alternative glycosylation on insulin receptor processing. \nThe mature insulin receptor is a cell surface heterotetrameric glycoprotein composed of two alpha- and two beta-subunits. In 3T3-L1 adipocytes as in other cell types, the receptor is synthesized as a single polypeptide consisting of uncleaved alpha- and beta-subunits, migrating as a 190-kDa glycoprotein. To examine the importance of N-linked glycosylation on insulin receptor processing, we have used glucose deprivation as a tool to alter protein glycosylation. Western blot analysis shows that glucose deprivation led to a time-dependent accumulation of an alternative proreceptor of 170 kDa in a subcellular fraction consistent with endoplasmic reticulum localization. Co-precipitation assays provide evidence that the alternative proreceptor bound GRP78, an endoplasmic reticulum molecular chaperone. N-Glycosidase F treatment shows that the alternative proreceptor contained N-linked oligosaccharides. Yet, endoglycosidase H insensitivity indicates an aberrant oligosaccharide structure. Using pulse-chase methodology, we show that the synthetic rate was similar between the normal and alternative proreceptor. However, the normal proreceptor was processed into alpha- and beta-subunits (t((1)/(2)) = 1.3 +/- 0.6 h), while the alternative proreceptor was degraded (t((1)/(2)) = 5.1 +/- 0.6 h). Upon refeeding cells that were initially deprived of glucose, the alternative proreceptor was processed to a higher molecular weight form and gained sensitivity to endoglycosidase H. This \"intermediate\" form of the proreceptor was also degraded, although a small fraction escaped degradation, resulting in cleavage to the alpha- and beta-subunits. These data provide evidence for the first time that glucose deprivation leads to the accumulation of an alternative proreceptor, which can be post-translationally glycosylated with the readdition of glucose inducing both accelerated degradation and maturation.\n"
],
"offsets": [
[
0,
1979
]
]
}
] | [
{
"id": "PMID-10428866_T1",
"type": "Protein",
"text": [
"insulin receptor"
],
"offsets": [
[
39,
55
]
],
"normalized": []
},
{
"id": "PMID-10428866_T2",
"type": "Protein",
"text": [
"insulin receptor"
],
"offsets": [
[
80,
96
]
],
"normalized": []
},
{
"id": "PMID-10428866_T3",
"type": "Protein",
"text": [
"insulin receptor"
],
"offsets": [
[
430,
446
]
],
"normalized": []
},
{
"id": "PMID-10428866_T4",
"type": "Protein",
"text": [
"GRP78"
],
"offsets": [
[
823,
828
]
],
"normalized": []
},
{
"id": "PMID-10428866_T5",
"type": "Protein",
"text": [
"N-Glycosidase F"
],
"offsets": [
[
876,
891
]
],
"normalized": []
},
{
"id": "PMID-10428866_T6",
"type": "Protein",
"text": [
"endoglycosidase H"
],
"offsets": [
[
983,
1000
]
],
"normalized": []
},
{
"id": "PMID-10428866_T7",
"type": "Protein",
"text": [
"endoglycosidase H"
],
"offsets": [
[
1534,
1551
]
],
"normalized": []
},
{
"id": "PMID-10428866_T11",
"type": "Entity",
"text": [
"oligosaccharides"
],
"offsets": [
[
960,
976
]
],
"normalized": []
}
] | [
{
"id": "PMID-10428866_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"glycosylation"
],
"offsets": [
[
22,
35
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10428866_T1"
}
]
},
{
"id": "PMID-10428866_E2",
"type": "Glycosylation",
"trigger": {
"text": [
"N-linked glycosylation"
],
"offsets": [
[
404,
426
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10428866_T3"
}
]
},
{
"id": "PMID-10428866_E3",
"type": "Glycosylation",
"trigger": {
"text": [
"N-linked"
],
"offsets": [
[
951,
959
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10428866_T3"
},
{
"role": "Sidechain",
"ref_id": "PMID-10428866_T11"
}
]
}
] | [] | [] |
6 | PMID-10443949 | [
{
"id": "PMID-10443949__text",
"type": "abstract",
"text": [
"Meat, metabolic genotypes and risk for colorectal cancer. \nPersuasive data exist as to the importance of environmental factors in the pathogenesis of sporadic colorectal cancer. One possibility is that the effect of environmental factors varies between individuals, perhaps on the basis of inherited variation (polymorphism) in genes which influence the activation or inactivation of dietary carcinogens. Thus far, the focus has been on acetylator genes (NAT1, NAT2) and the activation of heterocyclic amines, carcinogens generated by cooking meat for prolonged periods at high temperature. Three case-control studies and one prospective study have shown a consistent trend towards higher risks for cancer with higher intakes of meat in rapid acetylators for NAT1, NAT2 or both genotypes. Other links between meat, cooking methods, metabolic genotypes and risk for cancer might include enhanced activation of polycyclic aromatic hydrocarbons and N-nitroso compounds by variant genotypes of CYP1A1 and CYP2E1, respectively, and modulation by meat of the protective effect of the E4 allele of apolipoprotein E on risk for cancer of the proximal colon.\n"
],
"offsets": [
[
0,
1150
]
]
}
] | [
{
"id": "PMID-10443949_T1",
"type": "Protein",
"text": [
"NAT1"
],
"offsets": [
[
455,
459
]
],
"normalized": []
},
{
"id": "PMID-10443949_T2",
"type": "Protein",
"text": [
"NAT2"
],
"offsets": [
[
461,
465
]
],
"normalized": []
},
{
"id": "PMID-10443949_T3",
"type": "Protein",
"text": [
"NAT1"
],
"offsets": [
[
759,
763
]
],
"normalized": []
},
{
"id": "PMID-10443949_T4",
"type": "Protein",
"text": [
"NAT2"
],
"offsets": [
[
765,
769
]
],
"normalized": []
},
{
"id": "PMID-10443949_T5",
"type": "Protein",
"text": [
"CYP1A1"
],
"offsets": [
[
990,
996
]
],
"normalized": []
},
{
"id": "PMID-10443949_T6",
"type": "Protein",
"text": [
"CYP2E1"
],
"offsets": [
[
1001,
1007
]
],
"normalized": []
},
{
"id": "PMID-10443949_T7",
"type": "Protein",
"text": [
"E4"
],
"offsets": [
[
1078,
1080
]
],
"normalized": []
},
{
"id": "PMID-10443949_T8",
"type": "Protein",
"text": [
"apolipoprotein E"
],
"offsets": [
[
1091,
1107
]
],
"normalized": []
}
] | [] | [
{
"id": "PMID-10443949_1",
"entity_ids": [
"PMID-10443949_T7",
"PMID-10443949_T8"
]
}
] | [] |
7 | PMID-10457259 | [
{
"id": "PMID-10457259__text",
"type": "abstract",
"text": [
"Differential expression of human lysyl hydroxylase genes, lysine hydroxylation, and cross-linking of type I collagen during osteoblastic differentiation in vitro. \nThe pattern of lysyl hydroxylation in the nontriple helical domains of collagen is critical in determining the cross-linking pathways that are tissue specific. We hypothesized that the tissue specificity of type I collagen cross-linking is, in part, due to the differential expression of lysyl hydroxylase genes (Procollagen-lysine,2-oxyglutarate,5-dioxygenase 1, 2, and 3 [PLOD1, PLOD2, and PLOD3]). In this study, we have examined the expression patterns of these three genes during the course of in vitro differentiation of human osteoprogenitor cells (bone marrow stromal cells [BMSCs]) and normal skin fibroblasts (NSFs). In addition, using the medium and cell layer/matrix fractions in these cultures, lysine hydroxylation of type I collagen alpha chains and collagen cross-linking chemistries have been characterized. High levels of PLOD1 and PLOD3 genes were expressed in both BMSCs and NSFs, and the expression levels did not change in the course of differentiation. In contrast to the PLOD1 and PLOD3 genes, both cell types showed low PLOD2 gene expression in undifferentiated and early differentiated conditions. However, fully differentiated BMSCs, but not NSFs, exhibited a significantly elevated level (6-fold increase) of PLOD2 mRNA. This increase coincided with the onset of matrix mineralization and with the increase in lysyl hydroxylation in the nontriple helical domains of alpha chains of type I collagen molecule. Furthermore, the collagen cross-links that are derived from the nontriple helical hydroxylysine-aldehyde were found only in fully differentiated BMSC cultures. The data suggests that PLOD2 expression is associated with lysine hydroxylation in the nontriple helical domains of collagen and, thus, could be partially responsible for the tissue-specific collagen cross-linking pattern.\n"
],
"offsets": [
[
0,
1983
]
]
}
] | [
{
"id": "PMID-10457259_T1",
"type": "Protein",
"text": [
"Procollagen-lysine,2-oxyglutarate,5-dioxygenase 1"
],
"offsets": [
[
477,
526
]
],
"normalized": []
},
{
"id": "PMID-10457259_T2",
"type": "Protein",
"text": [
"2"
],
"offsets": [
[
528,
529
]
],
"normalized": []
},
{
"id": "PMID-10457259_T3",
"type": "Protein",
"text": [
"3"
],
"offsets": [
[
535,
536
]
],
"normalized": []
},
{
"id": "PMID-10457259_T4",
"type": "Protein",
"text": [
"PLOD1"
],
"offsets": [
[
538,
543
]
],
"normalized": []
},
{
"id": "PMID-10457259_T5",
"type": "Protein",
"text": [
"PLOD2"
],
"offsets": [
[
545,
550
]
],
"normalized": []
},
{
"id": "PMID-10457259_T6",
"type": "Protein",
"text": [
"PLOD3"
],
"offsets": [
[
556,
561
]
],
"normalized": []
},
{
"id": "PMID-10457259_T7",
"type": "Protein",
"text": [
"PLOD1"
],
"offsets": [
[
1004,
1009
]
],
"normalized": []
},
{
"id": "PMID-10457259_T8",
"type": "Protein",
"text": [
"PLOD3"
],
"offsets": [
[
1014,
1019
]
],
"normalized": []
},
{
"id": "PMID-10457259_T9",
"type": "Protein",
"text": [
"PLOD1"
],
"offsets": [
[
1159,
1164
]
],
"normalized": []
},
{
"id": "PMID-10457259_T10",
"type": "Protein",
"text": [
"PLOD3"
],
"offsets": [
[
1169,
1174
]
],
"normalized": []
},
{
"id": "PMID-10457259_T11",
"type": "Protein",
"text": [
"PLOD2"
],
"offsets": [
[
1209,
1214
]
],
"normalized": []
},
{
"id": "PMID-10457259_T12",
"type": "Protein",
"text": [
"PLOD2"
],
"offsets": [
[
1401,
1406
]
],
"normalized": []
},
{
"id": "PMID-10457259_T13",
"type": "Protein",
"text": [
"PLOD2"
],
"offsets": [
[
1783,
1788
]
],
"normalized": []
}
] | [] | [
{
"id": "PMID-10457259_1",
"entity_ids": [
"PMID-10457259_T1",
"PMID-10457259_T4"
]
},
{
"id": "PMID-10457259_2",
"entity_ids": [
"PMID-10457259_T2",
"PMID-10457259_T5"
]
},
{
"id": "PMID-10457259_3",
"entity_ids": [
"PMID-10457259_T3",
"PMID-10457259_T6"
]
}
] | [] |
8 | PMID-10460145 | [
{
"id": "PMID-10460145__text",
"type": "abstract",
"text": [
"Phenylalanine residues in the active site of tyrosine hydroxylase: mutagenesis of Phe300 and Phe309 to alanine and metal ion-catalyzed hydroxylation of Phe300. \nResidues Phe300 and Phe309 of tyrosine hydroxylase are located in the active site in the recently described three-dimensional structure of the enzyme, where they have been proposed to play roles in substrate binding. Also based on the structure, Phe300 has been reported to be hydroxylated due to a naturally occurring posttranslational modification [Goodwill, K. E., Sabatier, C., and Stevens, R. C. (1998) Biochemistry 37, 13437-13445]. Mutants of tyrosine hydroxylase with alanine substituted for Phe300 or Phe309 have now been purified and characterized. The F309A protein possesses 40% less activity than wild-type tyrosine hydroxylase in the production of DOPA, but full activity in the production of dihydropterin. The F300A protein shows a 2.5-fold decrease in activity in the production of both DOPA and dihydropterin. The K(6-MPH4) value for F300A tyrosine hydroxylase is twice the wild-type value. These results are consistent with Phe309 having a role in maintaining the integrity of the active site, while Phe300 contributes less than 1 kcal/mol to binding tetrahydropterin. Characterization of Phe300 by MALDI-TOF mass spectrometry and amino acid sequencing showed that hydroxylation only occurs in the isolated catalytic domain after incubation with a large excess of 7, 8-dihydropterin, DTT, and Fe(2+). The modification is not observed in the untreated catalytic domain or in the full-length protein, even in the presence of excess iron. These results establish that hydroxylation of Phe300 is an artifact of the crystallography conditions and is not relevant to catalysis.\n"
],
"offsets": [
[
0,
1752
]
]
}
] | [
{
"id": "PMID-10460145_T1",
"type": "Protein",
"text": [
"tyrosine hydroxylase"
],
"offsets": [
[
45,
65
]
],
"normalized": []
},
{
"id": "PMID-10460145_T2",
"type": "Protein",
"text": [
"tyrosine hydroxylase"
],
"offsets": [
[
191,
211
]
],
"normalized": []
},
{
"id": "PMID-10460145_T3",
"type": "Protein",
"text": [
"tyrosine hydroxylase"
],
"offsets": [
[
611,
631
]
],
"normalized": []
},
{
"id": "PMID-10460145_T4",
"type": "Protein",
"text": [
"tyrosine hydroxylase"
],
"offsets": [
[
781,
801
]
],
"normalized": []
},
{
"id": "PMID-10460145_T5",
"type": "Protein",
"text": [
"tyrosine hydroxylase"
],
"offsets": [
[
1019,
1039
]
],
"normalized": []
}
] | [] | [] | [] |
9 | PMID-10463816 | [
{
"id": "PMID-10463816__text",
"type": "abstract",
"text": [
"Development of an enzyme-linked immunosorbent assay, using a monoclonal antibody against alpha2-macroglobulin, for the diagnosis of systemic lupus erythematosus. \nOBJECTIVES: To develop an enzyme-linked immunosorbent assay (ELISA) using a monoclonal antibody (mab) directed against abnormally glycosylated serum alpha2-macroglobulin (alpha2-M) from patients with systemic lupus erythematosus (SLE). DESIGN AND METHODS: Serum alpha2-M purified by HPLC from patients with SLE was injected in a Balb/c, CB6 F1 female mouse and hybrid cell lines were screened using alpha2-M Glu-C fragments derived from SLE and normal donors (NHS). A mab was selected and used to develop an ELISA by which sera from NHS (n = 14), SLE (n = 34), rheumatoid arthritis (n = 15), Sjogren's syndrome (n = 11), mixed connective tissue diseases (n = 12), and liver diseases (n = 11) were analyzed. RESULTS: The affinity of the mab for alpha2-M from SLE, but not from the other diseases, was higher compared to NHS, as demonstrated by immunoblotting and ELISA. CONCLUSIONS: The ELISA was capable of recognizing changes of glycosylation of alpha2-M in SLE and may be useful for its differential diagnosis.\n"
],
"offsets": [
[
0,
1176
]
]
}
] | [
{
"id": "PMID-10463816_T1",
"type": "Protein",
"text": [
"alpha2-macroglobulin"
],
"offsets": [
[
89,
109
]
],
"normalized": []
},
{
"id": "PMID-10463816_T2",
"type": "Protein",
"text": [
"alpha2-macroglobulin"
],
"offsets": [
[
312,
332
]
],
"normalized": []
},
{
"id": "PMID-10463816_T3",
"type": "Protein",
"text": [
"alpha2-M"
],
"offsets": [
[
334,
342
]
],
"normalized": []
},
{
"id": "PMID-10463816_T4",
"type": "Protein",
"text": [
"alpha2-M"
],
"offsets": [
[
425,
433
]
],
"normalized": []
},
{
"id": "PMID-10463816_T5",
"type": "Protein",
"text": [
"alpha2-M"
],
"offsets": [
[
562,
570
]
],
"normalized": []
},
{
"id": "PMID-10463816_T6",
"type": "Protein",
"text": [
"alpha2-M"
],
"offsets": [
[
907,
915
]
],
"normalized": []
},
{
"id": "PMID-10463816_T7",
"type": "Protein",
"text": [
"alpha2-M"
],
"offsets": [
[
1110,
1118
]
],
"normalized": []
}
] | [
{
"id": "PMID-10463816_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"glycosylated"
],
"offsets": [
[
293,
305
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10463816_T2"
}
]
},
{
"id": "PMID-10463816_E2",
"type": "Glycosylation",
"trigger": {
"text": [
"glycosylation"
],
"offsets": [
[
1093,
1106
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10463816_T7"
}
]
}
] | [
{
"id": "PMID-10463816_1",
"entity_ids": [
"PMID-10463816_T2",
"PMID-10463816_T3"
]
}
] | [] |
10 | PMID-10485883 | [
{
"id": "PMID-10485883__text",
"type": "abstract",
"text": [
"Efficient adaptational demethylation of chemoreceptors requires the same enzyme-docking site as efficient methylation. \nThe mechanistic basis of sensory adaptation and gradient sensing in bacterial chemotaxis is reversible covalent modification of transmembrane chemoreceptors, methylation, and demethylation at specific glutamyl residues in their cytoplasmic domains. These reactions are catalyzed by a dedicated methyltransferase CheR and a dedicated methylesterase CheB. The esterase is also a deamidase that creates certain methyl-accepting glutamyls by hydrolysis of glutamine side chains. We investigated the action of CheB and its activated form, phospho-CheB, on a truncated form of the aspartate receptor of Escherichia coli that was missing the last 5 aa of the intact receptor. The deleted pentapeptide is conserved in several chemoreceptors in enteric and related bacteria. The truncated receptor was much less efficiently demethylated and deamidated than intact receptor, but essentially was unperturbed for kinase activation or transmembrane signaling. CheB bound specifically to an affinity column carrying the isolated pentapeptide, implying that in the intact receptor the pentapeptide serves as a docking site for the methylesterase/deamidase and that the truncated receptor was inefficiently modified because the enzyme could not dock. It is striking that the same pentapeptide serves as an activity-enhancing docking site for the methyltransferase CheR, the other enzyme involved in adaptational covalent modification of chemoreceptors. A shared docking site raises the tantalizing possibility that relative rates of methylation and demethylation could be influenced by competition between the two enzymes at that site.\n"
],
"offsets": [
[
0,
1740
]
]
}
] | [
{
"id": "PMID-10485883_T1",
"type": "Protein",
"text": [
"CheR"
],
"offsets": [
[
432,
436
]
],
"normalized": []
},
{
"id": "PMID-10485883_T2",
"type": "Protein",
"text": [
"CheB"
],
"offsets": [
[
468,
472
]
],
"normalized": []
},
{
"id": "PMID-10485883_T3",
"type": "Protein",
"text": [
"CheB"
],
"offsets": [
[
625,
629
]
],
"normalized": []
},
{
"id": "PMID-10485883_T4",
"type": "Protein",
"text": [
"CheB"
],
"offsets": [
[
662,
666
]
],
"normalized": []
},
{
"id": "PMID-10485883_T5",
"type": "Protein",
"text": [
"CheB"
],
"offsets": [
[
1067,
1071
]
],
"normalized": []
},
{
"id": "PMID-10485883_T6",
"type": "Protein",
"text": [
"CheR"
],
"offsets": [
[
1468,
1472
]
],
"normalized": []
}
] | [] | [] | [] |
11 | PMID-10490608 | [
{
"id": "PMID-10490608__text",
"type": "abstract",
"text": [
"Roles of cell division and gene transcription in the methylation of CpG islands. \nDe novo methylation of CpG islands within the promoters of eukaryotic genes is often associated with their transcriptional repression, yet the methylation of CpG islands located downstream of promoters does not block transcription. We investigated the kinetics of mRNA induction, demethylation, and remethylation of the p16 promoter and second-exon CpG islands in T24 cells after 5-aza-2'-deoxycytidine (5-Aza-CdR) treatment to explore the relationship between CpG island methylation and gene transcription. The rates of remethylation of both CpG islands were associated with time but not with the rate of cell division, and remethylation of the p16 exon 2 CpG island occurred at a higher rate than that of the p16 promoter. We also examined the relationship between the remethylation of coding sequence CpG islands and gene transcription. The kinetics of remethylation of the p16 exon 2, PAX-6 exon 5, c-ABL exon 11, and MYF-3 exon 3 loci were examined following 5-Aza-CdR treatment because these genes contain exonic CpG islands which are hypermethylated in T24 cells. Remethylation occurred most rapidly in the p16, PAX-6, and c-ABL genes, shown to be transcribed prior to drug treatment. These regions also exhibited higher levels of remethylation in single-cell clones and subclones derived from 5-Aza-CdR-treated T24 cells. Our data suggest that de novo methylation is not restricted to the S phase of the cell cycle and that transcription through CpG islands does not inhibit their remethylation.\n"
],
"offsets": [
[
0,
1586
]
]
}
] | [
{
"id": "PMID-10490608_T1",
"type": "Protein",
"text": [
"p16"
],
"offsets": [
[
402,
405
]
],
"normalized": []
},
{
"id": "PMID-10490608_T2",
"type": "Protein",
"text": [
"p16"
],
"offsets": [
[
728,
731
]
],
"normalized": []
},
{
"id": "PMID-10490608_T3",
"type": "Protein",
"text": [
"p16"
],
"offsets": [
[
793,
796
]
],
"normalized": []
},
{
"id": "PMID-10490608_T4",
"type": "Protein",
"text": [
"p16"
],
"offsets": [
[
959,
962
]
],
"normalized": []
},
{
"id": "PMID-10490608_T5",
"type": "Protein",
"text": [
"PAX-6"
],
"offsets": [
[
971,
976
]
],
"normalized": []
},
{
"id": "PMID-10490608_T6",
"type": "Protein",
"text": [
"c-ABL"
],
"offsets": [
[
985,
990
]
],
"normalized": []
},
{
"id": "PMID-10490608_T7",
"type": "Protein",
"text": [
"MYF-3"
],
"offsets": [
[
1004,
1009
]
],
"normalized": []
},
{
"id": "PMID-10490608_T8",
"type": "Protein",
"text": [
"p16"
],
"offsets": [
[
1196,
1199
]
],
"normalized": []
},
{
"id": "PMID-10490608_T9",
"type": "Protein",
"text": [
"PAX-6"
],
"offsets": [
[
1201,
1206
]
],
"normalized": []
},
{
"id": "PMID-10490608_T10",
"type": "Protein",
"text": [
"c-ABL"
],
"offsets": [
[
1212,
1217
]
],
"normalized": []
},
{
"id": "PMID-10490608_T13",
"type": "Entity",
"text": [
"promoter"
],
"offsets": [
[
406,
414
]
],
"normalized": []
},
{
"id": "PMID-10490608_T14",
"type": "Entity",
"text": [
"second-exon CpG islands"
],
"offsets": [
[
419,
442
]
],
"normalized": []
},
{
"id": "PMID-10490608_T15",
"type": "Entity",
"text": [
"CpG island"
],
"offsets": [
[
543,
553
]
],
"normalized": []
},
{
"id": "PMID-10490608_T18",
"type": "Entity",
"text": [
"exon 2 CpG island"
],
"offsets": [
[
732,
749
]
],
"normalized": []
},
{
"id": "PMID-10490608_T19",
"type": "Entity",
"text": [
"promoter"
],
"offsets": [
[
797,
805
]
],
"normalized": []
},
{
"id": "PMID-10490608_T21",
"type": "Entity",
"text": [
"exon 2"
],
"offsets": [
[
963,
969
]
],
"normalized": []
},
{
"id": "PMID-10490608_T22",
"type": "Entity",
"text": [
"exon 5"
],
"offsets": [
[
977,
983
]
],
"normalized": []
},
{
"id": "PMID-10490608_T23",
"type": "Entity",
"text": [
"exon 11"
],
"offsets": [
[
991,
998
]
],
"normalized": []
},
{
"id": "PMID-10490608_T24",
"type": "Entity",
"text": [
"exon 3"
],
"offsets": [
[
1010,
1016
]
],
"normalized": []
}
] | [
{
"id": "PMID-10490608_E1",
"type": "DNA_demethylation",
"trigger": {
"text": [
"demethylation"
],
"offsets": [
[
362,
375
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T1"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T13"
}
]
},
{
"id": "PMID-10490608_E2",
"type": "DNA_demethylation",
"trigger": {
"text": [
"demethylation"
],
"offsets": [
[
362,
375
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T1"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T14"
}
]
},
{
"id": "PMID-10490608_E3",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
381,
394
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T1"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T13"
}
]
},
{
"id": "PMID-10490608_E4",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
381,
394
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T1"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T14"
}
]
},
{
"id": "PMID-10490608_E5",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
554,
565
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T1"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T15"
}
]
},
{
"id": "PMID-10490608_E6",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
707,
720
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T2"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T18"
}
]
},
{
"id": "PMID-10490608_E7",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
707,
720
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T3"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T19"
}
]
},
{
"id": "PMID-10490608_E8",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
938,
951
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T6"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T23"
}
]
},
{
"id": "PMID-10490608_E9",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
938,
951
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T7"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T24"
}
]
},
{
"id": "PMID-10490608_E10",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
938,
951
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T4"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T21"
}
]
},
{
"id": "PMID-10490608_E11",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
938,
951
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T5"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T22"
}
]
},
{
"id": "PMID-10490608_E12",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypermethylated"
],
"offsets": [
[
1123,
1138
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T4"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T21"
}
]
},
{
"id": "PMID-10490608_E13",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypermethylated"
],
"offsets": [
[
1123,
1138
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T5"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T22"
}
]
},
{
"id": "PMID-10490608_E14",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypermethylated"
],
"offsets": [
[
1123,
1138
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T6"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T23"
}
]
},
{
"id": "PMID-10490608_E15",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypermethylated"
],
"offsets": [
[
1123,
1138
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T7"
},
{
"role": "Site",
"ref_id": "PMID-10490608_T24"
}
]
},
{
"id": "PMID-10490608_E16",
"type": "DNA_methylation",
"trigger": {
"text": [
"Remethylation"
],
"offsets": [
[
1153,
1166
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T8"
}
]
},
{
"id": "PMID-10490608_E17",
"type": "DNA_methylation",
"trigger": {
"text": [
"Remethylation"
],
"offsets": [
[
1153,
1166
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T9"
}
]
},
{
"id": "PMID-10490608_E18",
"type": "DNA_methylation",
"trigger": {
"text": [
"Remethylation"
],
"offsets": [
[
1153,
1166
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T10"
}
]
},
{
"id": "PMID-10490608_E19",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
1320,
1333
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T8"
}
]
},
{
"id": "PMID-10490608_E20",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
1320,
1333
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T9"
}
]
},
{
"id": "PMID-10490608_E21",
"type": "DNA_methylation",
"trigger": {
"text": [
"remethylation"
],
"offsets": [
[
1320,
1333
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10490608_T10"
}
]
}
] | [] | [] |
12 | PMID-10495421 | [
{
"id": "PMID-10495421__text",
"type": "abstract",
"text": [
"Distinct methylation pattern and microsatellite instability in sporadic gastric cancer. \nAberrant 5' CpG island methylation is an alternative mechanism of gene inactivation during the development of cancer as demonstrated for several tumor-suppressor genes. Also, marked relationship of microsatellite instability (MSI) and DNA methylation has been reported in sporadic colorectal cancer, which is a result of epigenetic inactivation of hMLH1 in association of promoter hypermethylation. In the present study, we investigated the 5' CpG island hypermethylation of hMLH1, E-cadherin and p16 in 61 primary gastric cancers (GCs) by using combined bisulfite restriction analysis (COBRA) and methylation-specific PCR (MSP), and their MSI status. Of 61 GCs investigated, 5 (8.1%) tumors presented hMLH1 methylation, 16 (26.2%) and 25 (40.9%) showed E-cadherin and p16 methylation respectively, and 8 (13.1%) presented high-frequency MSI (MSI-H). Of the 8 MSI-H patients, 5 presented hMLH1 methylation, whereas no low-frequency MSI (MSI-L) and microsatellite stable (MSS) cases exhibited hMLH1 methylation (5/8 vs. 0/43, p < 0.00001). Furthermore, these patients also presented E-cadherin and p16 hypermethylation. Our data showed a significant correlation between hMLH1 methylation and MSI in GC, and suggested that a common mechanism of aberrant de novo methylation can be postulated in these cancers.\n"
],
"offsets": [
[
0,
1397
]
]
}
] | [
{
"id": "PMID-10495421_T1",
"type": "Protein",
"text": [
"MLH1"
],
"offsets": [
[
438,
442
]
],
"normalized": []
},
{
"id": "PMID-10495421_T2",
"type": "Protein",
"text": [
"MLH1"
],
"offsets": [
[
565,
569
]
],
"normalized": []
},
{
"id": "PMID-10495421_T3",
"type": "Protein",
"text": [
"E-cadherin"
],
"offsets": [
[
571,
581
]
],
"normalized": []
},
{
"id": "PMID-10495421_T4",
"type": "Protein",
"text": [
"p16"
],
"offsets": [
[
586,
589
]
],
"normalized": []
},
{
"id": "PMID-10495421_T5",
"type": "Protein",
"text": [
"MLH1"
],
"offsets": [
[
792,
796
]
],
"normalized": []
},
{
"id": "PMID-10495421_T6",
"type": "Protein",
"text": [
"E-cadherin"
],
"offsets": [
[
843,
853
]
],
"normalized": []
},
{
"id": "PMID-10495421_T7",
"type": "Protein",
"text": [
"p16"
],
"offsets": [
[
858,
861
]
],
"normalized": []
},
{
"id": "PMID-10495421_T8",
"type": "Protein",
"text": [
"MLH1"
],
"offsets": [
[
978,
982
]
],
"normalized": []
},
{
"id": "PMID-10495421_T9",
"type": "Protein",
"text": [
"MLH1"
],
"offsets": [
[
1082,
1086
]
],
"normalized": []
},
{
"id": "PMID-10495421_T10",
"type": "Protein",
"text": [
"E-cadherin"
],
"offsets": [
[
1171,
1181
]
],
"normalized": []
},
{
"id": "PMID-10495421_T11",
"type": "Protein",
"text": [
"p16"
],
"offsets": [
[
1186,
1189
]
],
"normalized": []
},
{
"id": "PMID-10495421_T12",
"type": "Protein",
"text": [
"MLH1"
],
"offsets": [
[
1259,
1263
]
],
"normalized": []
},
{
"id": "PMID-10495421_T13",
"type": "Entity",
"text": [
"promoter"
],
"offsets": [
[
461,
469
]
],
"normalized": []
},
{
"id": "PMID-10495421_T15",
"type": "Entity",
"text": [
"5' CpG island"
],
"offsets": [
[
530,
543
]
],
"normalized": []
}
] | [
{
"id": "PMID-10495421_E1",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypermethylation"
],
"offsets": [
[
470,
486
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T1"
},
{
"role": "Site",
"ref_id": "PMID-10495421_T13"
}
]
},
{
"id": "PMID-10495421_E2",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypermethylation"
],
"offsets": [
[
544,
560
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T2"
},
{
"role": "Site",
"ref_id": "PMID-10495421_T15"
}
]
},
{
"id": "PMID-10495421_E3",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypermethylation"
],
"offsets": [
[
544,
560
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T3"
},
{
"role": "Site",
"ref_id": "PMID-10495421_T15"
}
]
},
{
"id": "PMID-10495421_E4",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypermethylation"
],
"offsets": [
[
544,
560
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T4"
},
{
"role": "Site",
"ref_id": "PMID-10495421_T15"
}
]
},
{
"id": "PMID-10495421_E5",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
797,
808
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T5"
}
]
},
{
"id": "PMID-10495421_E6",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
862,
873
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T6"
}
]
},
{
"id": "PMID-10495421_E7",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
862,
873
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T7"
}
]
},
{
"id": "PMID-10495421_E8",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
983,
994
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T8"
}
]
},
{
"id": "PMID-10495421_E9",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1087,
1098
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T9"
}
]
},
{
"id": "PMID-10495421_E10",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypermethylation"
],
"offsets": [
[
1190,
1206
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T10"
}
]
},
{
"id": "PMID-10495421_E11",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypermethylation"
],
"offsets": [
[
1190,
1206
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T11"
}
]
},
{
"id": "PMID-10495421_E12",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1264,
1275
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10495421_T12"
}
]
}
] | [] | [] |
13 | PMID-10532353 | [
{
"id": "PMID-10532353__text",
"type": "abstract",
"text": [
"Effect of HSP47 on prolyl 4-hydroxylation of collagen model peptides. \nProlyl 4-hydroxylation, the most important post-translational modification in collagen biosynthesis, is catalyzed by prolyl 4-hydroxylase, an endoplasmic reticulum-resident enzyme. HSP47 is a collagen-binding stress protein which also resides in the endoplasmic reticulum (Nagata, K. and Yamada, K.M. (1986) J. Biol. Chem., 261, 7531-7536). Both prolyl 4-hydroxylase and HSP47 interact with procollagen alpha-chains during their folding and/or modification in the endoplasmic reticulum. Recent study has revealed that a simple collagen model peptide, (Pro-Pro-Gly)n, is recognized by HSP47 as well as by prolyl 4-hydroxylase in vitro (Koide et al., manuscript submitted). In the present study, we investigated the effect of HSP47 on the prolyl 4-hydroxylation of such collagen model peptides. To monitor the enzymatic hydroxylation of the peptides, we developed a non-RI assay system based on reversed-phase HPLC. When HSP47 was added to the reaction mixture, substrate and less-hydroxylated materials accumulated. This effect depended on the peptide-binding activity of HSP47, because a mutant HSP47 without collagen-binding activity did not show any inhibitory effect on prolyl 4-hydroxylation. Kinetic analysis and other biochemical analyses suggest that HSP47 retards the enzymatic reaction competing for the substrate peptide.\n"
],
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0,
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] | [] | [] | [] |
14 | PMID-10564083 | [
{
"id": "PMID-10564083__text",
"type": "abstract",
"text": [
"Mouse K-Cl cotransporter KCC1: cloning, mapping, pathological expression, and functional regulation. \nAlthough K-Cl cotransporter (KCC1) mRNA is expressed in many tissues, K-Cl cotransport activity has been measured in few cell types, and detection of endogenous KCC1 polypeptide has not yet been reported. We have cloned the mouse erythroid KCC1 (mKCC1) cDNA and its flanking genomic regions and mapped the mKCC1 gene to chromosome 8. Three anti-peptide antibodies raised against recombinant mKCC1 function as immunoblot and immunoprecipitation reagents. The tissue distributions of mKCC1 mRNA and protein are widespread, and mKCC1 RNA is constitutively expressed during erythroid differentiation of ES cells. KCC1 polypeptide or related antigen is present in erythrocytes of multiple species in which K-Cl cotransport activity has been documented. Erythroid KCC1 polypeptide abundance is elevated in proportion to reticulocyte counts in density-fractionated cells, in bleeding-induced reticulocytosis, in mouse models of sickle cell disease and thalassemia, and in the corresponding human disorders. mKCC1-mediated uptake of (86)Rb into Xenopus oocytes requires extracellular Cl(-), is blocked by the diuretic R(+)-[2-n-butyl-6,7-dichloro-2-cyclopentyl-2, 3-dihydro-1-oxo-1H-indenyl-5-yl-)oxy]acetic acid, and exhibits an erythroid pattern of acute regulation, with activation by hypotonic swelling, N-ethylmaleimide, and staurosporine and inhibition by calyculin and okadaic acid. These reagents and findings will expedite studies of KCC1 structure-function relationships and of the pathobiology of KCC1-mediated K-Cl cotransport.\n"
],
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[
0,
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}
] | [] | [] | [] |
15 | PMID-10566667 | [
{
"id": "PMID-10566667__text",
"type": "abstract",
"text": [
"Progesterone metabolism in the human kidney and inhibition of 11beta-hydroxysteroid dehydrogenase type 2 by progesterone and its metabolites. \nProgesterone binds with high affinity to the mineralocorticoid (MC) receptor, but confers only very low agonistic MC activity. Therefore, progesterone is a potent MC antagonist in vitro. Although progesterone reaches up to 100 times higher plasma levels in late pregnancy than aldosterone, the in vivo MC antagonistic effect of progesterone seems to be relatively weak. One explanation for this phenomenon could be local metabolism of progesterone in the human kidney, similar to the inactivation of cortisol to cortisone by the 11beta-hydroxysteroid dehydrogenase (11beta-HSD) type 2. We studied the metabolism of progesterone in the human kidney in vitro and found reduction to 20alpha-dihydro (DH)-progesterone as the main metabolite. Ring-A reduction to 5alpha-DH-progesterone, 20alpha-DH-5alpha-DH-progesterone, and 3beta,5alpha-tetrahydro (TH)-progesterone was also documented. We further showed for the first time that 17-hydroxylation of progesterone (17alpha-OH-progesterone, 17alpha-OH, 20alpha-DH-progesterone), normally localized in the adrenals and the gonads, occurs in the human adult kidney. We found no formation of deoxycorticosterone from progesterone in the human adult kidney. Using human kidney cortex microsomes, we tested the inhibitory potency of progesterone and its metabolites on the 11beta-HSD type 2. The most potent inhibitor was progesterone itself (IC50 = 4.8 x 10(-8) mol/L), followed by 5alpha-DH-progesterone (IC50 = 2.4 x 10(-7) mol/L), 20alpha-DH-progesterone, 3beta,5alpha-TH-progesterone, 17alpha-OH-progesterone, and 20alpha-DH-5alpha-DH-progesterone (IC50 between 7.7 x 10(-7) mol/L and 1.3 x 10(-6) mol/L). The least potent inhibitor was 17alpha-OH,20alpha-DH-progesterone. In addition to progesterone metabolism by the kidney, the inhibition of 11beta-HSD type 2 by progesterone and its metabolites could be a second explanation for the weak MC-antagonist activity of progesterone in vivo. Inhibition of 11beta-HSD type 2 leads to an increase of intracellular cortisol in a way that the local equilibrium between the MC agonist cortisol and the antagonist progesterone is shifted to the agonist side.\n"
],
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[
0,
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"id": "PMID-10566667_T1",
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],
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"id": "PMID-10566667_T2",
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],
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}
] | [] | [] | [] |
16 | PMID-10593387 | [
{
"id": "PMID-10593387__text",
"type": "abstract",
"text": [
"Deglycosylation of a bifunctional lutropin-follitropin agonist reduced its follitropin activity more than its lutropin activity. \nOBJECTIVE: To design a drug that blocks the gonadal actions of lutropins and follitropins. DESIGN: Controlled in vitro study. SETTING: Academic laboratory. PATIENT(S): None. INTERVENTION(S): We removed three glycosylation signals from an hCG-hFSH chimera known to have high affinity for LH and FSH receptors, expecting this would create a bifunctional antagonist (dgCFC). To offset the inhibition of subunit combination caused by deglycosylation of alpha-subunit loop 2, we prepared dgCFC as a single-chain fusion protein containing the alpha-subunit downstream of the chimeric beta-subunit. MAIN OUTCOME MEASURE(S): Receptor binding, cyclic adenosine monophosphate accumulation. RESULT(S): dgCFC bound LH or FSH receptors similar to hCG or hFSH. It was a partial agonist and had one tenth the efficacy of hFSH and two thirds the efficacy of hCG. CONCLUSION(S): The surprising high residual lutropin activity of dgCFC indicated that its FSH residues offset the effects of deglycosylation, suggesting this approach to preparing a bifunctional antagonist is unlikely to lead to a useful drug. The increased lutropin efficacy of dgCFC relative to deglycosylated hCG supports the idea that oligosaccharides modulate glycoprotein hormone efficacy through an influence on hormone conformation.\n"
],
"offsets": [
[
0,
1418
]
]
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] | [
{
"id": "PMID-10593387_T1",
"type": "Protein",
"text": [
"LH"
],
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[
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},
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"id": "PMID-10593387_T2",
"type": "Protein",
"text": [
"FSH receptors"
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"id": "PMID-10593387_T3",
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"id": "PMID-10593387_T4",
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"FSH receptors"
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] | [] | [] | [] |
17 | PMID-10601977 | [
{
"id": "PMID-10601977__text",
"type": "abstract",
"text": [
"Regulation of thyrotropin receptor protein expression in insect cells. \nExpression of large quantities of conformationally intact thyrotropin receptor (TSHR) is essential to understand the structure-function relationship of the receptor. We expressed three different constructs of full-length human TSHR in insect cells: (a) a TSHR cDNA lacking signal sequence (TSHR-ns), (b) a TSHR cDNA containing human TSHR signal sequence (TSHR-hs) and (c) a TSHR cDNA with baculovirus envelope protein encoded signal sequence gp-67 (TSHR-gp). No unique protein band, corresponding to any of these recombinant proteins, was visible upon Coomassie Blue staining after SDS-PAGE. However, Western blot using TSHR specific monoclonal antibody showed unique bands around 80, 100 and 100 kDa in TSHR-ns, TSHR-hs and TSHR-gp virus infected insect cells respectively. All three full-length TSHR proteins could neutralize the TSH binding inhibitory immunoglobulin (TBII) activity from sera of experimental animals. However, only glycosylated proteins (TSHR-hs and TSHR-gp) neutralized the TBII activity of sera from autoimmune thyroid patients, confirming the importance of glycosylation for patient autoantibody reactivity. Expression levels of full-length TSHR proteins were much lower than the levels of similarly produced corresponding ectodomains of TSHR proteins. Southern blot and Northern blot analyses showed that DNA and RNA levels in full-length TSHR virus infected insect cells were comparable to the levels found in cells infected with viruses encoding only the ectodomain of TSHR. These data suggest that full-length TSHR expression is very low and is regulated at the translational level.\n"
],
"offsets": [
[
0,
1682
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]
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] | [
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"id": "PMID-10601977_T1",
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"id": "PMID-10601977_T2",
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"id": "PMID-10601977_T3",
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"id": "PMID-10601977_T4",
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] | [
{
"id": "PMID-10601977_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"glycosylated"
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"arguments": [
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"role": "Theme",
"ref_id": "PMID-10601977_T17"
}
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"id": "PMID-10601977_E2",
"type": "Glycosylation",
"trigger": {
"text": [
"glycosylated"
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]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10601977_T18"
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] | [
{
"id": "PMID-10601977_1",
"entity_ids": [
"PMID-10601977_T2",
"PMID-10601977_T3"
]
}
] | [] |
18 | PMID-10672186 | [
{
"id": "PMID-10672186__text",
"type": "abstract",
"text": [
"BasT, a membrane-bound transducer protein for amino acid detection in Halobacterium salinarum. \nHalophilic archaea, such as eubacteria, use methyl-accepting chemotaxis proteins (MCPs) to sense their environment. We show here that BasT is a halobacterial transducer protein (Htp) responsible for chemotaxis towards five attractant amino acids. The C-terminus of the protein exhibits the highly conserved regions that are diagnostic for MCPs: the signalling domain for communication with the histidine kinase and the methylation sites that interact with the methylation/demethylation enzymes for adaptation. Hydropathy analysis predicts an enterobacterial-type transducer protein topology for BasT, with an extracellular putative ligand-binding domain flanked by two transmembrane helices and a cytoplasmic domain. BasT-inactivated mutant cells are missing a membrane protein radiolabelled with L-[methyl-3H]-methionine in wild-type cells, confirming that BasT is methylatable and membrane bound. Behavioural analysis of the basT mutant cells by capillary and chemical-in-plug assays demonstrates complete loss of chemotactic responses towards five (leucine, isoleucine, valine, methionine and cysteine) of the six attractant amino acids for Halobacterium salinarum, whereas they still respond to arginine. The volatile methyl group production assays also corroborate these findings and confirm that BasT signalling induces methyl group turnover. Our data identify BasT as the chemotaxis transducer protein for the branched chain amino acids leucine, isoleucine and valine as well as for methionine and cysteine. Thus, BasT and the arginine sensor Car cover the entire spectrum of chemotactic responses towards attractant amino acids in H. salinarum.\n"
],
"offsets": [
[
0,
1749
]
]
}
] | [
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"id": "PMID-10672186_T1",
"type": "Protein",
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0,
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},
{
"id": "PMID-10672186_T2",
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"text": [
"BasT"
],
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230,
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]
],
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},
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"id": "PMID-10672186_T3",
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"BasT"
],
"offsets": [
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691,
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]
],
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},
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"id": "PMID-10672186_T4",
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"id": "PMID-10672186_T5",
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"id": "PMID-10672186_T6",
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"id": "PMID-10672186_T7",
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"id": "PMID-10672186_T8",
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"id": "PMID-10672186_T9",
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"id": "PMID-10672186_T10",
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"Car"
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[
1646,
1649
]
],
"normalized": []
}
] | [
{
"id": "PMID-10672186_E1",
"type": "Methylation",
"trigger": {
"text": [
"methylatable"
],
"offsets": [
[
962,
974
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10672186_T5"
}
]
}
] | [] | [] |
19 | PMID-10715549 | [
{
"id": "PMID-10715549__text",
"type": "abstract",
"text": [
"Additional N-glycosylation at Asn(13) rescues the human LHbeta-subunit from disulfide-linked aggregation. \nCG, LH, FSH, and TSH are a family of heterodimeric glycoprotein hormones that contain a common alpha-subunit, but differ in their hormone-specific beta-subunits. Despite the considerable homology between LHbeta and CGbeta, we previously demonstrated that, when expressed in GH(3) cells, the secreted form of LHbeta showed mispaired disulfide-linked aggregation in addition to monomer, whereas no aggregation was observed in CGbeta. To determine the domains which are associated with the LHbeta-aggregation and which prevent CGbeta-aggregation, mutant beta-subunits in glycosylation and carboxy-terminus were expressed in GH(3) cells, and the occurrence of aggregation was assessed by continuous labeling with [35S]methionine/cysteine, immunoprecipitation with anti-hCGbeta serum, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis in a non-reducing condition. No aggregation was seen when N-linked oligosaccharides were attached to the Asn(13) of LHbeta. Removal of the carbohydrate unit at the Asn(13) of CGbeta caused aggregation, although the amount was less than 10% of monomer. The carboxy-terminal regions of neither LHbeta nor CGbeta were associated with their aggregation. Both CGbeta wild-type (WT) and CGbeta lacking N-glycosylation at Asn(13) (CGbeta-N13) showed aggregates in lysate. However, in contrast to CGbeta-N13, CGbetaWT revealed no aggregation in medium. These results indicate that the backbone structure consisting of 114 amino acids and N-linked glycosylation at Asn(30) is involved in the aggregation of LHbeta. Moreover, N-glycosylation at Asn(13) does not prevent such aggregation, but instead plays an important role in correct folding for both LHbeta- and CGbeta-subunits to be secreted as monomer.\n"
],
"offsets": [
[
0,
1846
]
]
}
] | [
{
"id": "PMID-10715549_T1",
"type": "Protein",
"text": [
"LHbeta"
],
"offsets": [
[
56,
62
]
],
"normalized": []
},
{
"id": "PMID-10715549_T2",
"type": "Protein",
"text": [
"LHbeta"
],
"offsets": [
[
311,
317
]
],
"normalized": []
},
{
"id": "PMID-10715549_T3",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
322,
328
]
],
"normalized": []
},
{
"id": "PMID-10715549_T4",
"type": "Protein",
"text": [
"LHbeta"
],
"offsets": [
[
415,
421
]
],
"normalized": []
},
{
"id": "PMID-10715549_T5",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
531,
537
]
],
"normalized": []
},
{
"id": "PMID-10715549_T6",
"type": "Protein",
"text": [
"LHbeta"
],
"offsets": [
[
594,
600
]
],
"normalized": []
},
{
"id": "PMID-10715549_T7",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
631,
637
]
],
"normalized": []
},
{
"id": "PMID-10715549_T8",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
873,
879
]
],
"normalized": []
},
{
"id": "PMID-10715549_T9",
"type": "Protein",
"text": [
"LHbeta"
],
"offsets": [
[
1065,
1071
]
],
"normalized": []
},
{
"id": "PMID-10715549_T10",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
1124,
1130
]
],
"normalized": []
},
{
"id": "PMID-10715549_T11",
"type": "Protein",
"text": [
"LHbeta"
],
"offsets": [
[
1241,
1247
]
],
"normalized": []
},
{
"id": "PMID-10715549_T12",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
1252,
1258
]
],
"normalized": []
},
{
"id": "PMID-10715549_T13",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
1304,
1310
]
],
"normalized": []
},
{
"id": "PMID-10715549_T14",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
1330,
1336
]
],
"normalized": []
},
{
"id": "PMID-10715549_T15",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
1438,
1444
]
],
"normalized": []
},
{
"id": "PMID-10715549_T16",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
1450,
1456
]
],
"normalized": []
},
{
"id": "PMID-10715549_T17",
"type": "Protein",
"text": [
"LHbeta"
],
"offsets": [
[
1647,
1653
]
],
"normalized": []
},
{
"id": "PMID-10715549_T18",
"type": "Protein",
"text": [
"LHbeta"
],
"offsets": [
[
1791,
1797
]
],
"normalized": []
},
{
"id": "PMID-10715549_T19",
"type": "Protein",
"text": [
"CGbeta"
],
"offsets": [
[
1803,
1809
]
],
"normalized": []
},
{
"id": "PMID-10715549_T21",
"type": "Entity",
"text": [
"Asn(13)"
],
"offsets": [
[
30,
37
]
],
"normalized": []
},
{
"id": "PMID-10715549_T22",
"type": "Entity",
"text": [
"oligosaccharides"
],
"offsets": [
[
1016,
1032
]
],
"normalized": []
},
{
"id": "PMID-10715549_T24",
"type": "Entity",
"text": [
"Asn(13)"
],
"offsets": [
[
1054,
1061
]
],
"normalized": []
},
{
"id": "PMID-10715549_T26",
"type": "Entity",
"text": [
"carbohydrate"
],
"offsets": [
[
1088,
1100
]
],
"normalized": []
},
{
"id": "PMID-10715549_T27",
"type": "Entity",
"text": [
"Asn(13)"
],
"offsets": [
[
1113,
1120
]
],
"normalized": []
},
{
"id": "PMID-10715549_T29",
"type": "Entity",
"text": [
"Asn(13)"
],
"offsets": [
[
1364,
1371
]
],
"normalized": []
},
{
"id": "PMID-10715549_T31",
"type": "Entity",
"text": [
"Asn(30)"
],
"offsets": [
[
1605,
1612
]
],
"normalized": []
},
{
"id": "PMID-10715549_T33",
"type": "Entity",
"text": [
"Asn(13)"
],
"offsets": [
[
1684,
1691
]
],
"normalized": []
}
] | [
{
"id": "PMID-10715549_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"N-glycosylation"
],
"offsets": [
[
11,
26
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10715549_T1"
},
{
"role": "Site",
"ref_id": "PMID-10715549_T21"
}
]
},
{
"id": "PMID-10715549_E2",
"type": "Glycosylation",
"trigger": {
"text": [
"attached"
],
"offsets": [
[
1038,
1046
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10715549_T9"
},
{
"role": "Site",
"ref_id": "PMID-10715549_T24"
},
{
"role": "Sidechain",
"ref_id": "PMID-10715549_T22"
}
]
},
{
"id": "PMID-10715549_E3",
"type": "Deglycosylation",
"trigger": {
"text": [
"Removal"
],
"offsets": [
[
1073,
1080
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10715549_T10"
},
{
"role": "Site",
"ref_id": "PMID-10715549_T27"
},
{
"role": "Sidechain",
"ref_id": "PMID-10715549_T26"
}
]
},
{
"id": "PMID-10715549_E4",
"type": "Glycosylation",
"trigger": {
"text": [
"N-glycosylation"
],
"offsets": [
[
1345,
1360
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10715549_T14"
},
{
"role": "Site",
"ref_id": "PMID-10715549_T29"
}
]
},
{
"id": "PMID-10715549_E5",
"type": "Glycosylation",
"trigger": {
"text": [
"N-linked glycosylation"
],
"offsets": [
[
1579,
1601
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10715549_T17"
},
{
"role": "Site",
"ref_id": "PMID-10715549_T31"
}
]
},
{
"id": "PMID-10715549_E6",
"type": "Glycosylation",
"trigger": {
"text": [
"N-glycosylation"
],
"offsets": [
[
1665,
1680
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10715549_T17"
},
{
"role": "Site",
"ref_id": "PMID-10715549_T33"
}
]
}
] | [] | [] |
20 | PMID-10722741 | [
{
"id": "PMID-10722741__text",
"type": "abstract",
"text": [
"Type XIII collagen forms homotrimers with three triple helical collagenous domains and its association into disulfide-bonded trimers is enhanced by prolyl 4-hydroxylase. \nType XIII collagen is a type II transmembrane protein predicted to consist of a short cytosolic domain, a single transmembrane domain, and three collagenous domains flanked by noncollagenous sequences. Previous studies on mRNAs indicate that the structures of the collagenous domain closest to the cell membrane, COL1, the adjacent noncollagenous domain, NC2, and the C-terminal domains COL3 and NC4 are subject to alternative splicing. In order to extend studies of type XIII collagen from cDNAs to the protein level we have produced it in insect cells by means of baculoviruses. Type XIII collagen alpha chains were found to associate into disulfide-bonded trimers, and hydroxylation of proline residues dramatically enhanced this association. This protein contains altogether eight cysteine residues, and interchain disulfide bonds could be located in the NC1 domain and possibly at the junction of COL1 and NC2, while the two cysteine residues in NC4 are likely to form intrachain bonds. Pepsin and trypsin/chymotrypsin digestions indicated that the type XIII collagen alpha chains form homotrimers whose three collagenous domains are in triple helical conformation. The thermal stabilities (T(m)) of the COL1, COL2, and COL3 domains were 38, 49 and 40 degrees C, respectively. The T(m) of the central collagenous domain is unusually high, which in the light of this domain being invariant in terms of alternative splicing suggests that the central portion of the molecule may have an important role in the stability of the molecule. All in all, most of the type XIII collagen ectodomain appears to be present in triple helical conformation, which is in clear contrast to the short or highly interrupted triple helical domains of the other known collagenous transmembrane proteins.\n"
],
"offsets": [
[
0,
1957
]
]
}
] | [
{
"id": "PMID-10722741_T1",
"type": "Protein",
"text": [
"Type XIII collagen"
],
"offsets": [
[
0,
18
]
],
"normalized": []
},
{
"id": "PMID-10722741_T2",
"type": "Protein",
"text": [
"Type XIII collagen"
],
"offsets": [
[
171,
189
]
],
"normalized": []
},
{
"id": "PMID-10722741_T3",
"type": "Protein",
"text": [
"type XIII collagen"
],
"offsets": [
[
638,
656
]
],
"normalized": []
},
{
"id": "PMID-10722741_T4",
"type": "Protein",
"text": [
"Type XIII collagen alpha chains"
],
"offsets": [
[
752,
783
]
],
"normalized": []
},
{
"id": "PMID-10722741_T5",
"type": "Protein",
"text": [
"Pepsin"
],
"offsets": [
[
1163,
1169
]
],
"normalized": []
},
{
"id": "PMID-10722741_T6",
"type": "Protein",
"text": [
"type XIII collagen alpha chains"
],
"offsets": [
[
1225,
1256
]
],
"normalized": []
},
{
"id": "PMID-10722741_T7",
"type": "Protein",
"text": [
"type XIII collagen"
],
"offsets": [
[
1733,
1751
]
],
"normalized": []
},
{
"id": "PMID-10722741_T9",
"type": "Entity",
"text": [
"proline residues"
],
"offsets": [
[
860,
876
]
],
"normalized": []
}
] | [
{
"id": "PMID-10722741_E1",
"type": "Hydroxylation",
"trigger": {
"text": [
"hydroxylation"
],
"offsets": [
[
843,
856
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10722741_T4"
},
{
"role": "Site",
"ref_id": "PMID-10722741_T9"
}
]
}
] | [] | [] |
21 | PMID-10729220 | [
{
"id": "PMID-10729220__text",
"type": "abstract",
"text": [
"Symmetric and asymmetric DNA methylation in the human IGF2-H19 imprinted region. \nThe two contiguous IGF2 (human insulin-like growth factor II) and H19 genes are reciprocally imprinted in both human and mouse. In most tissues, IGF2 is transcribed only from the paternal chromosome while H19 is transcribed only from the maternal allele. The presence of a differential methylation region (DMR) on the two parental alleles at the 5' flanking region of H19 has been proposed to constitute the gametic imprint, which controls the reciprocal allelic expression of the two genes. Using bisulfite genomic sequencing, we have assessed the methylation status of cytosine (including 154 CpG sites) in six CpG-rich regions of the human IGF2-H19 genes. In a CpG island near promoter P3 of the IGF2 gene, more than 99.8% of all cytosines were converted to thymidine by sodium bisulfite mutagenesis, indicating that none of the CpGs was methylated. In the IGF2 exon 8-9 region, mosaic methylation of 56 CpG sites was observed in fetal tissues and in adult blood DNA. In contrast to the mosaic methylation of IGF2, the allelic methylation of the human H19 DMR was uniform. In the CpG region located 2 kb upstream (-2362 to -1911) of the H19 transcription site, all 25 CpG sites were completely methylated on only one parental allele. Uniform allele-specific methylation was also observed in the CpG island proximal to the H19 promoter (-711 to -290) with complete methylation of all 25 CpG sites in one parental allele. In contrast, the CpG region in the H19 promoter (-292 to +15) was mosaically methylated in all tissues. In addition, cytosine was methylated at three CpNpG and GpNpC sites on the top DNA strand and one CpNpG site on the bottom DNA strand from the fetal brain. The cytosines at CpG sites were methylated on both DNA strands (symmetric methylation) while cytosines at the CpNpG and GpNpC sites were methylated on only one DNA strand (asymmetric methylation). The asymmetric methylation was associated with tissue-specific disruption of H19 genomic imprinting in fetal brain.\n"
],
"offsets": [
[
0,
2078
]
]
}
] | [
{
"id": "PMID-10729220_T1",
"type": "Protein",
"text": [
"IGF2"
],
"offsets": [
[
54,
58
]
],
"normalized": []
},
{
"id": "PMID-10729220_T2",
"type": "Protein",
"text": [
"H19"
],
"offsets": [
[
59,
62
]
],
"normalized": []
},
{
"id": "PMID-10729220_T3",
"type": "Protein",
"text": [
"IGF2"
],
"offsets": [
[
101,
105
]
],
"normalized": []
},
{
"id": "PMID-10729220_T4",
"type": "Protein",
"text": [
"insulin-like growth factor II"
],
"offsets": [
[
113,
142
]
],
"normalized": []
},
{
"id": "PMID-10729220_T5",
"type": "Protein",
"text": [
"H19"
],
"offsets": [
[
148,
151
]
],
"normalized": []
},
{
"id": "PMID-10729220_T6",
"type": "Protein",
"text": [
"IGF2"
],
"offsets": [
[
227,
231
]
],
"normalized": []
},
{
"id": "PMID-10729220_T7",
"type": "Protein",
"text": [
"H19"
],
"offsets": [
[
287,
290
]
],
"normalized": []
},
{
"id": "PMID-10729220_T8",
"type": "Protein",
"text": [
"H19"
],
"offsets": [
[
450,
453
]
],
"normalized": []
},
{
"id": "PMID-10729220_T9",
"type": "Protein",
"text": [
"IGF2"
],
"offsets": [
[
725,
729
]
],
"normalized": []
},
{
"id": "PMID-10729220_T10",
"type": "Protein",
"text": [
"H19"
],
"offsets": [
[
730,
733
]
],
"normalized": []
},
{
"id": "PMID-10729220_T11",
"type": "Protein",
"text": [
"IGF2"
],
"offsets": [
[
781,
785
]
],
"normalized": []
},
{
"id": "PMID-10729220_T12",
"type": "Protein",
"text": [
"IGF2"
],
"offsets": [
[
942,
946
]
],
"normalized": []
},
{
"id": "PMID-10729220_T13",
"type": "Protein",
"text": [
"IGF2"
],
"offsets": [
[
1094,
1098
]
],
"normalized": []
},
{
"id": "PMID-10729220_T14",
"type": "Protein",
"text": [
"H19"
],
"offsets": [
[
1137,
1140
]
],
"normalized": []
},
{
"id": "PMID-10729220_T15",
"type": "Protein",
"text": [
"H19"
],
"offsets": [
[
1222,
1225
]
],
"normalized": []
},
{
"id": "PMID-10729220_T16",
"type": "Protein",
"text": [
"H19"
],
"offsets": [
[
1407,
1410
]
],
"normalized": []
},
{
"id": "PMID-10729220_T17",
"type": "Protein",
"text": [
"H19"
],
"offsets": [
[
1540,
1543
]
],
"normalized": []
},
{
"id": "PMID-10729220_T18",
"type": "Protein",
"text": [
"H19"
],
"offsets": [
[
2039,
2042
]
],
"normalized": []
},
{
"id": "PMID-10729220_T20",
"type": "Entity",
"text": [
"imprinted region"
],
"offsets": [
[
63,
79
]
],
"normalized": []
},
{
"id": "PMID-10729220_T22",
"type": "Entity",
"text": [
"5' flanking region"
],
"offsets": [
[
428,
446
]
],
"normalized": []
},
{
"id": "PMID-10729220_T24",
"type": "Entity",
"text": [
"cytosine"
],
"offsets": [
[
653,
661
]
],
"normalized": []
},
{
"id": "PMID-10729220_T25",
"type": "Entity",
"text": [
"CpG island"
],
"offsets": [
[
746,
756
]
],
"normalized": []
},
{
"id": "PMID-10729220_T28",
"type": "Entity",
"text": [
"CpG sites"
],
"offsets": [
[
989,
998
]
],
"normalized": []
},
{
"id": "PMID-10729220_T31",
"type": "Entity",
"text": [
"DMR"
],
"offsets": [
[
1141,
1144
]
],
"normalized": []
},
{
"id": "PMID-10729220_T32",
"type": "Entity",
"text": [
"25 CpG sites"
],
"offsets": [
[
1250,
1262
]
],
"normalized": []
},
{
"id": "PMID-10729220_T35",
"type": "Entity",
"text": [
"CpG island"
],
"offsets": [
[
1380,
1390
]
],
"normalized": []
},
{
"id": "PMID-10729220_T37",
"type": "Entity",
"text": [
"25 CpG sites"
],
"offsets": [
[
1468,
1480
]
],
"normalized": []
},
{
"id": "PMID-10729220_T38",
"type": "Entity",
"text": [
"CpG region"
],
"offsets": [
[
1522,
1532
]
],
"normalized": []
},
{
"id": "PMID-10729220_T41",
"type": "Entity",
"text": [
"CpNpG"
],
"offsets": [
[
1655,
1660
]
],
"normalized": []
},
{
"id": "PMID-10729220_T42",
"type": "Entity",
"text": [
"GpNpC"
],
"offsets": [
[
1665,
1670
]
],
"normalized": []
},
{
"id": "PMID-10729220_T43",
"type": "Entity",
"text": [
"CpNpG"
],
"offsets": [
[
1707,
1712
]
],
"normalized": []
},
{
"id": "PMID-10729220_T44",
"type": "Entity",
"text": [
"cytosines"
],
"offsets": [
[
1769,
1778
]
],
"normalized": []
},
{
"id": "PMID-10729220_T46",
"type": "Entity",
"text": [
"cytosines"
],
"offsets": [
[
1858,
1867
]
],
"normalized": []
}
] | [
{
"id": "PMID-10729220_E1",
"type": "DNA_methylation",
"trigger": {
"text": [
"DNA methylation"
],
"offsets": [
[
25,
40
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T1"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T20"
}
]
},
{
"id": "PMID-10729220_E2",
"type": "DNA_methylation",
"trigger": {
"text": [
"DNA methylation"
],
"offsets": [
[
25,
40
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T2"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T20"
}
]
},
{
"id": "PMID-10729220_E3",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
368,
379
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T8"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T22"
}
]
},
{
"id": "PMID-10729220_E4",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
631,
642
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T9"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T24"
}
]
},
{
"id": "PMID-10729220_E5",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
631,
642
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T10"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T24"
}
]
},
{
"id": "PMID-10729220_E6",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
923,
933
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T11"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T25"
}
]
},
{
"id": "PMID-10729220_E7",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
971,
982
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T12"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T28"
}
]
},
{
"id": "PMID-10729220_E8",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1079,
1090
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T13"
}
]
},
{
"id": "PMID-10729220_E9",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1112,
1123
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T14"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T31"
}
]
},
{
"id": "PMID-10729220_E10",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
1279,
1289
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T15"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T32"
}
]
},
{
"id": "PMID-10729220_E11",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1343,
1354
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T16"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T35"
}
]
},
{
"id": "PMID-10729220_E12",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1449,
1460
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T16"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T37"
}
]
},
{
"id": "PMID-10729220_E13",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
1582,
1592
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T17"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T38"
}
]
},
{
"id": "PMID-10729220_E14",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
1635,
1645
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T17"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T41"
}
]
},
{
"id": "PMID-10729220_E15",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
1635,
1645
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T17"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T42"
}
]
},
{
"id": "PMID-10729220_E16",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
1635,
1645
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T17"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T43"
}
]
},
{
"id": "PMID-10729220_E17",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
1797,
1807
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T17"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T44"
}
]
},
{
"id": "PMID-10729220_E18",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
1902,
1912
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T17"
},
{
"role": "Site",
"ref_id": "PMID-10729220_T46"
}
]
},
{
"id": "PMID-10729220_E19",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1977,
1988
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10729220_T18"
}
]
}
] | [
{
"id": "PMID-10729220_1",
"entity_ids": [
"PMID-10729220_T3",
"PMID-10729220_T4"
]
}
] | [] |
22 | PMID-10746157 | [
{
"id": "PMID-10746157__text",
"type": "abstract",
"text": [
"An increase in histone acetylation and IL-2 antagonizing the immunoinhibitory effect are necessary for augmentation by butyrate of in vitro anti-TNP antibody production. \nWe investigated the role of histone acetylation in the promotion of antigen-specific antibody production in murine B cells induced by sodium butyrate (NaBu) plus interleukin 2 (IL-2). NaBu dose dependently increased the acetylation levels of histone H4 at concentrations which effectively enhanced anti-trinitrophenyl (TNP) antibody production in the presence of IL-2. Among other short-chain fatty acids and NaBu analogs, propionate, valerate and vinylacetate were effective in the presence of IL-2 in increasing both antibody production and the histone H4 acetylation level, but acetate, alpha-, beta- and gamma-hydroxybutyrates and alpha-, beta- and gamma-aminobutyrates were not effective, even in the presence of IL-2. The effect of the specific histone deacetylase inhibitor trichostatin A (TSA), which enhances anti-TNP antibody production without IL-2, was markedly inhibited by adding NaBu simultaneously. However, the effect of TSA was neither inhibited nor potentiated by NaBu in the presence of IL-2. Splenic B cells treated with NaBu, TSA and both together in the presence or absence of IL-2 showed almost the same increased acetylation level of histone H4. These results suggest that the NaBu-induced enhancement of anti-TNP antibody production in the presence of IL-2 is mediated through a moderate increase in the level of histone acetylation and that NaBu has both stimulating and inhibiting activities for anti-TNP antibody production, the latter of which is overcome by IL-2.\n"
],
"offsets": [
[
0,
1666
]
]
}
] | [
{
"id": "PMID-10746157_T1",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
15,
22
]
],
"normalized": []
},
{
"id": "PMID-10746157_T2",
"type": "Protein",
"text": [
"IL-2"
],
"offsets": [
[
39,
43
]
],
"normalized": []
},
{
"id": "PMID-10746157_T3",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
199,
206
]
],
"normalized": []
},
{
"id": "PMID-10746157_T4",
"type": "Protein",
"text": [
"interleukin 2"
],
"offsets": [
[
333,
346
]
],
"normalized": []
},
{
"id": "PMID-10746157_T5",
"type": "Protein",
"text": [
"IL-2"
],
"offsets": [
[
348,
352
]
],
"normalized": []
},
{
"id": "PMID-10746157_T6",
"type": "Protein",
"text": [
"histone H4"
],
"offsets": [
[
413,
423
]
],
"normalized": []
},
{
"id": "PMID-10746157_T7",
"type": "Protein",
"text": [
"IL-2"
],
"offsets": [
[
534,
538
]
],
"normalized": []
},
{
"id": "PMID-10746157_T8",
"type": "Protein",
"text": [
"IL-2"
],
"offsets": [
[
666,
670
]
],
"normalized": []
},
{
"id": "PMID-10746157_T9",
"type": "Protein",
"text": [
"histone H4"
],
"offsets": [
[
718,
728
]
],
"normalized": []
},
{
"id": "PMID-10746157_T10",
"type": "Protein",
"text": [
"IL-2"
],
"offsets": [
[
889,
893
]
],
"normalized": []
},
{
"id": "PMID-10746157_T11",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
922,
929
]
],
"normalized": []
},
{
"id": "PMID-10746157_T12",
"type": "Protein",
"text": [
"IL-2"
],
"offsets": [
[
1026,
1030
]
],
"normalized": []
},
{
"id": "PMID-10746157_T13",
"type": "Protein",
"text": [
"IL-2"
],
"offsets": [
[
1178,
1182
]
],
"normalized": []
},
{
"id": "PMID-10746157_T14",
"type": "Protein",
"text": [
"IL-2"
],
"offsets": [
[
1271,
1275
]
],
"normalized": []
},
{
"id": "PMID-10746157_T15",
"type": "Protein",
"text": [
"histone H4"
],
"offsets": [
[
1330,
1340
]
],
"normalized": []
},
{
"id": "PMID-10746157_T16",
"type": "Protein",
"text": [
"IL-2"
],
"offsets": [
[
1449,
1453
]
],
"normalized": []
},
{
"id": "PMID-10746157_T17",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
1510,
1517
]
],
"normalized": []
},
{
"id": "PMID-10746157_T18",
"type": "Protein",
"text": [
"IL-2"
],
"offsets": [
[
1660,
1664
]
],
"normalized": []
}
] | [
{
"id": "PMID-10746157_E1",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
23,
34
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10746157_T1"
}
]
},
{
"id": "PMID-10746157_E2",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
207,
218
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10746157_T3"
}
]
},
{
"id": "PMID-10746157_E3",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
391,
402
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10746157_T6"
}
]
},
{
"id": "PMID-10746157_E4",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
729,
740
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10746157_T9"
}
]
},
{
"id": "PMID-10746157_E5",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
1309,
1320
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10746157_T15"
}
]
},
{
"id": "PMID-10746157_E6",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
1518,
1529
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10746157_T17"
}
]
}
] | [
{
"id": "PMID-10746157_1",
"entity_ids": [
"PMID-10746157_T4",
"PMID-10746157_T5"
]
}
] | [] |
23 | PMID-10799457 | [
{
"id": "PMID-10799457__text",
"type": "abstract",
"text": [
"New immunofluorescence assays for detection of Human herpesvirus 8-specific antibodies. \nSeveral assays have been developed for detection of immunoglobulin G antibodies to Human herpesvirus 8 (HHV-8), including immunofluorescence assays (IFAs) and enzyme-linked immunosorbent assays (ELISAs). However, the specificity and sensitivity of these assays are not completely defined due to the lack of a \"gold standard.\" Although IFAs based on primary effusion lymphoma (PEL) cell lines are used widely, the assays can be confounded by nonspecific reactions against cellular components and potential cross-reaction with antibodies against other herpesviruses. To provide more reliable IFAs, we established recombinant Semliki Forest viruses (rSFVs) expressing the HHV-8-specific proteins ORF73 and K8.1 and used BHK-21 cells infected with these rSFVs for IFA (ORF73-IFA and K8.1-IFA). Expression of the HHV-8-specific proteins at very high levels by the rSFV system allowed easy scoring for IFA and thereby increased specificity. The rSFV system also allowed detection of antibodies against glycosylation-dependent epitopes of K8.1. Titers measured by rSFV-based IFAs and PEL-based IFAs correlated well (correlation coefficients of >0.9), and concordances of seroreactivities between rSFV-based and PEL-based IFAs were >97% (kappa > 0.93). K8.1-IFA was more sensitive than either ORF73-IFA or peptide ELISAs. Using PEL-based lytic IFA as a reference assay, the sensitivity and specificity of K8.1-IFA were estimated to be 94 and 100%, respectively. HHV-8 prevalences determined by K8.1-IFA among the human immunodeficiency virus (HIV)-positive (HIV(+)) Kaposi's sarcoma (KS) patients, HIV(+) KS(-) patients, and healthy controls were 100, 65, and 6.7%, respectively, which were consistent with prior reports. Therefore, our rSFV-based IFAs may provide a specific and sensitive method for use in epidemiology studies. In addition, they will provide a basis for further development of diagnostic tests for HHV-8 infection.\n"
],
"offsets": [
[
0,
2016
]
]
}
] | [
{
"id": "PMID-10799457_T1",
"type": "Protein",
"text": [
"ORF73"
],
"offsets": [
[
783,
788
]
],
"normalized": []
},
{
"id": "PMID-10799457_T2",
"type": "Protein",
"text": [
"K8.1"
],
"offsets": [
[
793,
797
]
],
"normalized": []
},
{
"id": "PMID-10799457_T3",
"type": "Protein",
"text": [
"ORF73"
],
"offsets": [
[
855,
860
]
],
"normalized": []
},
{
"id": "PMID-10799457_T4",
"type": "Protein",
"text": [
"K8.1"
],
"offsets": [
[
869,
873
]
],
"normalized": []
},
{
"id": "PMID-10799457_T5",
"type": "Protein",
"text": [
"K8.1"
],
"offsets": [
[
1122,
1126
]
],
"normalized": []
},
{
"id": "PMID-10799457_T6",
"type": "Protein",
"text": [
"ORF73"
],
"offsets": [
[
1375,
1380
]
],
"normalized": []
},
{
"id": "PMID-10799457_T7",
"type": "Protein",
"text": [
"K8.1"
],
"offsets": [
[
1487,
1491
]
],
"normalized": []
},
{
"id": "PMID-10799457_T8",
"type": "Protein",
"text": [
"K8.1"
],
"offsets": [
[
1576,
1580
]
],
"normalized": []
}
] | [] | [] | [] |
24 | PMID-10880980 | [
{
"id": "PMID-10880980__text",
"type": "abstract",
"text": [
"Evidence that the lizard helospectin peptides are O-glycosylated. \nSix forms of helospectin (a vasoactive intestinal peptide analogue) were purified from the venom of the Heloderma horridum lizard. Their identification was performed by combining sequencing by automated Edman degradation and electrospray mass spectrometry analysis on the complete peptides and their tryptic fragments. The products resulting from the action of an O-glycosidase were also analysed. Two forms were identified as the previously named Hs1 and Hs2 of 38 and 37 amino-acid residues, respectively. Two forms corresponded to Hs1 and Hs2 O-glycosylated by a N-acetylhexosamine-hexose motif attached to the Ser32 residue. Two other forms were not completely characterized but might correspond to the O-glycosylated forms bearing a phosphate or a sulfate group. The glycosylation did not affect the capacity of the helospectins to recognize and to activate the human and the rat VPAC1 and VPAC2 receptors.\n"
],
"offsets": [
[
0,
979
]
]
}
] | [
{
"id": "PMID-10880980_T1",
"type": "Protein",
"text": [
"helospectin"
],
"offsets": [
[
25,
36
]
],
"normalized": []
},
{
"id": "PMID-10880980_T2",
"type": "Protein",
"text": [
"helospectin"
],
"offsets": [
[
80,
91
]
],
"normalized": []
},
{
"id": "PMID-10880980_T3",
"type": "Protein",
"text": [
"Hs1"
],
"offsets": [
[
515,
518
]
],
"normalized": []
},
{
"id": "PMID-10880980_T4",
"type": "Protein",
"text": [
"Hs2"
],
"offsets": [
[
523,
526
]
],
"normalized": []
},
{
"id": "PMID-10880980_T5",
"type": "Protein",
"text": [
"Hs1"
],
"offsets": [
[
601,
604
]
],
"normalized": []
},
{
"id": "PMID-10880980_T6",
"type": "Protein",
"text": [
"Hs2"
],
"offsets": [
[
609,
612
]
],
"normalized": []
},
{
"id": "PMID-10880980_T7",
"type": "Protein",
"text": [
"helospectins"
],
"offsets": [
[
888,
900
]
],
"normalized": []
},
{
"id": "PMID-10880980_T8",
"type": "Protein",
"text": [
"VPAC1"
],
"offsets": [
[
952,
957
]
],
"normalized": []
},
{
"id": "PMID-10880980_T9",
"type": "Protein",
"text": [
"VPAC2"
],
"offsets": [
[
962,
967
]
],
"normalized": []
},
{
"id": "PMID-10880980_T12",
"type": "Entity",
"text": [
"N-acetylhexosamine-hexose"
],
"offsets": [
[
633,
658
]
],
"normalized": []
},
{
"id": "PMID-10880980_T13",
"type": "Entity",
"text": [
"Ser32"
],
"offsets": [
[
681,
686
]
],
"normalized": []
}
] | [
{
"id": "PMID-10880980_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"O-glycosylated"
],
"offsets": [
[
50,
64
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10880980_T1"
}
]
},
{
"id": "PMID-10880980_E2",
"type": "Glycosylation",
"trigger": {
"text": [
"O-glycosylated"
],
"offsets": [
[
613,
627
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10880980_T5"
},
{
"role": "Site",
"ref_id": "PMID-10880980_T13"
},
{
"role": "Sidechain",
"ref_id": "PMID-10880980_T12"
}
]
},
{
"id": "PMID-10880980_E3",
"type": "Glycosylation",
"trigger": {
"text": [
"O-glycosylated"
],
"offsets": [
[
613,
627
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10880980_T6"
},
{
"role": "Site",
"ref_id": "PMID-10880980_T13"
},
{
"role": "Sidechain",
"ref_id": "PMID-10880980_T12"
}
]
}
] | [] | [] |
25 | PMID-10898761 | [
{
"id": "PMID-10898761__text",
"type": "abstract",
"text": [
"Changes in methionine adenosyltransferase and S-adenosylmethionine homeostasis in alcoholic rat liver. \nLiver-specific and non-liver-specific methionine adenosyltransferase (MAT) are products of two genes, MAT1A and MAT2A, respectively, that catalyze the formation of S-adenosylmethionine (SAM). We previously showed that MAT2A expression was associated with more rapid cell growth. Changes in MAT expression have not been examined in animal models of alcoholic liver injury, which is the focus of the current study. After rats were fed intragastrically with ethanol and high fat for 9 wk, the mRNA level of both MAT forms doubled but only the protein level of MAT2A increased. Although liver-specific MAT activity did not change, it was 32% lower after one and 68% lower after eight weekly enteral doses of lipopolysaccharide. Hepatic levels of methionine, SAM, and DNA methylation fell by approximately 40%. c-myc was hypomethylated, and its mRNA level increased. Genome-wide DNA strand break increased. Thus in the prefibrotic stage of alcoholic liver injury, there is already a switch in MAT expression, global DNA hypomethylation, increased c-myc expression, and genome-wide DNA strand break. These changes may be important in predisposing this liver disease to malignant degeneration.\n"
],
"offsets": [
[
0,
1291
]
]
}
] | [
{
"id": "PMID-10898761_T1",
"type": "Protein",
"text": [
"MAT1A"
],
"offsets": [
[
206,
211
]
],
"normalized": []
},
{
"id": "PMID-10898761_T2",
"type": "Protein",
"text": [
"MAT2A"
],
"offsets": [
[
216,
221
]
],
"normalized": []
},
{
"id": "PMID-10898761_T3",
"type": "Protein",
"text": [
"MAT2A"
],
"offsets": [
[
322,
327
]
],
"normalized": []
},
{
"id": "PMID-10898761_T4",
"type": "Protein",
"text": [
"MAT2A"
],
"offsets": [
[
661,
666
]
],
"normalized": []
},
{
"id": "PMID-10898761_T5",
"type": "Protein",
"text": [
"c-myc"
],
"offsets": [
[
910,
915
]
],
"normalized": []
},
{
"id": "PMID-10898761_T6",
"type": "Protein",
"text": [
"c-myc"
],
"offsets": [
[
1146,
1151
]
],
"normalized": []
}
] | [
{
"id": "PMID-10898761_E1",
"type": "DNA_methylation",
"trigger": {
"text": [
"hypomethylated"
],
"offsets": [
[
920,
934
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10898761_T5"
}
]
}
] | [] | [] |
26 | PMID-10903903 | [
{
"id": "PMID-10903903__text",
"type": "abstract",
"text": [
"Hsl7p, the yeast homologue of human JBP1, is a protein methyltransferase. \nThe yeast protein Hsl7p is a homologue of Janus kinase binding protein 1, JBP1, a newly characterized protein methyltransferase. In this report, Hsl7p also is shown to be a methyltransferase. It can be crosslinked to [(3)H]S-adenosylmethionine and exhibits in vitro protein methylation activity. Calf histones H2A and H4 and bovine myelin basic protein were methylated by Hsl7p, whereas histones H1, H2B, and H3 and bovine cytochrome c were not. We demonstrated that JBP1 can complement Saccharomyces cerevisiae with a disrupted HSL7 gene as judged by a reduction of the elongated bud phenotype, and a point mutation in the JBP1 S-adenosylmethionine consensus binding sequence eliminated all complementation by JBP1. Therefore, we conclude the yeast protein Hsl7p is a sequence and functional homologue of JBP1. These data provide evidence for an intricate link between protein methylation and macroscopic changes in yeast morphology.\n"
],
"offsets": [
[
0,
1010
]
]
}
] | [
{
"id": "PMID-10903903_T1",
"type": "Protein",
"text": [
"Hsl7p"
],
"offsets": [
[
0,
5
]
],
"normalized": []
},
{
"id": "PMID-10903903_T2",
"type": "Protein",
"text": [
"JBP1"
],
"offsets": [
[
36,
40
]
],
"normalized": []
},
{
"id": "PMID-10903903_T3",
"type": "Protein",
"text": [
"Hsl7p"
],
"offsets": [
[
93,
98
]
],
"normalized": []
},
{
"id": "PMID-10903903_T4",
"type": "Protein",
"text": [
"Janus kinase binding protein 1"
],
"offsets": [
[
117,
147
]
],
"normalized": []
},
{
"id": "PMID-10903903_T5",
"type": "Protein",
"text": [
"JBP1"
],
"offsets": [
[
149,
153
]
],
"normalized": []
},
{
"id": "PMID-10903903_T6",
"type": "Protein",
"text": [
"Hsl7p"
],
"offsets": [
[
220,
225
]
],
"normalized": []
},
{
"id": "PMID-10903903_T7",
"type": "Protein",
"text": [
"histones H2A"
],
"offsets": [
[
376,
388
]
],
"normalized": []
},
{
"id": "PMID-10903903_T8",
"type": "Protein",
"text": [
"H4"
],
"offsets": [
[
393,
395
]
],
"normalized": []
},
{
"id": "PMID-10903903_T9",
"type": "Protein",
"text": [
"myelin basic protein"
],
"offsets": [
[
407,
427
]
],
"normalized": []
},
{
"id": "PMID-10903903_T10",
"type": "Protein",
"text": [
"Hsl7p"
],
"offsets": [
[
447,
452
]
],
"normalized": []
},
{
"id": "PMID-10903903_T11",
"type": "Protein",
"text": [
"histones H1"
],
"offsets": [
[
462,
473
]
],
"normalized": []
},
{
"id": "PMID-10903903_T12",
"type": "Protein",
"text": [
"H2B"
],
"offsets": [
[
475,
478
]
],
"normalized": []
},
{
"id": "PMID-10903903_T13",
"type": "Protein",
"text": [
"H3"
],
"offsets": [
[
484,
486
]
],
"normalized": []
},
{
"id": "PMID-10903903_T14",
"type": "Protein",
"text": [
"cytochrome c"
],
"offsets": [
[
498,
510
]
],
"normalized": []
},
{
"id": "PMID-10903903_T15",
"type": "Protein",
"text": [
"JBP1"
],
"offsets": [
[
542,
546
]
],
"normalized": []
},
{
"id": "PMID-10903903_T16",
"type": "Protein",
"text": [
"HSL7"
],
"offsets": [
[
604,
608
]
],
"normalized": []
},
{
"id": "PMID-10903903_T17",
"type": "Protein",
"text": [
"JBP1"
],
"offsets": [
[
699,
703
]
],
"normalized": []
},
{
"id": "PMID-10903903_T18",
"type": "Protein",
"text": [
"JBP1"
],
"offsets": [
[
786,
790
]
],
"normalized": []
},
{
"id": "PMID-10903903_T19",
"type": "Protein",
"text": [
"Hsl7p"
],
"offsets": [
[
833,
838
]
],
"normalized": []
},
{
"id": "PMID-10903903_T20",
"type": "Protein",
"text": [
"JBP1"
],
"offsets": [
[
881,
885
]
],
"normalized": []
}
] | [
{
"id": "PMID-10903903_E1",
"type": "Methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
433,
443
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10903903_T7"
}
]
},
{
"id": "PMID-10903903_E2",
"type": "Methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
433,
443
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10903903_T14"
}
]
},
{
"id": "PMID-10903903_E3",
"type": "Catalysis",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
433,
443
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10903903_E1"
},
{
"role": "Cause",
"ref_id": "PMID-10903903_T10"
}
]
},
{
"id": "PMID-10903903_E4",
"type": "Methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
433,
443
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10903903_T8"
}
]
},
{
"id": "PMID-10903903_E5",
"type": "Catalysis",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
433,
443
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10903903_E4"
},
{
"role": "Cause",
"ref_id": "PMID-10903903_T10"
}
]
},
{
"id": "PMID-10903903_E6",
"type": "Methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
433,
443
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10903903_T9"
}
]
},
{
"id": "PMID-10903903_E7",
"type": "Catalysis",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
433,
443
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10903903_E6"
},
{
"role": "Cause",
"ref_id": "PMID-10903903_T10"
}
]
},
{
"id": "PMID-10903903_E8",
"type": "Methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
433,
443
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10903903_T11"
}
]
},
{
"id": "PMID-10903903_E9",
"type": "Methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
433,
443
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10903903_T12"
}
]
},
{
"id": "PMID-10903903_E10",
"type": "Methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
433,
443
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10903903_T13"
}
]
}
] | [
{
"id": "PMID-10903903_1",
"entity_ids": [
"PMID-10903903_T4",
"PMID-10903903_T5"
]
}
] | [] |
27 | PMID-10938272 | [
{
"id": "PMID-10938272__text",
"type": "abstract",
"text": [
"Rapid induction of histone hyperacetylation and cellular differentiation in human breast tumor cell lines following degradation of histone deacetylase-1. \nQuinidine inhibits proliferation and promotes cellular differentiation in human breast tumor epithelial cells. Previously we showed quinidine arrested MCF-7 cells in G(1) phase of the cell cycle and led to a G(1) to G(0) transition followed by apoptotic cell death. The present experiments demonstrated that MCF-7, MCF-7ras, T47D, MDA-MB-231, and MDA-MB-435 cells transiently differentiate before undergoing apoptosis in response to quinidine. The cells accumulated lipid droplets, and the cytokeratin 18 cytoskeleton was reorganized. Hyperacetylated histone H4 appeared within 2 h of the addition of quinidine to the medium, and levels were maximal by 24 h. Quinidine-treated MCF-7 cells showed elevated p21(WAF1), hypophosphorylation and suppression of retinoblastoma protein, and down-regulation of cyclin D1, similar to the cell cycle response observed with cells induced to differentiate by histone deacetylase inhibitors, trichostatin A, and trapoxin. Quinidine did not show evidence for direct inhibition of histone deacetylase enzymatic activity in vitro. HDAC1 was undetectable in MCF-7 cells 30 min after addition of quinidine to the growth medium. The proteasome inhibitors MG-132 and lactacystin completely protected HDAC1 from the action of quinidine. We conclude that quinidine is a breast tumor cell differentiating agent that causes the loss of HDAC1 via a proteasomal sensitive mechanism.\n"
],
"offsets": [
[
0,
1561
]
]
}
] | [
{
"id": "PMID-10938272_T1",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
19,
26
]
],
"normalized": []
},
{
"id": "PMID-10938272_T2",
"type": "Protein",
"text": [
"histone deacetylase-1"
],
"offsets": [
[
131,
152
]
],
"normalized": []
},
{
"id": "PMID-10938272_T3",
"type": "Protein",
"text": [
"cytokeratin 18"
],
"offsets": [
[
645,
659
]
],
"normalized": []
},
{
"id": "PMID-10938272_T4",
"type": "Protein",
"text": [
"histone H4"
],
"offsets": [
[
706,
716
]
],
"normalized": []
},
{
"id": "PMID-10938272_T5",
"type": "Protein",
"text": [
"p21"
],
"offsets": [
[
860,
863
]
],
"normalized": []
},
{
"id": "PMID-10938272_T6",
"type": "Protein",
"text": [
"WAF1"
],
"offsets": [
[
864,
868
]
],
"normalized": []
},
{
"id": "PMID-10938272_T7",
"type": "Protein",
"text": [
"retinoblastoma"
],
"offsets": [
[
910,
924
]
],
"normalized": []
},
{
"id": "PMID-10938272_T8",
"type": "Protein",
"text": [
"cyclin D1"
],
"offsets": [
[
957,
966
]
],
"normalized": []
},
{
"id": "PMID-10938272_T9",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
1051,
1058
]
],
"normalized": []
},
{
"id": "PMID-10938272_T10",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
1170,
1177
]
],
"normalized": []
},
{
"id": "PMID-10938272_T11",
"type": "Protein",
"text": [
"HDAC1"
],
"offsets": [
[
1219,
1224
]
],
"normalized": []
},
{
"id": "PMID-10938272_T12",
"type": "Protein",
"text": [
"HDAC1"
],
"offsets": [
[
1384,
1389
]
],
"normalized": []
},
{
"id": "PMID-10938272_T13",
"type": "Protein",
"text": [
"HDAC1"
],
"offsets": [
[
1516,
1521
]
],
"normalized": []
}
] | [
{
"id": "PMID-10938272_E1",
"type": "Acetylation",
"trigger": {
"text": [
"hyperacetylation"
],
"offsets": [
[
27,
43
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10938272_T1"
}
]
},
{
"id": "PMID-10938272_E2",
"type": "Acetylation",
"trigger": {
"text": [
"Hyperacetylated"
],
"offsets": [
[
690,
705
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10938272_T4"
}
]
},
{
"id": "PMID-10938272_E3",
"type": "Phosphorylation",
"trigger": {
"text": [
"hypophosphorylation"
],
"offsets": [
[
871,
890
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10938272_T5"
}
]
}
] | [
{
"id": "PMID-10938272_1",
"entity_ids": [
"PMID-10938272_T5",
"PMID-10938272_T6"
]
}
] | [] |
28 | PMID-10960154 | [
{
"id": "PMID-10960154__text",
"type": "abstract",
"text": [
"Glycosylation influences gating and pH sensitivity of I(sK). \nThe KvLQT1 and minK subunits that coassemble to form I(sK) channels, contain potential N-glycosylation sites. To examine the role of glycosylation in channel function, a Chinese hamster ovary cell line deficient in glycosylation (Lec-1) and its parental cell line (Pro-5) were transiently transfected with human KvLQT1 (hKvLQT1) cDNA, alone and in combination with the rat (rminK) or human minK (hminK) cDNA. Functional KvLQT1 and I(sK) currents were expressed in both cell lines, although amplitudes were larger in Pro-5 than Lec-1 cells transfected with hKvLQT1 and hKvLQT1/hminK. For I(sK), but not KvLQT1, the voltage-dependence of activation was shifted to more positive voltages and the activation kinetics were slower in the Lec-1 compared to the Pro-5 cells. The effect of extracellular acidification on recombinant KvLQT1 and I(sK) currents was investigated in Pro-5 and Lec-1 cells. Changing external pH (pH(o)) from 7.4 to 6.0 significantly decreased the amplitude and increased the half-activation voltage (V(1/2)) of KvLQT1 currents in Pro-5 and Lec-1 cells. In Pro-5 cells, decreasing pH(o) reduced I(sK) amplitude without increasing V(1/2), whether rminK or hminK was coexpressed with hKvLQT. In contrast, changing pH(o) from 7.4 to 6.0 did not significantly change I(sK) amplitude in Lec-1 cells. Thus, oligosaccharides attached to the minK subunit affect not only the gating properties, but also the pH sensitivity of I(sK).\n"
],
"offsets": [
[
0,
1504
]
]
}
] | [
{
"id": "PMID-10960154_T1",
"type": "Protein",
"text": [
"KvLQT1"
],
"offsets": [
[
66,
72
]
],
"normalized": []
},
{
"id": "PMID-10960154_T2",
"type": "Protein",
"text": [
"minK"
],
"offsets": [
[
77,
81
]
],
"normalized": []
},
{
"id": "PMID-10960154_T3",
"type": "Protein",
"text": [
"KvLQT1"
],
"offsets": [
[
374,
380
]
],
"normalized": []
},
{
"id": "PMID-10960154_T4",
"type": "Protein",
"text": [
"KvLQT1"
],
"offsets": [
[
383,
389
]
],
"normalized": []
},
{
"id": "PMID-10960154_T5",
"type": "Protein",
"text": [
"minK"
],
"offsets": [
[
437,
441
]
],
"normalized": []
},
{
"id": "PMID-10960154_T6",
"type": "Protein",
"text": [
"minK"
],
"offsets": [
[
452,
456
]
],
"normalized": []
},
{
"id": "PMID-10960154_T7",
"type": "Protein",
"text": [
"minK"
],
"offsets": [
[
459,
463
]
],
"normalized": []
},
{
"id": "PMID-10960154_T8",
"type": "Protein",
"text": [
"KvLQT1"
],
"offsets": [
[
482,
488
]
],
"normalized": []
},
{
"id": "PMID-10960154_T9",
"type": "Protein",
"text": [
"KvLQT1"
],
"offsets": [
[
619,
625
]
],
"normalized": []
},
{
"id": "PMID-10960154_T10",
"type": "Protein",
"text": [
"KvLQT1"
],
"offsets": [
[
631,
637
]
],
"normalized": []
},
{
"id": "PMID-10960154_T11",
"type": "Protein",
"text": [
"minK"
],
"offsets": [
[
639,
643
]
],
"normalized": []
},
{
"id": "PMID-10960154_T12",
"type": "Protein",
"text": [
"KvLQT1"
],
"offsets": [
[
664,
670
]
],
"normalized": []
},
{
"id": "PMID-10960154_T13",
"type": "Protein",
"text": [
"KvLQT1"
],
"offsets": [
[
886,
892
]
],
"normalized": []
},
{
"id": "PMID-10960154_T14",
"type": "Protein",
"text": [
"KvLQT1"
],
"offsets": [
[
1092,
1098
]
],
"normalized": []
},
{
"id": "PMID-10960154_T15",
"type": "Protein",
"text": [
"minK"
],
"offsets": [
[
1227,
1231
]
],
"normalized": []
},
{
"id": "PMID-10960154_T16",
"type": "Protein",
"text": [
"minK"
],
"offsets": [
[
1236,
1240
]
],
"normalized": []
},
{
"id": "PMID-10960154_T17",
"type": "Protein",
"text": [
"KvLQT"
],
"offsets": [
[
1263,
1268
]
],
"normalized": []
},
{
"id": "PMID-10960154_T18",
"type": "Protein",
"text": [
"minK"
],
"offsets": [
[
1414,
1418
]
],
"normalized": []
},
{
"id": "PMID-10960154_T19",
"type": "Entity",
"text": [
"oligosaccharides"
],
"offsets": [
[
1381,
1397
]
],
"normalized": []
}
] | [
{
"id": "PMID-10960154_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"attached"
],
"offsets": [
[
1398,
1406
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10960154_T18"
},
{
"role": "Sidechain",
"ref_id": "PMID-10960154_T19"
}
]
}
] | [] | [] |
29 | PMID-10973948 | [
{
"id": "PMID-10973948__text",
"type": "abstract",
"text": [
"A novel post-translational modification of yeast elongation factor 1A. Methylesterification at the C terminus. \nProtein methylation reactions can play important roles in cell physiology. After labeling intact Saccharomyces cerevisiae cells with S-adenosyl-l-[methyl-(3)H]methionine, we identified a major methylated 49-kDa polypeptide containing [(3)H]methyl groups in two distinct types of linkages. Peptide sequence analysis of the purified methylated protein revealed that it is eukaryotic elongation factor 1A (eEF1A, formerly EF-1alpha), the protein that forms a complex with GTP and aminoacyl-tRNAs for binding to the ribosomal A site during protein translation. Previous studies have shown that eEF1A is methylated on several internal lysine residues to give mono-, di-, and tri-N-epsilon-methyl-lysine derivatives. We confirm this finding but also detect methylation that is released as volatile methyl groups after base hydrolysis, characteristic of ester linkages. In cycloheximide-treated cells, methyl esterified eEF1A was detected largely in the ribosome and polysome fractions; little or no methylated protein was found in the soluble fraction. Because the base-labile, volatile [methyl-(3)H]radioactivity of eEF1A could be released by trypsin treatment but not by carboxypeptidase Y or chymotrypsin treatment, we suggest that the methyl ester is present on the alpha-carboxyl group of its C-terminal lysine residue. From the results of pulse-chase experiments using radiolabeled intact yeast cells, we find that the N-methylated lysine residues of eEF1A are stable over 4 h, whereas the eEF1A carboxyl methyl ester has a half-life of less than 10 min. The rapid turnover of the methyl ester suggests that the methylation/demethylation of eEF1A at the C-terminal carboxyl group may represent a novel mode of regulation of the activity of this protein in yeast.\n"
],
"offsets": [
[
0,
1876
]
]
}
] | [
{
"id": "PMID-10973948_T1",
"type": "Protein",
"text": [
"elongation factor 1A"
],
"offsets": [
[
49,
69
]
],
"normalized": []
},
{
"id": "PMID-10973948_T2",
"type": "Protein",
"text": [
"elongation factor 1A"
],
"offsets": [
[
494,
514
]
],
"normalized": []
},
{
"id": "PMID-10973948_T3",
"type": "Protein",
"text": [
"eEF1A"
],
"offsets": [
[
516,
521
]
],
"normalized": []
},
{
"id": "PMID-10973948_T4",
"type": "Protein",
"text": [
"EF-1alpha"
],
"offsets": [
[
532,
541
]
],
"normalized": []
},
{
"id": "PMID-10973948_T5",
"type": "Protein",
"text": [
"eEF1A"
],
"offsets": [
[
703,
708
]
],
"normalized": []
},
{
"id": "PMID-10973948_T6",
"type": "Protein",
"text": [
"eEF1A"
],
"offsets": [
[
1026,
1031
]
],
"normalized": []
},
{
"id": "PMID-10973948_T7",
"type": "Protein",
"text": [
"eEF1A"
],
"offsets": [
[
1224,
1229
]
],
"normalized": []
},
{
"id": "PMID-10973948_T8",
"type": "Protein",
"text": [
"carboxypeptidase Y"
],
"offsets": [
[
1280,
1298
]
],
"normalized": []
},
{
"id": "PMID-10973948_T9",
"type": "Protein",
"text": [
"chymotrypsin"
],
"offsets": [
[
1302,
1314
]
],
"normalized": []
},
{
"id": "PMID-10973948_T10",
"type": "Protein",
"text": [
"eEF1A"
],
"offsets": [
[
1564,
1569
]
],
"normalized": []
},
{
"id": "PMID-10973948_T11",
"type": "Protein",
"text": [
"eEF1A"
],
"offsets": [
[
1603,
1608
]
],
"normalized": []
},
{
"id": "PMID-10973948_T12",
"type": "Protein",
"text": [
"eEF1A"
],
"offsets": [
[
1754,
1759
]
],
"normalized": []
},
{
"id": "PMID-10973948_T14",
"type": "Entity",
"text": [
"C terminus"
],
"offsets": [
[
100,
110
]
],
"normalized": []
},
{
"id": "PMID-10973948_T16",
"type": "Entity",
"text": [
"lysine residues"
],
"offsets": [
[
743,
758
]
],
"normalized": []
},
{
"id": "PMID-10973948_T21",
"type": "Entity",
"text": [
"lysine residues"
],
"offsets": [
[
1545,
1560
]
],
"normalized": []
},
{
"id": "PMID-10973948_T24",
"type": "Entity",
"text": [
"C-terminal"
],
"offsets": [
[
1767,
1777
]
],
"normalized": []
}
] | [
{
"id": "PMID-10973948_E1",
"type": "Methylation",
"trigger": {
"text": [
"Methylesterification"
],
"offsets": [
[
72,
92
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10973948_T1"
},
{
"role": "Site",
"ref_id": "PMID-10973948_T14"
}
]
},
{
"id": "PMID-10973948_E2",
"type": "Methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
712,
722
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10973948_T5"
},
{
"role": "Site",
"ref_id": "PMID-10973948_T16"
}
]
},
{
"id": "PMID-10973948_E3",
"type": "Methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
864,
875
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10973948_T5"
}
]
},
{
"id": "PMID-10973948_E4",
"type": "Methylation",
"trigger": {
"text": [
"methyl esterified"
],
"offsets": [
[
1008,
1025
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10973948_T6"
}
]
},
{
"id": "PMID-10973948_E5",
"type": "Methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
1106,
1116
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10973948_T6"
}
]
},
{
"id": "PMID-10973948_E6",
"type": "Methylation",
"trigger": {
"text": [
"N-methylated"
],
"offsets": [
[
1532,
1544
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10973948_T10"
},
{
"role": "Site",
"ref_id": "PMID-10973948_T21"
}
]
},
{
"id": "PMID-10973948_E7",
"type": "Methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1725,
1736
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10973948_T12"
},
{
"role": "Site",
"ref_id": "PMID-10973948_T24"
}
]
},
{
"id": "PMID-10973948_E8",
"type": "Demethylation",
"trigger": {
"text": [
"demethylation"
],
"offsets": [
[
1737,
1750
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-10973948_T12"
},
{
"role": "Site",
"ref_id": "PMID-10973948_T24"
}
]
}
] | [
{
"id": "PMID-10973948_1",
"entity_ids": [
"PMID-10973948_T2",
"PMID-10973948_T3",
"PMID-10973948_T4"
]
}
] | [] |
30 | PMID-11013212 | [
{
"id": "PMID-11013212__text",
"type": "abstract",
"text": [
"Decreased UDP-GlcNAc levels abrogate proliferation control in EMeg32-deficient cells. \nThe hexosamine pathway provides UDP-N:-acetylhexosamine donor substrates used in cytosolic and Golgi-mediated glycosylation of proteins and for formation of glycosylphosphatidylinositol (GPI) anchors, which tether proteins to the outer plasma membrane. We have recently identified the murine glucosamine-6-phosphate (GlcN6P) acetyltransferase, EMeg32, as a developmentally regulated enzyme on the route to UDP-N:-acetylglucosamine (UDP-GlcNAc). Here we describe embryos and cells that have the EMeg32 gene inactivated by homologous recombination. Homozygous mutant embryos die at around embryonic day (E) 7.5 with a general proliferative delay of development. In vitro differentiated EMeg32(-/-) ES cells show reduced proliferation. Mouse embryonic fibroblasts (MEFs) deficient for EMeg32 exhibit defects in proliferation and adhesiveness, which could be complemented by stable re-expression of EMeg32 or by nutritional restoration of intracellular UDP-GlcNAc levels. Reduced UDP-GlcNAc levels predominantly translated into decreased O-GlcNAc modifications of cytosolic and nuclear proteins. Interestingly, growth-impaired EMeg32(-/-) MEFs withstand a number of apoptotic stimuli and express activated PKB/AKT. Thus, EMeg32-dependent UDP-GlcNAc levels influence cell cycle progression and susceptibility to apoptotic stimuli.\n"
],
"offsets": [
[
0,
1413
]
]
}
] | [
{
"id": "PMID-11013212_T1",
"type": "Protein",
"text": [
"EMeg32"
],
"offsets": [
[
62,
68
]
],
"normalized": []
},
{
"id": "PMID-11013212_T2",
"type": "Protein",
"text": [
"glucosamine-6-phosphate (GlcN6P) acetyltransferase"
],
"offsets": [
[
379,
429
]
],
"normalized": []
},
{
"id": "PMID-11013212_T3",
"type": "Protein",
"text": [
"EMeg32"
],
"offsets": [
[
431,
437
]
],
"normalized": []
},
{
"id": "PMID-11013212_T4",
"type": "Protein",
"text": [
"EMeg32"
],
"offsets": [
[
581,
587
]
],
"normalized": []
},
{
"id": "PMID-11013212_T5",
"type": "Protein",
"text": [
"EMeg32"
],
"offsets": [
[
771,
777
]
],
"normalized": []
},
{
"id": "PMID-11013212_T6",
"type": "Protein",
"text": [
"EMeg32"
],
"offsets": [
[
869,
875
]
],
"normalized": []
},
{
"id": "PMID-11013212_T7",
"type": "Protein",
"text": [
"EMeg32"
],
"offsets": [
[
982,
988
]
],
"normalized": []
},
{
"id": "PMID-11013212_T8",
"type": "Protein",
"text": [
"EMeg32"
],
"offsets": [
[
1210,
1216
]
],
"normalized": []
},
{
"id": "PMID-11013212_T9",
"type": "Protein",
"text": [
"PKB"
],
"offsets": [
[
1289,
1292
]
],
"normalized": []
},
{
"id": "PMID-11013212_T10",
"type": "Protein",
"text": [
"AKT"
],
"offsets": [
[
1293,
1296
]
],
"normalized": []
},
{
"id": "PMID-11013212_T11",
"type": "Protein",
"text": [
"EMeg32"
],
"offsets": [
[
1304,
1310
]
],
"normalized": []
}
] | [] | [
{
"id": "PMID-11013212_1",
"entity_ids": [
"PMID-11013212_T2",
"PMID-11013212_T3"
]
},
{
"id": "PMID-11013212_2",
"entity_ids": [
"PMID-11013212_T9",
"PMID-11013212_T10"
]
}
] | [] |
31 | PMID-11032800 | [
{
"id": "PMID-11032800__text",
"type": "abstract",
"text": [
"Post-translational hydroxylation at the N-terminus of the prion protein reveals presence of PPII structure in vivo. \nThe transmissible spongiform encephalopathies are characterized by conversion of a host protein, PrP(C) (cellular prion protein), to a protease-resistant isoform, PrP(Sc) (prion protein scrapie isoform). The importance of the highly flexible, N-terminal region of PrP has recently become more widely appreciated, particularly the biological activities associated with its metal ion-binding domain and its potential to form a poly(L-proline) II (PPII) helix. Circular dichroism spectroscopy of an N-terminal peptide, PrP(37-53), showed that the PPII helix is formed in aqueous buffer; as it also contains an Xaa-Pro-Gly consensus sequence, it may act as a substrate for the collagen-modifying enzyme prolyl 4-hydroxylase. Direct evidence for this modification was obtained by mass spectrometry and Edman sequencing in recombinant mouse PrP secreted from stably transfected Chinese hamster ovary cells. Almost complete conversion of proline to 4-hydroxyproline occurs specifically at residue Pro44 of this murine protein; the same hydroxylated residue was detected, at lower levels, in PrP(Sc) from the brains of scrapie-infected mice. Cation binding and/or post-translational hydroxylation of this region of PrP may regulate its role in the physiology and pathobiology of the cell.\n"
],
"offsets": [
[
0,
1398
]
]
}
] | [
{
"id": "PMID-11032800_T1",
"type": "Protein",
"text": [
"prion protein"
],
"offsets": [
[
58,
71
]
],
"normalized": []
},
{
"id": "PMID-11032800_T2",
"type": "Protein",
"text": [
"PrP(C)"
],
"offsets": [
[
214,
220
]
],
"normalized": []
},
{
"id": "PMID-11032800_T3",
"type": "Protein",
"text": [
"prion protein"
],
"offsets": [
[
231,
244
]
],
"normalized": []
},
{
"id": "PMID-11032800_T4",
"type": "Protein",
"text": [
"PrP"
],
"offsets": [
[
280,
283
]
],
"normalized": []
},
{
"id": "PMID-11032800_T5",
"type": "Protein",
"text": [
"prion protein"
],
"offsets": [
[
289,
302
]
],
"normalized": []
},
{
"id": "PMID-11032800_T6",
"type": "Protein",
"text": [
"PrP"
],
"offsets": [
[
381,
384
]
],
"normalized": []
},
{
"id": "PMID-11032800_T7",
"type": "Protein",
"text": [
"PrP"
],
"offsets": [
[
633,
636
]
],
"normalized": []
},
{
"id": "PMID-11032800_T8",
"type": "Protein",
"text": [
"PrP"
],
"offsets": [
[
952,
955
]
],
"normalized": []
},
{
"id": "PMID-11032800_T9",
"type": "Protein",
"text": [
"PrP"
],
"offsets": [
[
1201,
1204
]
],
"normalized": []
},
{
"id": "PMID-11032800_T10",
"type": "Protein",
"text": [
"PrP"
],
"offsets": [
[
1324,
1327
]
],
"normalized": []
},
{
"id": "PMID-11032800_T12",
"type": "Entity",
"text": [
"N-terminus"
],
"offsets": [
[
40,
50
]
],
"normalized": []
},
{
"id": "PMID-11032800_T14",
"type": "Entity",
"text": [
"Pro44"
],
"offsets": [
[
1107,
1112
]
],
"normalized": []
}
] | [
{
"id": "PMID-11032800_E1",
"type": "Hydroxylation",
"trigger": {
"text": [
"hydroxylation"
],
"offsets": [
[
19,
32
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11032800_T1"
},
{
"role": "Site",
"ref_id": "PMID-11032800_T12"
}
]
},
{
"id": "PMID-11032800_E2",
"type": "Hydroxylation",
"trigger": {
"text": [
"conversion"
],
"offsets": [
[
1034,
1044
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11032800_T8"
},
{
"role": "Site",
"ref_id": "PMID-11032800_T14"
}
]
},
{
"id": "PMID-11032800_E3",
"type": "Hydroxylation",
"trigger": {
"text": [
"hydroxylated"
],
"offsets": [
[
1146,
1158
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11032800_T9"
},
{
"role": "Site",
"ref_id": "PMID-11032800_T14"
}
]
},
{
"id": "PMID-11032800_E4",
"type": "Hydroxylation",
"trigger": {
"text": [
"hydroxylation"
],
"offsets": [
[
1292,
1305
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11032800_T10"
}
]
}
] | [
{
"id": "PMID-11032800_1",
"entity_ids": [
"PMID-11032800_T2",
"PMID-11032800_T3"
]
},
{
"id": "PMID-11032800_2",
"entity_ids": [
"PMID-11032800_T4",
"PMID-11032800_T5"
]
}
] | [] |
32 | PMID-11038366 | [
{
"id": "PMID-11038366__text",
"type": "abstract",
"text": [
"Carboxymethylation of the PP2A catalytic subunit in Saccharomyces cerevisiae is required for efficient interaction with the B-type subunits Cdc55p and Rts1p. \nProtein phosphatase 2A (PP2A) is an essential eukaryotic serine/threonine phosphatase known to play important roles in cell cycle regulation. Association of different B-type targeting subunits with the heterodimeric core (A/C) enzyme is known to be an important mechanism of regulating PP2A activity, substrate specificity, and localization. However, how the binding of these targeting subunits to the A/C heterodimer might be regulated is unknown. We have used the budding yeast Saccharomyces cerevisiae as a model system to investigate the hypothesis that covalent modification of the C subunit (Pph21p/Pph22p) carboxyl terminus modulates PP2A complex formation. Two approaches were taken. First, S. cerevisiae cells were generated whose survival depended on the expression of different carboxyl-terminal Pph21p mutants. Second, the major S. cerevisiae methyltransferase (Ppm1p) that catalyzes the methylation of the PP2A C subunit carboxyl-terminal leucine was identified, and cells deleted for this methyltransferase were utilized for our studies. Our results demonstrate that binding of the yeast B subunit, Cdc55p, to Pph21p was disrupted by either acidic substitution of potential carboxyl-terminal phosphorylation sites on Pph21p or by deletion of the gene for Ppm1p. Loss of Cdc55p association was accompanied in each case by a large reduction in binding of the yeast A subunit, Tpd3p, to Pph21p. Moreover, decreased Cdc55p and Tpd3p binding invariably resulted in nocodazole sensitivity, a known phenotype of CDC55 or TPD3 deletion. Furthermore, loss of methylation also greatly reduced the association of another yeast B-type subunit, Rts1p. Thus, methylation of Pph21p is important for formation of PP2A trimeric and dimeric complexes, and consequently, for PP2A function. Taken together, our results indicate that methylation and phosphorylation may be mechanisms by which the cell dynamically regulates PP2A complex formation and function.\n"
],
"offsets": [
[
0,
2113
]
]
}
] | [
{
"id": "PMID-11038366_T1",
"type": "Protein",
"text": [
"Cdc55p"
],
"offsets": [
[
140,
146
]
],
"normalized": []
},
{
"id": "PMID-11038366_T2",
"type": "Protein",
"text": [
"Rts1p"
],
"offsets": [
[
151,
156
]
],
"normalized": []
},
{
"id": "PMID-11038366_T3",
"type": "Protein",
"text": [
"Pph21p"
],
"offsets": [
[
757,
763
]
],
"normalized": []
},
{
"id": "PMID-11038366_T4",
"type": "Protein",
"text": [
"Pph22p"
],
"offsets": [
[
764,
770
]
],
"normalized": []
},
{
"id": "PMID-11038366_T5",
"type": "Protein",
"text": [
"Pph21p"
],
"offsets": [
[
966,
972
]
],
"normalized": []
},
{
"id": "PMID-11038366_T6",
"type": "Protein",
"text": [
"Ppm1p"
],
"offsets": [
[
1033,
1038
]
],
"normalized": []
},
{
"id": "PMID-11038366_T7",
"type": "Protein",
"text": [
"Cdc55p"
],
"offsets": [
[
1272,
1278
]
],
"normalized": []
},
{
"id": "PMID-11038366_T8",
"type": "Protein",
"text": [
"Pph21p"
],
"offsets": [
[
1283,
1289
]
],
"normalized": []
},
{
"id": "PMID-11038366_T9",
"type": "Protein",
"text": [
"Pph21p"
],
"offsets": [
[
1390,
1396
]
],
"normalized": []
},
{
"id": "PMID-11038366_T10",
"type": "Protein",
"text": [
"Ppm1p"
],
"offsets": [
[
1428,
1433
]
],
"normalized": []
},
{
"id": "PMID-11038366_T11",
"type": "Protein",
"text": [
"Cdc55p"
],
"offsets": [
[
1443,
1449
]
],
"normalized": []
},
{
"id": "PMID-11038366_T12",
"type": "Protein",
"text": [
"Tpd3p"
],
"offsets": [
[
1547,
1552
]
],
"normalized": []
},
{
"id": "PMID-11038366_T13",
"type": "Protein",
"text": [
"Pph21p"
],
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[
1557,
1563
]
],
"normalized": []
},
{
"id": "PMID-11038366_T14",
"type": "Protein",
"text": [
"Cdc55p"
],
"offsets": [
[
1585,
1591
]
],
"normalized": []
},
{
"id": "PMID-11038366_T15",
"type": "Protein",
"text": [
"Tpd3p"
],
"offsets": [
[
1596,
1601
]
],
"normalized": []
},
{
"id": "PMID-11038366_T16",
"type": "Protein",
"text": [
"CDC55"
],
"offsets": [
[
1678,
1683
]
],
"normalized": []
},
{
"id": "PMID-11038366_T17",
"type": "Protein",
"text": [
"TPD3"
],
"offsets": [
[
1687,
1691
]
],
"normalized": []
},
{
"id": "PMID-11038366_T18",
"type": "Protein",
"text": [
"Rts1p"
],
"offsets": [
[
1805,
1810
]
],
"normalized": []
},
{
"id": "PMID-11038366_T19",
"type": "Protein",
"text": [
"Pph21p"
],
"offsets": [
[
1833,
1839
]
],
"normalized": []
}
] | [
{
"id": "PMID-11038366_E1",
"type": "Methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1818,
1829
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11038366_T19"
}
]
}
] | [] | [] |
33 | PMID-11055323 | [
{
"id": "PMID-11055323__text",
"type": "abstract",
"text": [
"Safety and pharmacokinetic study with escalating doses of 3-acetyl-7-oxo-dehydroepiandrosterone in healthy male volunteers. \nOBJECTIVES: To evaluate the safety and pharmacokinetics of 3-acetyl-7-oxo-DHEA (3beta-acetoxyandrost-5-ene-7,17-dione) given orally. DESIGN: A randomized, double blind, placebo-controlled, escalating dose study. SETTING: The Chicago Center for Clinical Research. PARTICIPANTS: Twenty-two healthy men. STUDY METHOD: The participants received placebo (n = 6) or 3-acetyl-7-oxo-DHEA (n = 16) at 50 mg/d for 7 days followed by a 7-day washout; 100 mg/d for 7 days followed by a 7-day washout; and 200 mg/d for 28 days. OUTCOME MEASURES: Safety parameters, evaluated at each dose level, included measurement of total testosterone, free testosterone, dihydrotestosterone, estradiol, cortisol, thyroxin and insulin levels. Analyses for 7-oxo-DHEA-3beta-sulfate (DHEA-S), the only detectable metabolic product of the administered steroid, were conducted on plasma drawn from all subjects at 0.25, 0.5, 1, 2, 4, 6 and 12 hours after the final 100 mg dose of 3beta-acetyl-7-oxo-DHEA. RESULTS: There were no differences in the clinical laboratory values or in reported minor adverse experiences, between treatment and placebo groups. In general, blood hormone concentrations were unaffected by the treatment with 3beta-acetyl-7-oxo-DHEA and remained within the normal range. No changes in vital signs, blood chemistry or urinalysis occurred during treatment with 3beta-acetyl-7-oxo-DHEA compared to placebo. The administered steroid was not detected in the blood but was rapidly converted to 7-oxo-DHEA-S, the concentrations of which were proportional to dose. This steroid sulfate did not accumulate; plasma concentrations 12 hours after the 3beta-acetyl-7-oxo-DHEA dose at 7 and 28 days on the 200 mg/d dose were 15.8 and 16.3 microg/L respectively. The mean time to peak plasma level of 7-oxo-DHEA-S was 2.2 hours; the mean half life was 2.17 hours. The apparent clearance averaged 172 L/h, and the apparent mean volume of distribution was 540 L. CONCLUSION: These results indicate that 3beta-acetyl-7-oxo-DHEA is safe and well tolerated in normal healthy men at doses up to 200 mg/d for 4 weeks.\n"
],
"offsets": [
[
0,
2214
]
]
}
] | [
{
"id": "PMID-11055323_T1",
"type": "Protein",
"text": [
"insulin"
],
"offsets": [
[
825,
832
]
],
"normalized": []
}
] | [] | [] | [] |
34 | PMID-11073455 | [
{
"id": "PMID-11073455__text",
"type": "abstract",
"text": [
"Aureusidin synthase: a polyphenol oxidase homolog responsible for flower coloration. \nAurones are plant flavonoids that provide yellow color to the flowers of some popular ornamental plants, such as snapdragon and cosmos. In this study, we have identified an enzyme responsible for the synthesis of aurone from chalcones in the yellow snapdragon flower. The enzyme (aureusidin synthase) is a 39-kilodalton, copper-containing glycoprotein catalyzing the hydroxylation and/or oxidative cyclization of the precursor chalcones, 2',4',6',4-tetrahydroxychalcone and 2',4',6',3,4-pentahydroxychalcone. The complementary DNA encoding aureusidin synthase is expressed in the petals of aurone-containing varieties. DNA sequence analysis revealed that aureusidin synthase belongs to the plant polyphenol oxidase family, providing an unequivocal example of the function of the polyphenol oxidase homolog in plants, i.e., flower coloration.\n"
],
"offsets": [
[
0,
928
]
]
}
] | [
{
"id": "PMID-11073455_T1",
"type": "Protein",
"text": [
"Aureusidin synthase"
],
"offsets": [
[
0,
19
]
],
"normalized": []
},
{
"id": "PMID-11073455_T2",
"type": "Protein",
"text": [
"aureusidin synthase"
],
"offsets": [
[
366,
385
]
],
"normalized": []
},
{
"id": "PMID-11073455_T3",
"type": "Protein",
"text": [
"aureusidin synthase"
],
"offsets": [
[
626,
645
]
],
"normalized": []
},
{
"id": "PMID-11073455_T4",
"type": "Protein",
"text": [
"aureusidin synthase"
],
"offsets": [
[
741,
760
]
],
"normalized": []
}
] | [] | [] | [] |
35 | PMID-11106238 | [
{
"id": "PMID-11106238__text",
"type": "abstract",
"text": [
"E-cadherin expression is silenced by 5' CpG island methylation in acute leukemia. \nE-Cadherin is a transmembrane glycoprotein that mediates Ca2+-dependent intercellular adhesion in normal epithelium. In tumors of epithelial origin, E-cadherin expression frequently is reduced, an event that contributes to tumor invasion and metastasis. The role of E-cadherin in hematopoietic tissues is less clear. In normal bone marrow, E-cadherin is expressed on erythroid progenitors, CD34+ stem cells, and stromal cells, where it likely contributes to intercellular interactions during hematopoiesis. In this study, we used a nested-PCR approach to examine the methylation status of the E-cadherin 5' CpG island in blood and bone marrow samples from normal donors and in bone marrow from patients with acute leukemia. In normal peripheral blood mononuclear cells and bone marrow, E-cadherin was completely unmethylated. In peripheral blood mononuclear cells, expression was evident by reverse transcription-PCR. Immunoblotting confirmed E-cadherin protein expression in two lymphoblastoid cell lines derived from normal donors. In contrast, E-cadherin was aberrantly methylated in 4 of 4 (100%) leukemia cell lines, 14 of 44 (32%) acute myelogenous leukemias, and 18 of 33 (53%) acute lymphoblastic leukemias. Genomic bisulfite sequencing of primary leukemias confirmed dense methylation across the CpG island. Methylation was associated with loss of E-cadherin RNA and protein in leukemia cell lines and primary leukemias. Following treatment with 5-aza-2'-deoxycytidine, a methylated leukemia cell line expressed both E-cadherin transcript and protein. Our results show that methylation of E-cadherin occurs commonly in acute leukemia and suggests a hypothesis for E-cadherin down-regulation in leukemogenesis.\n"
],
"offsets": [
[
0,
1802
]
]
}
] | [
{
"id": "PMID-11106238_T1",
"type": "Protein",
"text": [
"E-cadherin"
],
"offsets": [
[
0,
10
]
],
"normalized": []
},
{
"id": "PMID-11106238_T2",
"type": "Protein",
"text": [
"E-Cadherin"
],
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[
83,
93
]
],
"normalized": []
},
{
"id": "PMID-11106238_T3",
"type": "Protein",
"text": [
"E-cadherin"
],
"offsets": [
[
232,
242
]
],
"normalized": []
},
{
"id": "PMID-11106238_T4",
"type": "Protein",
"text": [
"E-cadherin"
],
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[
349,
359
]
],
"normalized": []
},
{
"id": "PMID-11106238_T5",
"type": "Protein",
"text": [
"E-cadherin"
],
"offsets": [
[
423,
433
]
],
"normalized": []
},
{
"id": "PMID-11106238_T6",
"type": "Protein",
"text": [
"CD34"
],
"offsets": [
[
473,
477
]
],
"normalized": []
},
{
"id": "PMID-11106238_T7",
"type": "Protein",
"text": [
"E-cadherin"
],
"offsets": [
[
676,
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]
],
"normalized": []
},
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"id": "PMID-11106238_T8",
"type": "Protein",
"text": [
"E-cadherin"
],
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869,
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]
],
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},
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"id": "PMID-11106238_T9",
"type": "Protein",
"text": [
"E-cadherin"
],
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1026,
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],
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},
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"id": "PMID-11106238_T10",
"type": "Protein",
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"E-cadherin"
],
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[
1130,
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],
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},
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"id": "PMID-11106238_T11",
"type": "Protein",
"text": [
"E-cadherin"
],
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1440,
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],
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},
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"id": "PMID-11106238_T12",
"type": "Protein",
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"E-cadherin"
],
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1609,
1619
]
],
"normalized": []
},
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"id": "PMID-11106238_T13",
"type": "Protein",
"text": [
"E-cadherin"
],
"offsets": [
[
1681,
1691
]
],
"normalized": []
},
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"id": "PMID-11106238_T14",
"type": "Protein",
"text": [
"E-cadherin"
],
"offsets": [
[
1756,
1766
]
],
"normalized": []
},
{
"id": "PMID-11106238_T15",
"type": "Entity",
"text": [
"5' CpG island"
],
"offsets": [
[
37,
50
]
],
"normalized": []
},
{
"id": "PMID-11106238_T18",
"type": "Entity",
"text": [
"5' CpG island"
],
"offsets": [
[
687,
700
]
],
"normalized": []
},
{
"id": "PMID-11106238_T22",
"type": "Entity",
"text": [
"CpG island"
],
"offsets": [
[
1388,
1398
]
],
"normalized": []
}
] | [
{
"id": "PMID-11106238_E1",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
51,
62
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11106238_T1"
},
{
"role": "Site",
"ref_id": "PMID-11106238_T15"
}
]
},
{
"id": "PMID-11106238_E2",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
650,
661
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11106238_T7"
},
{
"role": "Site",
"ref_id": "PMID-11106238_T18"
}
]
},
{
"id": "PMID-11106238_E3",
"type": "DNA_methylation",
"trigger": {
"text": [
"unmethylated"
],
"offsets": [
[
895,
907
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11106238_T8"
}
]
},
{
"id": "PMID-11106238_E4",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
1156,
1166
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11106238_T10"
}
]
},
{
"id": "PMID-11106238_E5",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1365,
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]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11106238_T10"
},
{
"role": "Site",
"ref_id": "PMID-11106238_T22"
}
]
},
{
"id": "PMID-11106238_E6",
"type": "DNA_methylation",
"trigger": {
"text": [
"Methylation"
],
"offsets": [
[
1400,
1411
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11106238_T11"
}
]
},
{
"id": "PMID-11106238_E7",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
1564,
1574
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11106238_T12"
}
]
},
{
"id": "PMID-11106238_E8",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
1666,
1677
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11106238_T13"
}
]
}
] | [] | [] |
36 | PMID-11159919 | [
{
"id": "PMID-11159919__text",
"type": "abstract",
"text": [
"Defect in N-glycosylation of proteins is tissue-dependent in congenital disorders of glycosylation Ia. \nThe biochemical hallmark of Congenital Disorders of Glycosylation (CDG) including type Ia is a defective N-glycosylation of serum glycoproteins. Hypoglycosylated forms of alpha1-antitrypsin have been detected by Western blot in serum from CDG Ia patients. In contrast we were not able to detect hypoglycosylation in alpha1-antitrypsin synthesized by fibroblasts, keratinocytes, enterocytes, and leukocytes. Similarly no hypoglycosylation was detectable in a membrane-associated N-linked glycoprotein, the facilitative glucose transporter GLUT-1 and also in serum immunoglobulin G isolated from sera of CDG Ia patients. We conclude that the phenotypic expression of CDG Ia is tissue-dependent.\n"
],
"offsets": [
[
0,
797
]
]
}
] | [
{
"id": "PMID-11159919_T1",
"type": "Protein",
"text": [
"alpha1-antitrypsin"
],
"offsets": [
[
275,
293
]
],
"normalized": []
},
{
"id": "PMID-11159919_T2",
"type": "Protein",
"text": [
"alpha1-antitrypsin"
],
"offsets": [
[
420,
438
]
],
"normalized": []
},
{
"id": "PMID-11159919_T3",
"type": "Protein",
"text": [
"GLUT-1"
],
"offsets": [
[
642,
648
]
],
"normalized": []
}
] | [
{
"id": "PMID-11159919_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"Hypoglycosylated"
],
"offsets": [
[
249,
265
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11159919_T1"
}
]
},
{
"id": "PMID-11159919_E2",
"type": "Glycosylation",
"trigger": {
"text": [
"hypoglycosylation"
],
"offsets": [
[
399,
416
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11159919_T2"
}
]
},
{
"id": "PMID-11159919_E3",
"type": "Glycosylation",
"trigger": {
"text": [
"hypoglycosylation"
],
"offsets": [
[
524,
541
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11159919_T3"
}
]
}
] | [] | [] |
37 | PMID-11162640 | [
{
"id": "PMID-11162640__text",
"type": "abstract",
"text": [
"Molecular cloning and characterization of CHM1L, a novel membrane molecule similar to chondromodulin-I. \nChondromodulin-I (ChM-I) is a cartilage-specific glycoprotein that stimulates the growth of chondrocytes and inhibits the tube formation of endothelial cells. In the present study, we identified a novel ChM-I like molecule, designated ChM1L. Cloning of full length cDNAs of human, mouse, and rat ChM1L revealed that ChM1L encodes 317 amino acids novel type II transmembrane protein. ChM1L protein was expressed on the cell surface as N-glycosylated and non-N-glycosylated protein with molecular mass of 45 and 40 kDa, respectively. In adult mouse tissues, ChM1L mRNA was highly expressed in eye, skeletal muscle, and whole rib. The temporal pattern of ChM1L mRNA was examined using whole embryo at day 10 to 19 of gestation. After day 11, ChM1L mRNA was detected and its level was progressively elevated in association with development of mouse embryo. These data suggest that ChM1L is a novel membrane molecule which is similar to ChM-I that plays a regulatory role in eye, skeletal muscle, and development of embryo.\n"
],
"offsets": [
[
0,
1124
]
]
}
] | [
{
"id": "PMID-11162640_T1",
"type": "Protein",
"text": [
"CHM1L"
],
"offsets": [
[
42,
47
]
],
"normalized": []
},
{
"id": "PMID-11162640_T2",
"type": "Protein",
"text": [
"chondromodulin-I"
],
"offsets": [
[
86,
102
]
],
"normalized": []
},
{
"id": "PMID-11162640_T3",
"type": "Protein",
"text": [
"Chondromodulin-I"
],
"offsets": [
[
105,
121
]
],
"normalized": []
},
{
"id": "PMID-11162640_T4",
"type": "Protein",
"text": [
"ChM-I"
],
"offsets": [
[
123,
128
]
],
"normalized": []
},
{
"id": "PMID-11162640_T5",
"type": "Protein",
"text": [
"ChM-I"
],
"offsets": [
[
308,
313
]
],
"normalized": []
},
{
"id": "PMID-11162640_T6",
"type": "Protein",
"text": [
"ChM1L"
],
"offsets": [
[
340,
345
]
],
"normalized": []
},
{
"id": "PMID-11162640_T7",
"type": "Protein",
"text": [
"ChM1L"
],
"offsets": [
[
401,
406
]
],
"normalized": []
},
{
"id": "PMID-11162640_T8",
"type": "Protein",
"text": [
"ChM1L"
],
"offsets": [
[
421,
426
]
],
"normalized": []
},
{
"id": "PMID-11162640_T9",
"type": "Protein",
"text": [
"ChM1L"
],
"offsets": [
[
488,
493
]
],
"normalized": []
},
{
"id": "PMID-11162640_T10",
"type": "Protein",
"text": [
"ChM1L"
],
"offsets": [
[
661,
666
]
],
"normalized": []
},
{
"id": "PMID-11162640_T11",
"type": "Protein",
"text": [
"ChM1L"
],
"offsets": [
[
757,
762
]
],
"normalized": []
},
{
"id": "PMID-11162640_T12",
"type": "Protein",
"text": [
"ChM1L"
],
"offsets": [
[
844,
849
]
],
"normalized": []
},
{
"id": "PMID-11162640_T13",
"type": "Protein",
"text": [
"ChM1L"
],
"offsets": [
[
982,
987
]
],
"normalized": []
},
{
"id": "PMID-11162640_T14",
"type": "Protein",
"text": [
"ChM-I"
],
"offsets": [
[
1037,
1042
]
],
"normalized": []
}
] | [
{
"id": "PMID-11162640_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"N-glycosylated"
],
"offsets": [
[
539,
553
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11162640_T9"
}
]
},
{
"id": "PMID-11162640_E2",
"type": "Glycosylation",
"trigger": {
"text": [
"non-N-glycosylated"
],
"offsets": [
[
558,
576
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11162640_T9"
}
]
}
] | [
{
"id": "PMID-11162640_1",
"entity_ids": [
"PMID-11162640_T3",
"PMID-11162640_T4"
]
}
] | [] |
38 | PMID-11281648 | [
{
"id": "PMID-11281648__text",
"type": "abstract",
"text": [
"Targeting of calsequestrin to the sarcoplasmic reticulum of skeletal muscle upon deletion of its glycosylation site. \nThe glycoprotein calsequestrin (CS) is segregated to the junctional sarcoplasmic reticulum (jSR) and is responsible for intraluminal Ca(2+) binding. A chimeric CS-hemoagglutinin 1 (HA1), obtained by adding the nine amino acid viral epitope hemoagglutinin to the carboxy terminal of CS and shown to be correctly segregated to skeletal muscle jSR [A. Nori, K. A. Nadalini, A. Martini, R. Rizzuto, A. Villa, and P. Volpe (1997). Chimeric calsequestrin and its targeting to the junctional sarcoplasmic reticulum of skeletal muscle. Am. J. Physiol. 272, C1420-C1428] lends itself as a molecular tool to investigate the targeting domains of CS. A putative targeting mechanism of CS to jSR implies glycosylation-dependent steps in the endoplasmic reticulum (ER) and Golgi complex. To test this hypothesis, CS-HA1DeltaGly, a mutant in which the unique N-glycosylation site Asn316 was changed to Ile, was engineered by site-directed mutagenesis. The mutant cDNA was transiently transfected in either HeLa cells, myoblasts of rat skeletal muscle primary cultures, or regenerating soleus muscle fibers of adult rats. The expression and intracellular localization of CS-HA1DeltaGly was studied by double-labeling epifluorescence by means of antibodies against either CS, HA1, or the ryanodine receptor calcium release channel. CS-HA1DeltaGly was expressed and retained to ER and ER/sarcoplasmic reticulum of HeLa cells and myotubes, respectively, and expressed, sorted, and correctly segregated to jSR of regenerating soleus muscle fibers. Thus, the targeting mechanism of CS in vivo appears not to be affected by glycosylation-that is, the sorting, docking, and segregation of CS are independent of cotranslational and posttranslational glycosylation or glycosylations.\n"
],
"offsets": [
[
0,
1877
]
]
}
] | [
{
"id": "PMID-11281648_T1",
"type": "Protein",
"text": [
"hemoagglutinin 1"
],
"offsets": [
[
281,
297
]
],
"normalized": []
},
{
"id": "PMID-11281648_T2",
"type": "Protein",
"text": [
"HA1"
],
"offsets": [
[
299,
302
]
],
"normalized": []
},
{
"id": "PMID-11281648_T3",
"type": "Protein",
"text": [
"hemoagglutinin"
],
"offsets": [
[
358,
372
]
],
"normalized": []
},
{
"id": "PMID-11281648_T4",
"type": "Protein",
"text": [
"HA1"
],
"offsets": [
[
920,
923
]
],
"normalized": []
},
{
"id": "PMID-11281648_T5",
"type": "Protein",
"text": [
"HA1"
],
"offsets": [
[
1276,
1279
]
],
"normalized": []
},
{
"id": "PMID-11281648_T6",
"type": "Protein",
"text": [
"HA1"
],
"offsets": [
[
1377,
1380
]
],
"normalized": []
},
{
"id": "PMID-11281648_T7",
"type": "Protein",
"text": [
"HA1"
],
"offsets": [
[
1436,
1439
]
],
"normalized": []
}
] | [] | [
{
"id": "PMID-11281648_1",
"entity_ids": [
"PMID-11281648_T1",
"PMID-11281648_T2"
]
}
] | [] |
39 | PMID-11292861 | [
{
"id": "PMID-11292861__text",
"type": "abstract",
"text": [
"Targeting of HIF-alpha to the von Hippel-Lindau ubiquitylation complex by O2-regulated prolyl hydroxylation. \nHypoxia-inducible factor (HIF) is a transcriptional complex that plays a central role in the regulation of gene expression by oxygen. In oxygenated and iron replete cells, HIF-alpha subunits are rapidly destroyed by a mechanism that involves ubiquitylation by the von Hippel-Lindau tumor suppressor (pVHL) E3 ligase complex. This process is suppressed by hypoxia and iron chelation, allowing transcriptional activation. Here we show that the interaction between human pVHL and a specific domain of the HIF-1alpha subunit is regulated through hydroxylation of a proline residue (HIF-1alpha P564) by an enzyme we have termed HIF-alpha prolyl-hydroxylase (HIF-PH). An absolute requirement for dioxygen as a cosubstrate and iron as cofactor suggests that HIF-PH functions directly as a cellular oxygen sensor.\n"
],
"offsets": [
[
0,
916
]
]
}
] | [
{
"id": "PMID-11292861_T1",
"type": "Protein",
"text": [
"von Hippel-Lindau"
],
"offsets": [
[
30,
47
]
],
"normalized": []
},
{
"id": "PMID-11292861_T2",
"type": "Protein",
"text": [
"von Hippel-Lindau tumor suppressor"
],
"offsets": [
[
374,
408
]
],
"normalized": []
},
{
"id": "PMID-11292861_T3",
"type": "Protein",
"text": [
"pVHL"
],
"offsets": [
[
410,
414
]
],
"normalized": []
},
{
"id": "PMID-11292861_T4",
"type": "Protein",
"text": [
"pVHL"
],
"offsets": [
[
578,
582
]
],
"normalized": []
},
{
"id": "PMID-11292861_T5",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
612,
622
]
],
"normalized": []
},
{
"id": "PMID-11292861_T6",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
688,
698
]
],
"normalized": []
},
{
"id": "PMID-11292861_T8",
"type": "Entity",
"text": [
"P564"
],
"offsets": [
[
699,
703
]
],
"normalized": []
}
] | [
{
"id": "PMID-11292861_E1",
"type": "Hydroxylation",
"trigger": {
"text": [
"hydroxylation"
],
"offsets": [
[
652,
665
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11292861_T5"
},
{
"role": "Site",
"ref_id": "PMID-11292861_T8"
}
]
}
] | [
{
"id": "PMID-11292861_1",
"entity_ids": [
"PMID-11292861_T2",
"PMID-11292861_T3"
]
}
] | [] |
40 | PMID-11292862 | [
{
"id": "PMID-11292862__text",
"type": "abstract",
"text": [
"HIFalpha targeted for VHL-mediated destruction by proline hydroxylation: implications for O2 sensing. \nHIF (hypoxia-inducible factor) is a transcription factor that plays a pivotal role in cellular adaptation to changes in oxygen availability. In the presence of oxygen, HIF is targeted for destruction by an E3 ubiquitin ligase containing the von Hippel-Lindau tumor suppressor protein (pVHL). We found that human pVHL binds to a short HIF-derived peptide when a conserved proline residue at the core of this peptide is hydroxylated. Because proline hydroxylation requires molecular oxygen and Fe(2+), this protein modification may play a key role in mammalian oxygen sensing.\n"
],
"offsets": [
[
0,
678
]
]
}
] | [
{
"id": "PMID-11292862_T1",
"type": "Protein",
"text": [
"VHL"
],
"offsets": [
[
22,
25
]
],
"normalized": []
},
{
"id": "PMID-11292862_T2",
"type": "Protein",
"text": [
"ubiquitin"
],
"offsets": [
[
312,
321
]
],
"normalized": []
},
{
"id": "PMID-11292862_T3",
"type": "Protein",
"text": [
"von Hippel-Lindau tumor suppressor"
],
"offsets": [
[
344,
378
]
],
"normalized": []
},
{
"id": "PMID-11292862_T4",
"type": "Protein",
"text": [
"pVHL"
],
"offsets": [
[
388,
392
]
],
"normalized": []
},
{
"id": "PMID-11292862_T5",
"type": "Protein",
"text": [
"pVHL"
],
"offsets": [
[
415,
419
]
],
"normalized": []
}
] | [] | [
{
"id": "PMID-11292862_1",
"entity_ids": [
"PMID-11292862_T3",
"PMID-11292862_T4"
]
}
] | [] |
41 | PMID-11306499 | [
{
"id": "PMID-11306499__text",
"type": "abstract",
"text": [
"Genetic and clinical features of human pancreatic ductal adenocarcinomas with widespread microsatellite instability. \nThe incidences of microsatellite instability (MSI) and underlying DNA mismatch repair (MMR) defects in pancreatic carcinogenesis have not been well established. We analyzed 100 sporadic and 3 hereditary pancreatic ductal adenocarcinomas for MSI, and high-frequency MSI (MSI-H) and low-frequency MSI (MSI-L) tumors were further analyzed for frameshift mutations of possible target genes and for promoter methylation and mutation of DNA MMR genes, including hMLH1, hMSH2, hMSH3, and hMSH6 genes. Among the 100 sporadic tumors, 13 (13%) were MSI-H, 13 (13%) were MSI-L, and 74 (74%) were microsatellite stable (MSS) tumors. All of the three hereditary tumors from hereditary nonpolyposis colorectal cancer (HNPCC) patients were MSI-H. MSI-H tumors were significantly associated with poor differentiation and the presence of wild-type K-RAS and p53 genes. Patients with MSI-H tumors had a significantly longer overall survival time than did those with MSI-L or MSS tumors (P = 0.0057). Frameshift mutations of hMSH3, hMLH3, BRCA-2, TGF-beta type II receptor, and BAX genes were detected in MSI-H tumors. Hypermethylation of the hMLH1 promoter was observed in 6 (46%) of the 13 sporadic MSI-H tumors but not in any of the 3 hereditary MSI-H tumors or 13 MSI-L tumors. All of the 3 HNPCC cases had germ-line hMLH1 mutation accompanied by loss of heterogeneity or other mutation in the tumor. Our results suggest that pancreatic carcinomas with MSI-H represent a distinctive oncogenic pathway because they exhibit peculiar clinical, pathological, and molecular characteristics. Our results also suggest the principal involvement of epigenetic or genetic inactivation of the hMLH1 gene in the pathogenesis of pancreatic carcinoma with MSI-H.\n"
],
"offsets": [
[
0,
1852
]
]
}
] | [
{
"id": "PMID-11306499_T1",
"type": "Protein",
"text": [
"MLH1"
],
"offsets": [
[
575,
579
]
],
"normalized": []
},
{
"id": "PMID-11306499_T2",
"type": "Protein",
"text": [
"MSH2"
],
"offsets": [
[
582,
586
]
],
"normalized": []
},
{
"id": "PMID-11306499_T3",
"type": "Protein",
"text": [
"MSH3"
],
"offsets": [
[
589,
593
]
],
"normalized": []
},
{
"id": "PMID-11306499_T4",
"type": "Protein",
"text": [
"MSH6"
],
"offsets": [
[
600,
604
]
],
"normalized": []
},
{
"id": "PMID-11306499_T5",
"type": "Protein",
"text": [
"K-RAS"
],
"offsets": [
[
949,
954
]
],
"normalized": []
},
{
"id": "PMID-11306499_T6",
"type": "Protein",
"text": [
"p53"
],
"offsets": [
[
959,
962
]
],
"normalized": []
},
{
"id": "PMID-11306499_T7",
"type": "Protein",
"text": [
"MSH3"
],
"offsets": [
[
1125,
1129
]
],
"normalized": []
},
{
"id": "PMID-11306499_T8",
"type": "Protein",
"text": [
"MLH3"
],
"offsets": [
[
1132,
1136
]
],
"normalized": []
},
{
"id": "PMID-11306499_T9",
"type": "Protein",
"text": [
"BRCA-2"
],
"offsets": [
[
1138,
1144
]
],
"normalized": []
},
{
"id": "PMID-11306499_T10",
"type": "Protein",
"text": [
"TGF-beta type II receptor"
],
"offsets": [
[
1146,
1171
]
],
"normalized": []
},
{
"id": "PMID-11306499_T11",
"type": "Protein",
"text": [
"BAX"
],
"offsets": [
[
1177,
1180
]
],
"normalized": []
},
{
"id": "PMID-11306499_T12",
"type": "Protein",
"text": [
"MLH1"
],
"offsets": [
[
1243,
1247
]
],
"normalized": []
},
{
"id": "PMID-11306499_T13",
"type": "Protein",
"text": [
"MLH1"
],
"offsets": [
[
1421,
1425
]
],
"normalized": []
},
{
"id": "PMID-11306499_T14",
"type": "Protein",
"text": [
"MLH1"
],
"offsets": [
[
1786,
1790
]
],
"normalized": []
},
{
"id": "PMID-11306499_T15",
"type": "Entity",
"text": [
"promoter"
],
"offsets": [
[
512,
520
]
],
"normalized": []
},
{
"id": "PMID-11306499_T18",
"type": "Entity",
"text": [
"promoter"
],
"offsets": [
[
1248,
1256
]
],
"normalized": []
}
] | [
{
"id": "PMID-11306499_E1",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
521,
532
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11306499_T1"
},
{
"role": "Site",
"ref_id": "PMID-11306499_T15"
}
]
},
{
"id": "PMID-11306499_E2",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
521,
532
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11306499_T2"
},
{
"role": "Site",
"ref_id": "PMID-11306499_T15"
}
]
},
{
"id": "PMID-11306499_E3",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
521,
532
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11306499_T3"
},
{
"role": "Site",
"ref_id": "PMID-11306499_T15"
}
]
},
{
"id": "PMID-11306499_E4",
"type": "DNA_methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
521,
532
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11306499_T4"
},
{
"role": "Site",
"ref_id": "PMID-11306499_T15"
}
]
},
{
"id": "PMID-11306499_E5",
"type": "DNA_methylation",
"trigger": {
"text": [
"Hypermethylation"
],
"offsets": [
[
1218,
1234
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11306499_T12"
},
{
"role": "Site",
"ref_id": "PMID-11306499_T18"
}
]
}
] | [] | [] |
42 | PMID-11327822 | [
{
"id": "PMID-11327822__text",
"type": "abstract",
"text": [
"The acetylation state of human fetal hemoglobin modulates the strength of its subunit interactions: long-range effects and implications for histone interactions in the nucleosome. \nThe source of the 70-fold increased tetramer strength of liganded fetal hemoglobin relative to that of adult hemoglobin between pH 6.0 and 7.5 reported earlier [Dumoulin et al. (1997) J. Biol. Chem. 272, 31326] has been identified as the N-terminal Gly residue of the gamma-chain, which is replaced by Val in adult hemoglobin. This was revealed by extending the study of the pH dependence of the tetramer-dimer equilibrium of these hemoglobins into the alkaline range as far as pH 9. From pH 7.5 to 9.0, the 70-fold difference in the association equilibrium constant between hemoglobins F and A lessened progressively. This behavior was attributed to the difference in the pK(a) 8.1 of Gly-1(gamma) compared to the pK(a) 7.1 value of Val-1(beta) of hemoglobins F and A, respectively. Evidence for this conclusion was obtained by demonstrating that natural hemoglobin F(1), which is specifically acetylated at Gly-1(gamma) and hence unable to be protonated, behaves like HbA and not HbF in its tetramer-dimer association properties over the pH range studied. An increased degree of protonation of the gamma-chain N-terminus of hemoglobin F from pH 9.0 to 8.0 is therefore suggested as responsible for its increased tetramer strength representing an example of transmission of a signal from its positively charged N-terminal tail to the distant subunit allosteric interface where the equilibrium constant is measured. An analogy is made between the effects of acetylation of the fetal hemoglobin tetramer on the strength of its subunit interactions and acetylation of some internal Lys residues within the N-terminal segments of the histone octamer around which DNA is wrapped in the nucleosome.\n"
],
"offsets": [
[
0,
1875
]
]
}
] | [
{
"id": "PMID-11327822_T1",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
140,
147
]
],
"normalized": []
}
] | [] | [] | [] |
43 | PMID-11352938 | [
{
"id": "PMID-11352938__text",
"type": "abstract",
"text": [
"Synergism of Xist RNA, DNA methylation, and histone hypoacetylation in maintaining X chromosome inactivation. \nXist RNA expression, methylation of CpG islands, and hypoacetylation of histone H4 are distinguishing features of inactive X chromatin. Here, we show that these silencing mechanisms act synergistically to maintain the inactive state. Xist RNA has been shown to be essential for initiation of X inactivation, but not required for maintenance. We have developed a system in which the reactivation frequency of individual X-linked genes can be assessed quantitatively. Using a conditional mutant Xist allele, we provide direct evidence for that loss of Xist RNA destabilizes the inactive state in somatic cells, leading to an increased reactivation frequency of an X-linked GFP transgene and of the endogenous hypoxanthine phosphoribosyl transferase (Hprt) gene in mouse embryonic fibroblasts. Demethylation of DNA, using 5-azadC or by introducing a mutation in Dnmt1, and inhibition of histone hypoacetylation using trichostatin A further increases reactivation in Xist mutant fibroblasts, indicating a synergistic interaction of X chromosome silencing mechanisms.\n"
],
"offsets": [
[
0,
1174
]
]
}
] | [
{
"id": "PMID-11352938_T1",
"type": "Protein",
"text": [
"Xist"
],
"offsets": [
[
13,
17
]
],
"normalized": []
},
{
"id": "PMID-11352938_T2",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
44,
51
]
],
"normalized": []
},
{
"id": "PMID-11352938_T3",
"type": "Protein",
"text": [
"Xist"
],
"offsets": [
[
111,
115
]
],
"normalized": []
},
{
"id": "PMID-11352938_T4",
"type": "Protein",
"text": [
"histone H4"
],
"offsets": [
[
183,
193
]
],
"normalized": []
},
{
"id": "PMID-11352938_T5",
"type": "Protein",
"text": [
"Xist"
],
"offsets": [
[
345,
349
]
],
"normalized": []
},
{
"id": "PMID-11352938_T6",
"type": "Protein",
"text": [
"Xist"
],
"offsets": [
[
604,
608
]
],
"normalized": []
},
{
"id": "PMID-11352938_T7",
"type": "Protein",
"text": [
"Xist"
],
"offsets": [
[
661,
665
]
],
"normalized": []
},
{
"id": "PMID-11352938_T8",
"type": "Protein",
"text": [
"GFP"
],
"offsets": [
[
782,
785
]
],
"normalized": []
},
{
"id": "PMID-11352938_T9",
"type": "Protein",
"text": [
"hypoxanthine phosphoribosyl transferase"
],
"offsets": [
[
818,
857
]
],
"normalized": []
},
{
"id": "PMID-11352938_T10",
"type": "Protein",
"text": [
"Hprt"
],
"offsets": [
[
859,
863
]
],
"normalized": []
},
{
"id": "PMID-11352938_T11",
"type": "Protein",
"text": [
"Dnmt1"
],
"offsets": [
[
970,
975
]
],
"normalized": []
},
{
"id": "PMID-11352938_T12",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
995,
1002
]
],
"normalized": []
},
{
"id": "PMID-11352938_T13",
"type": "Protein",
"text": [
"Xist"
],
"offsets": [
[
1074,
1078
]
],
"normalized": []
}
] | [
{
"id": "PMID-11352938_E1",
"type": "Acetylation",
"trigger": {
"text": [
"hypoacetylation"
],
"offsets": [
[
52,
67
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11352938_T2"
}
]
},
{
"id": "PMID-11352938_E2",
"type": "Acetylation",
"trigger": {
"text": [
"hypoacetylation"
],
"offsets": [
[
164,
179
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11352938_T4"
}
]
},
{
"id": "PMID-11352938_E3",
"type": "Acetylation",
"trigger": {
"text": [
"hypoacetylation"
],
"offsets": [
[
1003,
1018
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11352938_T12"
}
]
}
] | [
{
"id": "PMID-11352938_1",
"entity_ids": [
"PMID-11352938_T9",
"PMID-11352938_T10"
]
}
] | [] |
44 | PMID-11357511 | [
{
"id": "PMID-11357511__text",
"type": "abstract",
"text": [
"Expression of Pichia anomala INV1 gene in Saccharomyces cerevisiae results in two different active forms of hypoglycosylated invertase. \nThe Pichia anomala invertase gene (INV1) was introduced at different copy numbers into a sucrose-nonfermenting mutant of Saccharomyces cerevisiae and expressed from its own promoter sequences. The level reached in the production of invertase by the transformants (up to 540 units/10(10) cells) was in agreement with the INV1 gene dosage. Two forms of multimeric active and glycosylated invertase displaying different subcellular locations and molecular masses could be detected in the transformants. One was found to be present in the culture medium and in the periplasm, and the other could only be detected inside the cell. Each of the two heterologous forms of invertase was shown to be an oligomer composed of identical subunits. The difference found in the apparent molecular masses of their monomers (81.5 and 78.3 kDa, respectively) seems to be due to the size of their N-linked oligosaccharide chains (on average 2.4 and 1.9 kDa, respectively), since the number of sugar chains (9) and the molecular mass of the protein moiety (60.5 kDa) are identical in both forms. The shorter size of their oligosaccharides must also be the reason for the lower apparent molecular masses of the heterologous invertases when compared with the enzyme purified from P. anomala. The hypoglycosylated invertase accumulated within the cells of the transformants to an unusual level (up to 130 units/10(10) cells). Such accumulation of active enzyme inside the cells, as well as its underglycosylation, could be due to intrinsic properties of the P. anomala invertase that are determined by the particular primary structure of its protein moiety.\n"
],
"offsets": [
[
0,
1771
]
]
}
] | [
{
"id": "PMID-11357511_T1",
"type": "Protein",
"text": [
"INV1"
],
"offsets": [
[
29,
33
]
],
"normalized": []
},
{
"id": "PMID-11357511_T2",
"type": "Protein",
"text": [
"invertase"
],
"offsets": [
[
125,
134
]
],
"normalized": []
},
{
"id": "PMID-11357511_T3",
"type": "Protein",
"text": [
"invertase"
],
"offsets": [
[
156,
165
]
],
"normalized": []
},
{
"id": "PMID-11357511_T4",
"type": "Protein",
"text": [
"INV1"
],
"offsets": [
[
172,
176
]
],
"normalized": []
},
{
"id": "PMID-11357511_T5",
"type": "Protein",
"text": [
"invertase"
],
"offsets": [
[
369,
378
]
],
"normalized": []
},
{
"id": "PMID-11357511_T6",
"type": "Protein",
"text": [
"INV1"
],
"offsets": [
[
457,
461
]
],
"normalized": []
},
{
"id": "PMID-11357511_T7",
"type": "Protein",
"text": [
"invertase"
],
"offsets": [
[
523,
532
]
],
"normalized": []
},
{
"id": "PMID-11357511_T8",
"type": "Protein",
"text": [
"invertase"
],
"offsets": [
[
801,
810
]
],
"normalized": []
},
{
"id": "PMID-11357511_T9",
"type": "Protein",
"text": [
"invertase"
],
"offsets": [
[
1427,
1436
]
],
"normalized": []
},
{
"id": "PMID-11357511_T10",
"type": "Protein",
"text": [
"invertase"
],
"offsets": [
[
1682,
1691
]
],
"normalized": []
},
{
"id": "PMID-11357511_T14",
"type": "Entity",
"text": [
"oligosaccharide chains"
],
"offsets": [
[
1023,
1045
]
],
"normalized": []
}
] | [
{
"id": "PMID-11357511_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"hypoglycosylated"
],
"offsets": [
[
108,
124
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11357511_T1"
}
]
},
{
"id": "PMID-11357511_E2",
"type": "Glycosylation",
"trigger": {
"text": [
"glycosylated"
],
"offsets": [
[
510,
522
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11357511_T7"
}
]
},
{
"id": "PMID-11357511_E3",
"type": "Glycosylation",
"trigger": {
"text": [
"N-linked"
],
"offsets": [
[
1014,
1022
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11357511_T8"
},
{
"role": "Sidechain",
"ref_id": "PMID-11357511_T14"
}
]
},
{
"id": "PMID-11357511_E4",
"type": "Glycosylation",
"trigger": {
"text": [
"hypoglycosylated"
],
"offsets": [
[
1410,
1426
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11357511_T9"
}
]
},
{
"id": "PMID-11357511_E5",
"type": "Glycosylation",
"trigger": {
"text": [
"underglycosylation"
],
"offsets": [
[
1607,
1625
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11357511_T10"
}
]
}
] | [
{
"id": "PMID-11357511_1",
"entity_ids": [
"PMID-11357511_T1",
"PMID-11357511_T2"
]
},
{
"id": "PMID-11357511_2",
"entity_ids": [
"PMID-11357511_T3",
"PMID-11357511_T4"
]
}
] | [] |
45 | PMID-11384967 | [
{
"id": "PMID-11384967__text",
"type": "abstract",
"text": [
"The histone acetyltransferase, hGCN5, interacts with and acetylates the HIV transactivator, Tat. \nFactor acetyltransferase activity associated with several histone acetyltransferases plays a key role in the control of transcription. Here we report that hGCN5, a well known histone acetyltransferase, specifically interacts with and acetylates the human immunodeficiency virus type 1 (HIV-1) transactivator protein, Tat. The interaction between Tat and hGCN5 is direct and involves the acetyltransferase and the bromodomain regions of hGCN5, as well as a limited region of Tat encompassing the cysteine-rich domain of the protein. Tat lysines 50 and 51, target of acetylation by p300/CBP, were also found to be acetylated by hGCN5. The acetylation of these two lysines by p300/CBP has been recently shown to stimulate Tat transcriptional activity and accordingly, we have found that hGCN5 can considerably enhance Tat-dependent transcription of the HIV-1 long terminal repeat. These data highlight the importance of the acetylation of lysines 50 and 51 in the function of Tat, since different histone acetyltransferases involved in distinct signaling pathways, GCN5 and p300/CBP, converge to acetylate Tat on the same site.\n"
],
"offsets": [
[
0,
1223
]
]
}
] | [
{
"id": "PMID-11384967_T1",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
4,
11
]
],
"normalized": []
},
{
"id": "PMID-11384967_T2",
"type": "Protein",
"text": [
"GCN5"
],
"offsets": [
[
32,
36
]
],
"normalized": []
},
{
"id": "PMID-11384967_T3",
"type": "Protein",
"text": [
"Tat"
],
"offsets": [
[
92,
95
]
],
"normalized": []
},
{
"id": "PMID-11384967_T4",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
156,
163
]
],
"normalized": []
},
{
"id": "PMID-11384967_T5",
"type": "Protein",
"text": [
"GCN5"
],
"offsets": [
[
254,
258
]
],
"normalized": []
},
{
"id": "PMID-11384967_T6",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
273,
280
]
],
"normalized": []
},
{
"id": "PMID-11384967_T7",
"type": "Protein",
"text": [
"Tat"
],
"offsets": [
[
415,
418
]
],
"normalized": []
},
{
"id": "PMID-11384967_T8",
"type": "Protein",
"text": [
"Tat"
],
"offsets": [
[
444,
447
]
],
"normalized": []
},
{
"id": "PMID-11384967_T9",
"type": "Protein",
"text": [
"GCN5"
],
"offsets": [
[
453,
457
]
],
"normalized": []
},
{
"id": "PMID-11384967_T10",
"type": "Protein",
"text": [
"GCN5"
],
"offsets": [
[
535,
539
]
],
"normalized": []
},
{
"id": "PMID-11384967_T11",
"type": "Protein",
"text": [
"Tat"
],
"offsets": [
[
572,
575
]
],
"normalized": []
},
{
"id": "PMID-11384967_T12",
"type": "Protein",
"text": [
"Tat"
],
"offsets": [
[
630,
633
]
],
"normalized": []
},
{
"id": "PMID-11384967_T13",
"type": "Protein",
"text": [
"p300"
],
"offsets": [
[
678,
682
]
],
"normalized": []
},
{
"id": "PMID-11384967_T14",
"type": "Protein",
"text": [
"CBP"
],
"offsets": [
[
683,
686
]
],
"normalized": []
},
{
"id": "PMID-11384967_T15",
"type": "Protein",
"text": [
"GCN5"
],
"offsets": [
[
725,
729
]
],
"normalized": []
},
{
"id": "PMID-11384967_T16",
"type": "Protein",
"text": [
"p300"
],
"offsets": [
[
771,
775
]
],
"normalized": []
},
{
"id": "PMID-11384967_T17",
"type": "Protein",
"text": [
"CBP"
],
"offsets": [
[
776,
779
]
],
"normalized": []
},
{
"id": "PMID-11384967_T18",
"type": "Protein",
"text": [
"Tat"
],
"offsets": [
[
817,
820
]
],
"normalized": []
},
{
"id": "PMID-11384967_T19",
"type": "Protein",
"text": [
"GCN5"
],
"offsets": [
[
883,
887
]
],
"normalized": []
},
{
"id": "PMID-11384967_T20",
"type": "Protein",
"text": [
"Tat"
],
"offsets": [
[
913,
916
]
],
"normalized": []
},
{
"id": "PMID-11384967_T21",
"type": "Protein",
"text": [
"Tat"
],
"offsets": [
[
1071,
1074
]
],
"normalized": []
},
{
"id": "PMID-11384967_T22",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
1092,
1099
]
],
"normalized": []
},
{
"id": "PMID-11384967_T23",
"type": "Protein",
"text": [
"GCN5"
],
"offsets": [
[
1160,
1164
]
],
"normalized": []
},
{
"id": "PMID-11384967_T24",
"type": "Protein",
"text": [
"p300"
],
"offsets": [
[
1169,
1173
]
],
"normalized": []
},
{
"id": "PMID-11384967_T25",
"type": "Protein",
"text": [
"CBP"
],
"offsets": [
[
1174,
1177
]
],
"normalized": []
},
{
"id": "PMID-11384967_T26",
"type": "Protein",
"text": [
"Tat"
],
"offsets": [
[
1201,
1204
]
],
"normalized": []
},
{
"id": "PMID-11384967_T31",
"type": "Entity",
"text": [
"lysines 50"
],
"offsets": [
[
634,
644
]
],
"normalized": []
},
{
"id": "PMID-11384967_T32",
"type": "Entity",
"text": [
"51"
],
"offsets": [
[
649,
651
]
],
"normalized": []
},
{
"id": "PMID-11384967_T37",
"type": "Entity",
"text": [
"lysines"
],
"offsets": [
[
760,
767
]
],
"normalized": []
},
{
"id": "PMID-11384967_T39",
"type": "Entity",
"text": [
"lysines 50"
],
"offsets": [
[
1034,
1044
]
],
"normalized": []
},
{
"id": "PMID-11384967_T40",
"type": "Entity",
"text": [
"51"
],
"offsets": [
[
1049,
1051
]
],
"normalized": []
}
] | [
{
"id": "PMID-11384967_E1",
"type": "Acetylation",
"trigger": {
"text": [
"acetylates"
],
"offsets": [
[
57,
67
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T3"
}
]
},
{
"id": "PMID-11384967_E2",
"type": "Catalysis",
"trigger": {
"text": [
"acetylates"
],
"offsets": [
[
57,
67
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T3"
},
{
"role": "Cause",
"ref_id": "PMID-11384967_T2"
}
]
},
{
"id": "PMID-11384967_E3",
"type": "Acetylation",
"trigger": {
"text": [
"acetylates"
],
"offsets": [
[
332,
342
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T7"
}
]
},
{
"id": "PMID-11384967_E4",
"type": "Catalysis",
"trigger": {
"text": [
"acetylates"
],
"offsets": [
[
332,
342
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_E3"
},
{
"role": "Cause",
"ref_id": "PMID-11384967_T5"
}
]
},
{
"id": "PMID-11384967_E5",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
663,
674
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T12"
},
{
"role": "Site",
"ref_id": "PMID-11384967_T31"
}
]
},
{
"id": "PMID-11384967_E6",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
663,
674
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T12"
},
{
"role": "Site",
"ref_id": "PMID-11384967_T32"
}
]
},
{
"id": "PMID-11384967_E7",
"type": "Acetylation",
"trigger": {
"text": [
"acetylated"
],
"offsets": [
[
710,
720
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T12"
},
{
"role": "Site",
"ref_id": "PMID-11384967_T31"
}
]
},
{
"id": "PMID-11384967_E8",
"type": "Catalysis",
"trigger": {
"text": [
"acetylated"
],
"offsets": [
[
710,
720
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_E7"
},
{
"role": "Cause",
"ref_id": "PMID-11384967_T15"
}
]
},
{
"id": "PMID-11384967_E9",
"type": "Acetylation",
"trigger": {
"text": [
"acetylated"
],
"offsets": [
[
710,
720
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T12"
},
{
"role": "Site",
"ref_id": "PMID-11384967_T32"
}
]
},
{
"id": "PMID-11384967_E10",
"type": "Catalysis",
"trigger": {
"text": [
"acetylated"
],
"offsets": [
[
710,
720
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_E9"
},
{
"role": "Cause",
"ref_id": "PMID-11384967_T15"
}
]
},
{
"id": "PMID-11384967_E11",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
735,
746
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T12"
},
{
"role": "Site",
"ref_id": "PMID-11384967_T37"
}
]
},
{
"id": "PMID-11384967_E12",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
1019,
1030
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T21"
},
{
"role": "Site",
"ref_id": "PMID-11384967_T39"
}
]
},
{
"id": "PMID-11384967_E13",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
1019,
1030
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T21"
},
{
"role": "Site",
"ref_id": "PMID-11384967_T40"
}
]
},
{
"id": "PMID-11384967_E14",
"type": "Acetylation",
"trigger": {
"text": [
"acetylate"
],
"offsets": [
[
1191,
1200
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T26"
},
{
"role": "Site",
"ref_id": "PMID-11384967_T39"
}
]
},
{
"id": "PMID-11384967_E15",
"type": "Catalysis",
"trigger": {
"text": [
"acetylate"
],
"offsets": [
[
1191,
1200
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_E14"
},
{
"role": "Cause",
"ref_id": "PMID-11384967_T23"
}
]
},
{
"id": "PMID-11384967_E16",
"type": "Acetylation",
"trigger": {
"text": [
"acetylate"
],
"offsets": [
[
1191,
1200
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_T26"
},
{
"role": "Site",
"ref_id": "PMID-11384967_T40"
}
]
},
{
"id": "PMID-11384967_E17",
"type": "Catalysis",
"trigger": {
"text": [
"acetylate"
],
"offsets": [
[
1191,
1200
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11384967_E16"
},
{
"role": "Cause",
"ref_id": "PMID-11384967_T23"
}
]
}
] | [] | [] |
46 | PMID-113854 | [
{
"id": "PMID-113854__text",
"type": "abstract",
"text": [
"Hydroxylating activity of frog epidermis tyrosinase. \nTrypsin activated in a similar way both the tyrosine hydroxylase and the dopa-oxidasa activities of frog epidermis tyrosinase. Several electron donors reduced or eliminated the lag period for the hydroxylating enzyme. 4 x 10(-5) M dopa was particularly effective, but without affecting the stationary activity after lag period. Tyrosine hydroxylase had KM = 2.6 X 10(-3) M for tyrosine and 2 x 10(-3) M dopa was a competitive inhibitor with Ki = 5 x 10(-4) M. The enzyme was inactivated during its actuation. Data on thermal denaturation were similar to other obtained from dopa oxidase. Our results tend to confirm our previous hypothesis that the activatory process of the enzyme is accompanied by a spatial unfolding of the enzyme molecule.\n"
],
"offsets": [
[
0,
798
]
]
}
] | [
{
"id": "PMID-113854_T1",
"type": "Protein",
"text": [
"tyrosinase"
],
"offsets": [
[
41,
51
]
],
"normalized": []
},
{
"id": "PMID-113854_T2",
"type": "Protein",
"text": [
"tyrosine hydroxylase"
],
"offsets": [
[
98,
118
]
],
"normalized": []
},
{
"id": "PMID-113854_T3",
"type": "Protein",
"text": [
"tyrosinase"
],
"offsets": [
[
169,
179
]
],
"normalized": []
},
{
"id": "PMID-113854_T4",
"type": "Protein",
"text": [
"Tyrosine hydroxylase"
],
"offsets": [
[
382,
402
]
],
"normalized": []
}
] | [] | [] | [] |
47 | PMID-11393792 | [
{
"id": "PMID-11393792__text",
"type": "abstract",
"text": [
"Canine COL1A2 mutation resulting in C-terminal truncation of pro-alpha2(I) and severe osteogenesis imperfecta. \nRNA and type I collagen were analyzed from cultured skin fibroblasts of a Beagle puppy with fractures consistent with type III osteogenesis imperfecta (OI). In a nonisotopic RNAse cleavage assay (NIRCA), the proband's RNA had a unique cleavage pattern in the region of COL1A2 encoding the C-propeptide. DNA sequence analyses identified a mutation in which nucleotides 3991-3994 (\"CTAG\") were replaced with \"TGTCATTGG.\" The first seven bases of the inserted sequence were identical to nucleotides 4002-4008 of the normal canine COL1A2 sequence. The resulting frameshift changed 30 amino acids and introduced a premature stop codon. Reverse-transcription polymerase chain reaction (RT-PCR) with primers flanking the mutation site amplified two complementary DNA (cDNA) fragments for the proband and a single product for the control. Restriction enzyme digestions also were consistent with a heterozygous mutation in the proband. Type I procollagen labeled with [3H]proline was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Increased density of pC-alpha2(I) suggested comigration with the similarly sized pro-alpha2(I) derived from the mutant allele. Furthermore, a-chains were overhydroxylated and the ratio of alpha1(I):alpha2(I) was 3.2:1, consistent with the presence of alpha1(I) homotrimers. Analyses of COL1A2 and type I collagen were both consistent with the described heterozygous mutation affecting the pro-alpha2(I) C-propeptide and confirmed a diagnosis of OI.\n"
],
"offsets": [
[
0,
1618
]
]
}
] | [
{
"id": "PMID-11393792_T1",
"type": "Protein",
"text": [
"COL1A2"
],
"offsets": [
[
7,
13
]
],
"normalized": []
},
{
"id": "PMID-11393792_T2",
"type": "Protein",
"text": [
"COL1A2"
],
"offsets": [
[
381,
387
]
],
"normalized": []
},
{
"id": "PMID-11393792_T3",
"type": "Protein",
"text": [
"C-propeptide"
],
"offsets": [
[
401,
413
]
],
"normalized": []
},
{
"id": "PMID-11393792_T4",
"type": "Protein",
"text": [
"COL1A2"
],
"offsets": [
[
639,
645
]
],
"normalized": []
},
{
"id": "PMID-11393792_T5",
"type": "Protein",
"text": [
"pC-alpha2(I)"
],
"offsets": [
[
1190,
1202
]
],
"normalized": []
},
{
"id": "PMID-11393792_T6",
"type": "Protein",
"text": [
"alpha2(I)"
],
"offsets": [
[
1254,
1263
]
],
"normalized": []
},
{
"id": "PMID-11393792_T7",
"type": "Protein",
"text": [
"alpha1(I)"
],
"offsets": [
[
1357,
1366
]
],
"normalized": []
},
{
"id": "PMID-11393792_T8",
"type": "Protein",
"text": [
"alpha2(I)"
],
"offsets": [
[
1367,
1376
]
],
"normalized": []
},
{
"id": "PMID-11393792_T9",
"type": "Protein",
"text": [
"alpha1(I)"
],
"offsets": [
[
1420,
1429
]
],
"normalized": []
},
{
"id": "PMID-11393792_T10",
"type": "Protein",
"text": [
"COL1A2"
],
"offsets": [
[
1455,
1461
]
],
"normalized": []
},
{
"id": "PMID-11393792_T11",
"type": "Protein",
"text": [
"alpha2(I)"
],
"offsets": [
[
1562,
1571
]
],
"normalized": []
}
] | [
{
"id": "PMID-11393792_E1",
"type": "Hydroxylation",
"trigger": {
"text": [
"overhydroxylated"
],
"offsets": [
[
1323,
1339
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11393792_T7"
}
]
},
{
"id": "PMID-11393792_E2",
"type": "Hydroxylation",
"trigger": {
"text": [
"overhydroxylated"
],
"offsets": [
[
1323,
1339
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11393792_T8"
}
]
}
] | [] | [] |
48 | PMID-11445559 | [
{
"id": "PMID-11445559__text",
"type": "abstract",
"text": [
"Linking global histone acetylation to the transcription enhancement of X-chromosomal genes in Drosophila males. \nIt has become well established for several genes that targeting of histone acetylation to promoters is required for the activation of transcription. In contrast, global patterns of acetylation have not been ascribed to any particular regulatory function. In Drosophila, a specific modification of H4, acetylation at lysine 16, is enriched at hundreds of sites on the male X chromosome due to the activity of the male-specific lethal (MSL) dosage compensation complex. Utilizing chromatin immunoprecipitation, we have determined that H4Ac16 is present along the entire length of X-linked genes targeted by the MSL complex with relatively modest levels of acetylation at the promoter regions and high levels in the middle and/or 3' end of the transcription units. We propose that global acetylation by the MSL complex increases the expression of X-linked genes by facilitating transcription elongation rather than by enhancing promoter accessibility. We have also determined that H4Ac16 is absent from a region of the X chromosome that includes a gene known to be dosage-compensated by a MSL-independent mechanism. This study represents the first biochemical interpretation of the very large body of cytological observations on the chromosomal distribution of the MSL complex.\n"
],
"offsets": [
[
0,
1388
]
]
}
] | [
{
"id": "PMID-11445559_T1",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
15,
22
]
],
"normalized": []
},
{
"id": "PMID-11445559_T2",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
180,
187
]
],
"normalized": []
},
{
"id": "PMID-11445559_T3",
"type": "Protein",
"text": [
"H4"
],
"offsets": [
[
410,
412
]
],
"normalized": []
},
{
"id": "PMID-11445559_T4",
"type": "Protein",
"text": [
"H4"
],
"offsets": [
[
646,
648
]
],
"normalized": []
},
{
"id": "PMID-11445559_T5",
"type": "Protein",
"text": [
"H4"
],
"offsets": [
[
1091,
1093
]
],
"normalized": []
},
{
"id": "PMID-11445559_T10",
"type": "Entity",
"text": [
"lysine 16"
],
"offsets": [
[
429,
438
]
],
"normalized": []
},
{
"id": "PMID-11445559_T11",
"type": "Entity",
"text": [
"16"
],
"offsets": [
[
650,
652
]
],
"normalized": []
}
] | [
{
"id": "PMID-11445559_E1",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
23,
34
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11445559_T1"
}
]
},
{
"id": "PMID-11445559_E2",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
188,
199
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11445559_T2"
}
]
},
{
"id": "PMID-11445559_E3",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
294,
305
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11445559_T2"
}
]
},
{
"id": "PMID-11445559_E4",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
414,
425
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11445559_T3"
},
{
"role": "Site",
"ref_id": "PMID-11445559_T10"
}
]
},
{
"id": "PMID-11445559_E5",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
767,
778
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11445559_T4"
},
{
"role": "Site",
"ref_id": "PMID-11445559_T11"
}
]
},
{
"id": "PMID-11445559_E6",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
898,
909
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11445559_T4"
}
]
}
] | [] | [] |
49 | PMID-11498546 | [
{
"id": "PMID-11498546__text",
"type": "abstract",
"text": [
"Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. \nMethylation of histones at specific residues plays an important role in transcriptional regulation. Chromatin immunoprecipitation of dimethylated lysine 9 on histone H3 across 53 kilobases of the chicken beta-globin locus during erythropoiesis shows an almost complete anticorrelation between regions of elevated lysine 9 methylation and acetylation. Lysine 9 is methylated most over constitutive condensed chromatin and developmentally inactive globin genes. In contrast, lysine 4 methylation of histone H3 correlates with H3 acetylation. These results lead us to propose a mechanism by which the insulator in the beta-globin locus can protect the globin genes from being silenced by adjacent condensed chromatin.\n"
],
"offsets": [
[
0,
823
]
]
}
] | [
{
"id": "PMID-11498546_T1",
"type": "Protein",
"text": [
"histone"
],
"offsets": [
[
20,
27
]
],
"normalized": []
},
{
"id": "PMID-11498546_T2",
"type": "Protein",
"text": [
"beta-globin"
],
"offsets": [
[
88,
99
]
],
"normalized": []
},
{
"id": "PMID-11498546_T3",
"type": "Protein",
"text": [
"histones"
],
"offsets": [
[
123,
131
]
],
"normalized": []
},
{
"id": "PMID-11498546_T4",
"type": "Protein",
"text": [
"histone H3"
],
"offsets": [
[
266,
276
]
],
"normalized": []
},
{
"id": "PMID-11498546_T5",
"type": "Protein",
"text": [
"beta-globin"
],
"offsets": [
[
312,
323
]
],
"normalized": []
},
{
"id": "PMID-11498546_T6",
"type": "Protein",
"text": [
"histone H3"
],
"offsets": [
[
605,
615
]
],
"normalized": []
},
{
"id": "PMID-11498546_T7",
"type": "Protein",
"text": [
"H3"
],
"offsets": [
[
632,
634
]
],
"normalized": []
},
{
"id": "PMID-11498546_T8",
"type": "Protein",
"text": [
"beta-globin"
],
"offsets": [
[
723,
734
]
],
"normalized": []
},
{
"id": "PMID-11498546_T9",
"type": "Entity",
"text": [
"lysine"
],
"offsets": [
[
28,
34
]
],
"normalized": []
},
{
"id": "PMID-11498546_T13",
"type": "Entity",
"text": [
"lysine 9"
],
"offsets": [
[
254,
262
]
],
"normalized": []
},
{
"id": "PMID-11498546_T14",
"type": "Entity",
"text": [
"lysine 9"
],
"offsets": [
[
421,
429
]
],
"normalized": []
},
{
"id": "PMID-11498546_T17",
"type": "Entity",
"text": [
"Lysine 9"
],
"offsets": [
[
459,
467
]
],
"normalized": []
},
{
"id": "PMID-11498546_T19",
"type": "Entity",
"text": [
"lysine 4"
],
"offsets": [
[
581,
589
]
],
"normalized": []
}
] | [
{
"id": "PMID-11498546_E1",
"type": "Methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
35,
46
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11498546_T1"
},
{
"role": "Site",
"ref_id": "PMID-11498546_T9"
},
{
"role": "Contextgene",
"ref_id": "PMID-11498546_T2"
}
]
},
{
"id": "PMID-11498546_E2",
"type": "Methylation",
"trigger": {
"text": [
"Methylation"
],
"offsets": [
[
108,
119
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11498546_T3"
}
]
},
{
"id": "PMID-11498546_E3",
"type": "Methylation",
"trigger": {
"text": [
"dimethylated"
],
"offsets": [
[
241,
253
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11498546_T4"
},
{
"role": "Site",
"ref_id": "PMID-11498546_T13"
},
{
"role": "Contextgene",
"ref_id": "PMID-11498546_T5"
}
]
},
{
"id": "PMID-11498546_E4",
"type": "Methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
430,
441
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11498546_T4"
},
{
"role": "Site",
"ref_id": "PMID-11498546_T14"
}
]
},
{
"id": "PMID-11498546_E5",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
446,
457
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11498546_T4"
}
]
},
{
"id": "PMID-11498546_E6",
"type": "Methylation",
"trigger": {
"text": [
"methylated"
],
"offsets": [
[
471,
481
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11498546_T4"
},
{
"role": "Site",
"ref_id": "PMID-11498546_T17"
},
{
"role": "Contextgene",
"ref_id": "PMID-11498546_T5"
}
]
},
{
"id": "PMID-11498546_E7",
"type": "Methylation",
"trigger": {
"text": [
"methylation"
],
"offsets": [
[
590,
601
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11498546_T6"
},
{
"role": "Site",
"ref_id": "PMID-11498546_T19"
},
{
"role": "Contextgene",
"ref_id": "PMID-11498546_T5"
}
]
},
{
"id": "PMID-11498546_E8",
"type": "Acetylation",
"trigger": {
"text": [
"acetylation"
],
"offsets": [
[
635,
646
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11498546_T7"
},
{
"role": "Contextgene",
"ref_id": "PMID-11498546_T5"
}
]
}
] | [] | [] |
50 | PMID-11502179 | [
{
"id": "PMID-11502179__text",
"type": "abstract",
"text": [
"Purification and characterization of a soluble bioactive amino-terminal extracellular domain of the human thyrotropin receptor. \nThe amino-terminal ectodomain of the human TSH receptor has been expressed at the surface of CHO cells as a glycosylphosphatidylinositol-anchored molecule containing a 10-residue histidine tag close to its C terminus. The soluble ectodomain could be released from the cells by treatment with a glycosylphosphatidylinositol-phospholipase C and purified to apparent homogeneity by cobalt-Sepharose chromatography. Two nanomoles of material was obtained, which was suitable for analysis by mass spectrometry. This allowed the identification of four out of the six potential N-glycosylation sites as being effectively glycosylated. A proportion of the purified soluble ectodomain displayed specific binding of (125)I-labeled TSH, allowing for the first time performance of classical saturation binding experiments. Two classes of high-affinity binding sites were identified: site A, K(d) 0.014 nM; site B, K(d) 0.83 nM. The significance of site A, whose affinity is much higher than for the holoreceptor at the surface of intact cells, remains to be clarified. The purified ectodomain was capable of inhibiting efficiently the thyroid stimulating activity of immunoglobulins from patients with Graves' disease. It allowed computation of the amounts of these immunoglobulins in patient's serum, giving values up to 10 microg/mL. Contrary to all currently available assays, the soluble ectodomain of the TSH receptor purified in a functionally competent conformation allows direct studies of its interactions with TSH and autoantibodies and opens the way to structural studies.\n"
],
"offsets": [
[
0,
1701
]
]
}
] | [
{
"id": "PMID-11502179_T1",
"type": "Protein",
"text": [
"thyrotropin receptor"
],
"offsets": [
[
106,
126
]
],
"normalized": []
},
{
"id": "PMID-11502179_T2",
"type": "Protein",
"text": [
"TSH receptor"
],
"offsets": [
[
172,
184
]
],
"normalized": []
},
{
"id": "PMID-11502179_T3",
"type": "Protein",
"text": [
"glycosylphosphatidylinositol-phospholipase C"
],
"offsets": [
[
423,
467
]
],
"normalized": []
},
{
"id": "PMID-11502179_T4",
"type": "Protein",
"text": [
"TSH"
],
"offsets": [
[
850,
853
]
],
"normalized": []
},
{
"id": "PMID-11502179_T5",
"type": "Protein",
"text": [
"TSH receptor"
],
"offsets": [
[
1527,
1539
]
],
"normalized": []
},
{
"id": "PMID-11502179_T6",
"type": "Protein",
"text": [
"TSH"
],
"offsets": [
[
1637,
1640
]
],
"normalized": []
},
{
"id": "PMID-11502179_T7",
"type": "Entity",
"text": [
"glycosylphosphatidylinositol"
],
"offsets": [
[
237,
265
]
],
"normalized": []
},
{
"id": "PMID-11502179_T9",
"type": "Entity",
"text": [
"N-glycosylation sites"
],
"offsets": [
[
700,
721
]
],
"normalized": []
}
] | [
{
"id": "PMID-11502179_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"anchored"
],
"offsets": [
[
266,
274
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11502179_T2"
},
{
"role": "Sidechain",
"ref_id": "PMID-11502179_T7"
}
]
},
{
"id": "PMID-11502179_E2",
"type": "Glycosylation",
"trigger": {
"text": [
"glycosylated"
],
"offsets": [
[
743,
755
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11502179_T2"
},
{
"role": "Site",
"ref_id": "PMID-11502179_T9"
}
]
}
] | [] | [] |
51 | PMID-11504942 | [
{
"id": "PMID-11504942__text",
"type": "abstract",
"text": [
"HIF-1alpha binding to VHL is regulated by stimulus-sensitive proline hydroxylation. \nHypoxia-inducible factor-1alpha (HIF-1alpha) is a global transcriptional regulator of the hypoxic response. Under normoxic conditions, HIF-1alpha is recognized by the von Hippel-Lindau tumor-suppressor protein (VHL), a component of an E3 ubiquitin ligase complex. This interaction thereby promotes the rapid degradation of HIF-1alpha. Under hypoxic conditions, HIF-1alpha is stabilized. We have previously shown that VHL binds in a hypoxia-sensitive manner to a 27-aa segment of HIF-1alpha, and that this regulation depends on a posttranslational modification of HIF-1alpha. Through a combination of in vivo coimmunoprecipitation assays using VHL and a panel of point mutants of HIF-1alpha in this region, as well as MS and in vitro binding assays, we now provide evidence that this modification, which occurs under normoxic conditions, is hydroxylation of Pro-564 of HIF-1alpha. The data furthermore show that this proline hydroxylation is the primary regulator of VHL binding.\n"
],
"offsets": [
[
0,
1064
]
]
}
] | [
{
"id": "PMID-11504942_T1",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
0,
10
]
],
"normalized": []
},
{
"id": "PMID-11504942_T2",
"type": "Protein",
"text": [
"VHL"
],
"offsets": [
[
22,
25
]
],
"normalized": []
},
{
"id": "PMID-11504942_T3",
"type": "Protein",
"text": [
"Hypoxia-inducible factor-1alpha"
],
"offsets": [
[
85,
116
]
],
"normalized": []
},
{
"id": "PMID-11504942_T4",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
118,
128
]
],
"normalized": []
},
{
"id": "PMID-11504942_T5",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
220,
230
]
],
"normalized": []
},
{
"id": "PMID-11504942_T6",
"type": "Protein",
"text": [
"von Hippel-Lindau tumor-suppressor"
],
"offsets": [
[
252,
286
]
],
"normalized": []
},
{
"id": "PMID-11504942_T7",
"type": "Protein",
"text": [
"VHL"
],
"offsets": [
[
296,
299
]
],
"normalized": []
},
{
"id": "PMID-11504942_T8",
"type": "Protein",
"text": [
"ubiquitin"
],
"offsets": [
[
323,
332
]
],
"normalized": []
},
{
"id": "PMID-11504942_T9",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
408,
418
]
],
"normalized": []
},
{
"id": "PMID-11504942_T10",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
446,
456
]
],
"normalized": []
},
{
"id": "PMID-11504942_T11",
"type": "Protein",
"text": [
"VHL"
],
"offsets": [
[
502,
505
]
],
"normalized": []
},
{
"id": "PMID-11504942_T12",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
564,
574
]
],
"normalized": []
},
{
"id": "PMID-11504942_T13",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
648,
658
]
],
"normalized": []
},
{
"id": "PMID-11504942_T14",
"type": "Protein",
"text": [
"VHL"
],
"offsets": [
[
728,
731
]
],
"normalized": []
},
{
"id": "PMID-11504942_T15",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
764,
774
]
],
"normalized": []
},
{
"id": "PMID-11504942_T16",
"type": "Protein",
"text": [
"HIF-1alpha"
],
"offsets": [
[
953,
963
]
],
"normalized": []
},
{
"id": "PMID-11504942_T17",
"type": "Protein",
"text": [
"VHL"
],
"offsets": [
[
1051,
1054
]
],
"normalized": []
},
{
"id": "PMID-11504942_T18",
"type": "Entity",
"text": [
"proline"
],
"offsets": [
[
61,
68
]
],
"normalized": []
},
{
"id": "PMID-11504942_T21",
"type": "Entity",
"text": [
"Pro-564"
],
"offsets": [
[
942,
949
]
],
"normalized": []
}
] | [
{
"id": "PMID-11504942_E1",
"type": "Hydroxylation",
"trigger": {
"text": [
"hydroxylation"
],
"offsets": [
[
69,
82
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11504942_T1"
},
{
"role": "Site",
"ref_id": "PMID-11504942_T18"
}
]
},
{
"id": "PMID-11504942_E2",
"type": "Hydroxylation",
"trigger": {
"text": [
"hydroxylation"
],
"offsets": [
[
925,
938
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11504942_T16"
},
{
"role": "Site",
"ref_id": "PMID-11504942_T21"
}
]
}
] | [
{
"id": "PMID-11504942_1",
"entity_ids": [
"PMID-11504942_T3",
"PMID-11504942_T4"
]
},
{
"id": "PMID-11504942_2",
"entity_ids": [
"PMID-11504942_T6",
"PMID-11504942_T7"
]
}
] | [] |
52 | PMID-11513145 | [
{
"id": "PMID-11513145__text",
"type": "abstract",
"text": [
"2B4 (CD244) and CS1: novel members of the CD2 subset of the immunoglobulin superfamily molecules expressed on natural killer cells and other leukocytes. \n2B4 is a member of the CD2 subset of the immunoglobulin superfamily molecules expressed on natural killer (NK) cells and other leukocytes. It is the high affinity ligand for CD48. Engagement of 2B4 on NK-cell surfaces with specific antibodies or CD48 can trigger cell-mediated cytotoxicity, interferon-gamma secretion, phosphoinositol turnover and NK-cell invasiveness. The function of 2B4 in CD8+ T cells and myeloid cells remains unknown. The cytoplasmic domain of 2B4 contains unique tyrosine motifs (TxYxxV/I) that associate with src homology 2 domain-containing protein or signaling lymphocyte activation molecule (SLAM)-associated protein, whose mutation is the underlying genetic defect in the X-linked lymphoproliferative disease (XLPD). Impaired signaling via 2B4 and SLAM is implicated in the immunopathogenesis of XLPD. CS1 is a novel member of the CD2 subset that contains two of the unique tyrosine motifs present in 2B4 and SLAM. Signaling through 2B4, CS1 and other members of the CD2 subset may play a major role in the regulation of NK cells and other leukocyte functions.\n"
],
"offsets": [
[
0,
1244
]
]
}
] | [
{
"id": "PMID-11513145_T1",
"type": "Protein",
"text": [
"2B4"
],
"offsets": [
[
0,
3
]
],
"normalized": []
},
{
"id": "PMID-11513145_T2",
"type": "Protein",
"text": [
"CD244"
],
"offsets": [
[
5,
10
]
],
"normalized": []
},
{
"id": "PMID-11513145_T3",
"type": "Protein",
"text": [
"CS1"
],
"offsets": [
[
16,
19
]
],
"normalized": []
},
{
"id": "PMID-11513145_T4",
"type": "Protein",
"text": [
"CD2"
],
"offsets": [
[
42,
45
]
],
"normalized": []
},
{
"id": "PMID-11513145_T5",
"type": "Protein",
"text": [
"2B4"
],
"offsets": [
[
154,
157
]
],
"normalized": []
},
{
"id": "PMID-11513145_T6",
"type": "Protein",
"text": [
"CD2"
],
"offsets": [
[
177,
180
]
],
"normalized": []
},
{
"id": "PMID-11513145_T7",
"type": "Protein",
"text": [
"CD48"
],
"offsets": [
[
328,
332
]
],
"normalized": []
},
{
"id": "PMID-11513145_T8",
"type": "Protein",
"text": [
"2B4"
],
"offsets": [
[
348,
351
]
],
"normalized": []
},
{
"id": "PMID-11513145_T9",
"type": "Protein",
"text": [
"CD48"
],
"offsets": [
[
400,
404
]
],
"normalized": []
},
{
"id": "PMID-11513145_T10",
"type": "Protein",
"text": [
"interferon-gamma"
],
"offsets": [
[
445,
461
]
],
"normalized": []
},
{
"id": "PMID-11513145_T11",
"type": "Protein",
"text": [
"2B4"
],
"offsets": [
[
540,
543
]
],
"normalized": []
},
{
"id": "PMID-11513145_T12",
"type": "Protein",
"text": [
"CD8+"
],
"offsets": [
[
547,
551
]
],
"normalized": []
},
{
"id": "PMID-11513145_T13",
"type": "Protein",
"text": [
"2B4"
],
"offsets": [
[
621,
624
]
],
"normalized": []
},
{
"id": "PMID-11513145_T14",
"type": "Protein",
"text": [
"signaling lymphocyte activation molecule (SLAM)-associated protein"
],
"offsets": [
[
732,
798
]
],
"normalized": []
},
{
"id": "PMID-11513145_T15",
"type": "Protein",
"text": [
"2B4"
],
"offsets": [
[
923,
926
]
],
"normalized": []
},
{
"id": "PMID-11513145_T16",
"type": "Protein",
"text": [
"CS1"
],
"offsets": [
[
985,
988
]
],
"normalized": []
},
{
"id": "PMID-11513145_T17",
"type": "Protein",
"text": [
"CD2"
],
"offsets": [
[
1014,
1017
]
],
"normalized": []
},
{
"id": "PMID-11513145_T18",
"type": "Protein",
"text": [
"2B4"
],
"offsets": [
[
1084,
1087
]
],
"normalized": []
},
{
"id": "PMID-11513145_T19",
"type": "Protein",
"text": [
"2B4"
],
"offsets": [
[
1116,
1119
]
],
"normalized": []
},
{
"id": "PMID-11513145_T20",
"type": "Protein",
"text": [
"CS1"
],
"offsets": [
[
1121,
1124
]
],
"normalized": []
},
{
"id": "PMID-11513145_T21",
"type": "Protein",
"text": [
"CD2"
],
"offsets": [
[
1150,
1153
]
],
"normalized": []
}
] | [] | [
{
"id": "PMID-11513145_1",
"entity_ids": [
"PMID-11513145_T1",
"PMID-11513145_T2"
]
}
] | [] |
53 | PMID-11595658 | [
{
"id": "PMID-11595658__text",
"type": "abstract",
"text": [
"N-glycosylation of CRF receptor type 1 is important for its ligand-specific interaction. \nThe corticotropin-releasing factor (CRF) receptor type 1 (CRFR1) contains five potential N-glycosylation sites: N38, N45, N78, N90, and N98. Cells expressing CRFR1 were treated with tunicamycin to block receptor glycosylation. The nonglycosylated receptor did not bind the radioligand and had a decreased cAMP stimulation potency in response to CRF. To determine which of the polysaccharide chain(s) is/are involved in ligand interaction, the polysaccharide chains were deleted using site-directed mutagenesis of the glycosylation consensus, N-X-S/T. Two sets of mutations were performed for each glycosylation site: N to Q and S/T to A, respectively. The single mutants Q38, Q45, Q78, Q90, Q98, A40, A47, A80, A92, and A100 and the double mutants A40/A47 and A80/A100 were well expressed, bound CRF, sauvagine (SVG), and urotensin-I (UTS-I) with a normal affinity, and increased cAMP accumulation with a high efficiency. In contrast, the combined mutations A80/A92/A100, A40/A80/A92/A100, and A40/A47/A80/A92/A100 had low levels of expression, did not bind the radioligand, and had a decreased cAMP stimulation. These data indicate the requirement for three or more polysaccharide chains for normal CRFR1 function.\n"
],
"offsets": [
[
0,
1306
]
]
}
] | [
{
"id": "PMID-11595658_T1",
"type": "Protein",
"text": [
"CRF receptor type 1"
],
"offsets": [
[
19,
38
]
],
"normalized": []
},
{
"id": "PMID-11595658_T2",
"type": "Protein",
"text": [
"corticotropin-releasing factor (CRF) receptor type 1"
],
"offsets": [
[
94,
146
]
],
"normalized": []
},
{
"id": "PMID-11595658_T3",
"type": "Protein",
"text": [
"CRFR1"
],
"offsets": [
[
148,
153
]
],
"normalized": []
},
{
"id": "PMID-11595658_T4",
"type": "Protein",
"text": [
"CRFR1"
],
"offsets": [
[
248,
253
]
],
"normalized": []
},
{
"id": "PMID-11595658_T5",
"type": "Protein",
"text": [
"CRF"
],
"offsets": [
[
435,
438
]
],
"normalized": []
},
{
"id": "PMID-11595658_T6",
"type": "Protein",
"text": [
"CRF"
],
"offsets": [
[
886,
889
]
],
"normalized": []
},
{
"id": "PMID-11595658_T7",
"type": "Protein",
"text": [
"sauvagine"
],
"offsets": [
[
891,
900
]
],
"normalized": []
},
{
"id": "PMID-11595658_T8",
"type": "Protein",
"text": [
"SVG"
],
"offsets": [
[
902,
905
]
],
"normalized": []
},
{
"id": "PMID-11595658_T9",
"type": "Protein",
"text": [
"urotensin-I"
],
"offsets": [
[
912,
923
]
],
"normalized": []
},
{
"id": "PMID-11595658_T10",
"type": "Protein",
"text": [
"UTS-I"
],
"offsets": [
[
925,
930
]
],
"normalized": []
},
{
"id": "PMID-11595658_T11",
"type": "Protein",
"text": [
"CRFR1"
],
"offsets": [
[
1290,
1295
]
],
"normalized": []
}
] | [
{
"id": "PMID-11595658_E1",
"type": "Glycosylation",
"trigger": {
"text": [
"N-glycosylation"
],
"offsets": [
[
0,
15
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMID-11595658_T1"
}
]
}
] | [
{
"id": "PMID-11595658_1",
"entity_ids": [
"PMID-11595658_T2",
"PMID-11595658_T3"
]
},
{
"id": "PMID-11595658_2",
"entity_ids": [
"PMID-11595658_T7",
"PMID-11595658_T8"
]
},
{
"id": "PMID-11595658_3",
"entity_ids": [
"PMID-11595658_T9",
"PMID-11595658_T10"
]
}
] | [] |
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Dataset Card for BioNLP 2011 EPI
The dataset of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011.
Citation Information
@inproceedings{ohta-etal-2011-overview,
title = "Overview of the Epigenetics and Post-translational
Modifications ({EPI}) task of {B}io{NLP} Shared Task 2011",
author = "Ohta, Tomoko and
Pyysalo, Sampo and
Tsujii, Jun{'}ichi",
booktitle = "Proceedings of {B}io{NLP} Shared Task 2011 Workshop",
month = jun,
year = "2011",
address = "Portland, Oregon, USA",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/W11-1803",
pages = "16--25",
}
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